Contacts of the helix formed by residues 102 - 128 (chain I) in PDB entry 1VEQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 102 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I VAL* 3.8 17.7 - - + -
43I VAL 3.2 11.8 + - - +
44I GLY* 3.9 12.3 - - - +
45I PRO* 4.7 1.3 - - + -
46I ASN* 3.6 36.1 - - - +
47I PHE 4.6 0.7 - - - +
50I VAL* 3.2 38.4 - - + -
101I THR* 1.3 73.6 - - - +
103I GLN* 1.3 76.9 + - + +
104I ALA 3.1 0.9 + - - -
105I HIS* 3.2 2.4 + - - +
106I LEU* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PRO* 4.6 17.1 - - - +
46I ASN* 4.7 5.7 + - - +
101I THR* 3.5 11.2 - - - +
102I VAL* 1.3 89.9 - - + +
104I ALA* 1.3 66.9 + - - +
106I LEU* 3.4 4.5 + - - +
107I ALA* 3.0 24.4 + - - +
155I HIS* 4.0 21.4 + - - +
156I LEU* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I VAL* 4.8 6.3 - - + -
100I ASP* 3.5 29.2 - - + +
101I THR* 2.9 23.8 + - - +
103I GLN* 1.3 78.8 - - - +
105I HIS* 1.3 66.0 - - - +
107I ALA* 3.2 5.1 + - - +
108I ALA* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 4.0 18.2 - - + +
41I ASN* 3.1 29.9 + - + -
42I VAL* 3.6 25.4 - - + -
50I VAL* 6.5 0.4 - - + -
95I TYR* 2.6 40.2 + + - +
97I VAL* 3.0 31.0 - - + +
98I GLU 3.1 12.2 + - - -
100I ASP* 3.6 7.4 + - + -
101I THR 3.4 19.0 + - - -
102I VAL 3.2 5.2 + - - +
104I ALA* 1.3 78.8 - - - +
106I LEU* 1.3 55.9 + - + +
108I ALA* 2.8 3.2 + - - -
109I LEU* 2.5 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 6.5 0.9 - - + -
50I VAL* 3.9 11.2 - - + -
53I MET* 4.1 16.6 - - + -
54I ILE* 6.1 1.3 - - + -
102I VAL* 3.1 39.4 + - + +
103I GLN* 3.8 5.4 - - - +
105I HIS* 1.3 78.1 - - + +
107I ALA* 1.3 52.6 + - - +
109I LEU* 4.0 10.3 - - + -
110I ASP* 2.7 30.8 + - - +
152I VAL* 3.0 41.7 - - + +
155I HIS* 3.4 37.2 - - + -
156I LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I GLN 3.0 18.7 + - - +
104I ALA* 3.5 4.9 - - - +
106I LEU* 1.3 75.2 - - - +
108I ALA* 1.3 65.0 + - - +
110I ASP* 3.0 7.9 - - - +
111I LEU* 3.0 25.1 - - + +
156I LEU* 3.8 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I TYR* 3.5 24.5 - - + +
97I VAL* 4.1 12.6 - - + -
104I ALA 3.0 11.1 + - - +
105I HIS 2.8 7.3 + - - +
107I ALA* 1.3 76.2 - - - +
109I LEU* 1.3 62.7 + - - +
111I LEU* 3.2 20.3 + - - +
112I VAL* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LEU* 5.6 0.4 - - + -
34I THR* 4.7 8.5 - - + -
35I LEU* 3.9 28.3 - - + -
38I VAL* 4.3 25.6 - - + -
54I ILE* 5.5 2.7 - - + -
95I TYR* 4.3 12.3 - - + -
105I HIS* 2.5 21.2 + - + +
106I LEU* 3.5 15.0 - - + +
108I ALA* 1.3 70.0 - - - +
110I ASP* 1.3 67.3 + - - +
112I VAL* 3.0 29.2 + - + +
113I TYR* 3.0 27.8 + - + -
148I PHE* 4.2 17.7 - - + -
152I VAL* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I LEU 2.7 16.7 + - - +
107I ALA* 3.0 17.0 + - - +
109I LEU* 1.3 74.4 - - - +
111I LEU* 1.3 68.2 + - + +
113I TYR* 3.2 3.6 + - - +
114I ASN* 2.8 27.6 + - - +
149I GLN* 3.4 8.5 + - - +
152I VAL* 4.1 8.5 - - + +
153I ARG* 2.8 47.4 + - - +
156I LEU* 4.6 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I ALA* 3.0 20.9 - - + +
108I ALA* 3.5 11.2 - - - +
109I LEU 3.1 0.4 - - - -
110I ASP* 1.3 85.1 - - + +
112I VAL* 1.3 67.3 + - + +
114I ASN* 2.9 29.5 + - + +
115I GLY* 3.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ASP* 4.9 11.9 - - - +
31I LEU* 4.6 17.5 - - + -
34I THR* 5.2 8.3 - - + -
92I TRP* 5.7 6.6 - - + -
95I TYR* 4.3 14.4 - - + -
108I ALA 3.1 18.8 - - - +
109I LEU* 3.4 25.1 - - + +
111I LEU* 1.3 76.5 - - + +
113I TYR* 1.3 64.1 + - + +
115I GLY* 3.2 3.2 + - - -
116I VAL* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LEU* 3.4 30.8 - - + +
35I LEU* 3.6 16.8 - - + +
57I GLN* 3.1 30.5 + - - +
109I LEU* 3.0 26.7 + - + +
110I ASP* 3.6 4.3 - - - +
112I VAL* 1.3 74.2 - - + +
114I ASN* 1.3 57.9 + - - +
116I VAL* 4.1 5.4 - - + -
117I ILE* 2.7 41.4 + - + +
145I LEU* 3.5 44.0 - - + -
148I PHE* 3.4 32.3 - + - -
149I GLN* 3.5 27.4 - - + +
152I VAL* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G PRO* 3.8 22.4 - - + +
110I ASP* 2.8 28.3 + - - +
111I LEU* 2.9 18.4 + - - +
113I TYR* 1.3 76.0 - - - +
115I GLY* 1.3 57.8 + - - +
117I ILE* 3.9 1.0 - - - +
118I GLU* 2.9 35.6 + - - +
149I GLN* 2.9 15.9 + - - +
153I ARG* 3.1 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I TRP* 4.2 14.8 - - - -
111I LEU 3.1 8.1 + - - -
112I VAL* 3.2 4.7 + - - -
114I ASN* 1.3 79.3 - - - +
116I VAL* 1.3 58.2 + - - +
118I GLU* 4.2 7.2 - - - -
119I ASP* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLN* 5.5 0.4 - - - +
27I THR* 4.0 30.6 - - + +
28I TYR* 4.7 9.0 - - + -
31I LEU* 4.5 31.2 - - + -
92I TRP* 4.7 6.1 - - + -
112I VAL* 3.1 22.0 + - + +
113I TYR* 3.0 11.5 + - + +
115I GLY* 1.3 78.8 - - - +
117I ILE* 1.3 60.3 + - + +
118I GLU 3.3 0.2 - - - -
119I ASP* 3.8 2.2 + - - +
120I THR* 2.7 38.8 + - - +
145I LEU* 4.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.4 9.0 - - + -
7G PRO* 4.4 11.4 - - + +
113I TYR* 2.7 23.5 + - + +
114I ASN 4.1 1.8 - - - +
116I VAL* 1.3 71.0 - - + +
118I GLU* 1.3 61.0 + - - +
120I THR* 3.3 5.5 + - - -
121I ARG* 2.8 42.7 + - + +
142I ALA* 5.6 2.9 - - + -
145I LEU* 4.6 11.4 - - + -
146I GLU* 3.5 55.6 - - + +
149I GLN* 3.4 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G PRO* 4.0 30.9 + - + +
8G GLY* 5.5 2.0 - - - -
114I ASN* 2.9 20.3 + - - +
115I GLY* 4.4 5.5 - - - +
117I ILE* 1.3 74.6 - - - +
119I ASP* 1.3 71.4 + - - +
120I THR 3.0 1.4 + - - -
121I ARG* 3.2 5.1 + - + +
122I LYS* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LYS* 3.4 33.7 + - - -
24I GLN* 4.7 7.9 - - - +
27I THR* 5.2 9.4 + - + +
91I THR* 5.1 3.5 + - - -
92I TRP* 5.0 10.6 - - - -
115I GLY* 3.1 25.2 + - - +
116I VAL* 4.2 4.0 - - - +
117I ILE 3.5 0.2 - - - -
118I GLU* 1.3 84.0 - - - +
120I THR* 1.3 56.6 + - - +
122I LYS* 3.8 5.8 + - - +
123I SER* 3.1 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLN* 2.7 23.9 + - - +
28I TYR* 4.8 2.3 + - - +
116I VAL* 2.7 26.1 + - - +
117I ILE* 3.4 7.6 - - - -
118I GLU 3.0 0.4 - - - -
119I ASP* 1.3 75.3 - - - +
121I ARG* 1.3 70.2 + - + +
123I SER* 2.7 16.8 + - - -
124I ILE* 2.8 28.4 + - + +
138I LEU* 3.6 28.5 - - + +
141I HIS* 5.7 0.7 - - + -
142I ALA* 4.4 14.6 - - + +
145I LEU* 5.7 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.4 20.5 - - - +
7G PRO 4.3 9.9 - - - +
8G GLY* 5.2 9.4 + - - -
9G LEU* 4.3 17.7 - - - +
71G ARG* 3.8 5.5 - - - +
130G LEU 5.5 0.2 + - - -
131G ASP* 2.8 33.0 + - - +
132G LEU* 4.9 2.6 - - - +
133G VAL* 4.0 7.9 - - - +
117I ILE* 2.8 30.5 + - + +
118I GLU* 3.5 5.4 - - + +
120I THR* 1.3 73.4 - - + +
122I LYS* 1.3 62.5 + - - +
124I ILE* 2.9 26.9 + - + +
125I GLU* 3.1 15.3 + - - +
142I ALA* 5.8 1.1 - - + -
146I GLU* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I GLU 3.1 13.5 + - - +
119I ASP* 3.9 6.7 - - - +
121I ARG* 1.3 78.5 - - - +
123I SER* 1.3 64.3 + - - +
124I ILE 3.1 0.2 + - - -
125I GLU* 3.3 6.4 + - - +
126I LYS* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 3.3 30.8 + - - +
23I LYS* 5.7 3.1 - - - +
24I GLN* 4.3 11.3 + - - -
119I ASP 3.1 16.3 + - - -
120I THR* 2.7 17.0 + - - -
122I LYS* 1.3 72.5 - - - +
124I ILE* 1.3 58.0 + - - +
126I LYS* 3.8 8.9 + - - +
127I LEU* 3.0 34.7 + - - +
138I LEU* 5.1 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.7 12.6 - - + -
133G VAL* 5.2 4.5 - - + -
120I THR* 2.8 33.9 + - + +
121I ARG* 2.9 17.5 + - - +
123I SER* 1.3 73.2 - - - +
125I GLU* 1.3 61.2 + - - +
126I LYS 3.1 1.1 - - - -
127I LEU* 2.7 34.0 + - - +
128I GLU 3.2 5.7 + - - -
135I GLN* 3.4 27.1 + - + +
138I LEU* 4.1 15.9 - - + -
139I ILE* 3.9 34.3 - - + -
142I ALA* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.7 16.9 - - + +
121I ARG 3.1 8.0 + - - +
122I LYS* 3.8 9.6 - - - +
124I ILE* 1.3 81.2 - - - +
126I LYS* 1.3 62.0 + - - +
127I LEU 3.2 1.0 + - - -
128I GLU* 3.4 27.0 + - - +
129I ASP* 4.6 6.2 - - - +
135I GLN* 5.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 4.5 25.9 - - + +
122I LYS* 3.0 28.8 + - - +
123I SER* 4.0 7.6 - - - +
125I GLU* 1.3 76.6 - - - +
127I LEU* 1.3 61.2 + - - +
129I ASP* 4.1 9.7 + - - +
130I LEU* 3.6 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 4.0 26.5 - - + -
20I LEU* 4.1 11.9 - - + -
21I LEU* 4.9 7.6 - - + -
123I SER* 3.0 23.5 + - - +
124I ILE* 2.7 19.7 + - - +
126I LYS* 1.3 68.9 - - - +
128I GLU* 1.3 49.9 + - - -
129I ASP 2.7 17.8 + - - -
130I LEU* 2.8 35.9 + - + +
131I ASP 3.2 22.2 + - - +
134I SER* 3.3 28.3 - - - +
135I GLN* 4.2 13.9 - - + -
138I LEU* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G GLU* 4.3 12.3 - - - +
132G LEU* 4.7 15.8 - - + +
128H GLU* 4.1 17.7 - - - +
124I ILE 3.2 5.9 + - - -
125I GLU* 3.4 23.3 + - - +
127I LEU* 1.3 73.8 - - - +
129I ASP* 1.3 64.3 + - - +
130I LEU 5.2 0.4 - - - -
132I LEU* 4.5 23.9 - - + +
135I GLN* 3.3 28.9 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il