Contacts of the helix formed by residues 83 - 108 (chain A) in PDB entry 3VG9
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 PHE 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.9 3.1 - - + -
58A LEU* 3.3 41.5 - - + -
59A ALA* 4.8 4.3 - - - -
62A PHE* 4.2 19.1 - + + -
79A PHE* 3.3 39.2 + + + +
80A ILE 4.7 0.8 + - - +
81A ALA 3.9 2.8 + - - -
82A CYS* 1.3 74.5 - - - +
84A VAL* 1.3 59.5 + - + +
85A LEU 2.7 14.4 + - - +
86A VAL* 2.8 46.5 + - + +
87A LEU* 3.5 29.3 + - + +
133A PHE* 4.3 17.9 - + - -
137A LEU* 5.4 3.6 - - + -
406A STE 5.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.9 5.4 - - + -
59A ALA* 3.2 40.4 - - + +
62A PHE* 5.8 2.5 - - + -
80A ILE 5.9 1.1 - - - +
81A ALA 5.5 6.1 - - - +
83A PHE* 1.3 77.0 - - + +
85A LEU* 1.3 68.9 + - + +
86A VAL 3.5 0.2 - - - -
87A LEU* 3.6 13.8 - - - +
88A THR* 2.8 38.2 + - - +
246A TRP* 4.2 22.0 - - + -
274A ILE* 6.0 3.1 - - + -
278A HIS* 4.7 13.0 - - + +
401A ZMA 4.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A CYS* 3.8 27.4 - - + -
83A PHE 2.7 2.6 + - - +
84A VAL* 1.3 85.7 - - + +
86A VAL* 1.3 56.8 + - - +
88A THR* 3.6 4.6 - - - -
89A GLN* 3.0 28.2 + - - +
135A ILE 5.4 1.3 - - - +
136A GLY* 3.1 26.2 - - - +
168A PHE* 4.9 3.6 - - + -
177A MET* 4.1 18.8 - - + -
181A ASN* 3.7 31.0 - - - +
401A ZMA 3.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 2.8 40.6 + - + +
85A LEU* 1.3 72.3 - - - +
87A LEU* 1.3 69.1 + - + +
89A GLN* 3.3 3.1 + - - +
90A SER* 2.9 21.8 + - - -
129A TRP* 5.0 4.0 - - + -
132A SER* 3.0 33.3 - - - +
133A PHE* 3.0 44.9 - - + -
136A GLY* 3.7 11.6 - - - -
137A LEU* 5.1 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.5 13.4 - - - +
54A ALA* 3.4 20.4 - - + -
55A VAL* 3.3 50.0 - - + +
59A ALA* 4.6 1.6 - - + -
83A PHE* 3.5 31.6 + - + +
84A VAL* 3.6 12.3 - - - +
85A LEU 3.3 0.2 - - - -
86A VAL* 1.3 81.7 - - + +
88A THR* 1.3 64.8 + - - +
90A SER* 2.9 7.6 + - - -
91A SER* 2.9 26.1 + - - -
129A TRP* 4.3 21.3 - - + -
133A PHE* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 2.8 23.9 + - - +
85A LEU* 3.6 6.1 - - - -
87A LEU* 1.3 71.0 - - - +
89A GLN* 1.3 64.9 + - - +
91A SER* 3.1 11.8 + - - -
92A ILE* 3.0 28.6 + - + +
181A ASN* 6.4 0.2 - - - +
186A VAL* 5.1 6.5 - - + -
242A PHE* 3.5 24.5 - - + -
246A TRP* 3.0 45.1 - - + +
250A HIS* 6.0 1.8 - - + -
280A ASN* 6.1 0.7 - - - +
401A ZMA 5.3 3.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 3.0 17.3 + - - +
86A VAL* 3.5 9.2 - - - +
88A THR* 1.3 77.8 - - - +
90A SER* 1.3 58.6 + - - +
92A ILE* 3.2 12.5 + - - +
93A PHE* 2.9 62.6 + - + -
132A SER* 3.8 7.9 - - - +
135A ILE* 4.4 15.4 - - + +
136A GLY* 5.1 2.5 - - - -
181A ASN* 4.7 6.6 - - - +
185A CYS* 2.8 53.6 + - - +
186A VAL* 4.2 9.0 - - - +
189A PRO* 5.2 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.4 3.8 + - - -
48A LEU* 4.9 0.4 - - - -
51A ALA* 4.5 3.5 - - - +
86A VAL 2.9 10.3 + - - -
87A LEU* 2.9 8.6 + - - -
89A GLN* 1.3 72.9 - - - +
91A SER* 1.3 66.4 + - - +
93A PHE* 3.2 5.4 + - - +
94A SER* 2.9 27.1 + - - -
128A CYS* 4.6 3.3 + - - +
129A TRP* 3.4 47.4 + - - -
132A SER* 3.1 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.3 20.3 - - - +
51A ALA* 4.3 7.8 + - - +
52A ASP* 3.6 20.4 + - - -
87A LEU 2.9 16.9 + - - -
88A THR* 3.2 11.5 - - - -
90A SER* 1.3 76.3 - - - +
92A ILE* 1.3 57.5 - - - -
95A LEU* 2.9 35.4 + - - +
242A PHE* 3.6 21.0 - - - -
280A ASN* 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.0 18.3 + - + +
89A GLN* 3.2 14.1 + - - +
91A SER* 1.3 76.8 - - - +
93A PHE* 1.3 70.0 + - + +
95A LEU* 3.1 10.7 + - + +
96A LEU* 2.9 23.9 + - + +
185A CYS 4.2 5.6 - - - +
186A VAL* 3.5 35.4 - - + +
189A PRO* 3.8 33.9 - - + -
190A LEU* 5.2 7.9 - - + +
193A MET* 4.5 4.1 - - + +
242A PHE* 3.3 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 2.9 50.6 + - + -
90A SER* 3.6 7.0 - - - +
92A ILE* 1.3 79.7 - - + +
94A SER* 1.3 58.5 + - - +
96A LEU* 3.4 16.5 + - + +
97A ALA* 2.9 27.1 + - - +
128A CYS* 3.2 44.5 - - + -
131A LEU* 4.4 18.2 - - + -
132A SER* 3.3 26.0 - - - -
135A ILE* 4.4 13.2 - - + -
185A CYS* 6.0 0.2 - - - -
189A PRO* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.8 18.4 - - - -
47A SER* 2.8 29.1 + - - -
48A LEU* 3.3 26.0 - - - +
90A SER* 2.9 13.2 + - - -
93A PHE* 1.3 74.7 - - - +
95A LEU* 1.3 65.7 - - - +
97A ALA* 2.9 9.4 + - - +
98A ILE* 2.9 27.9 + - - +
125A ILE* 6.0 0.2 - - - +
128A CYS* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.7 24.4 - - + +
91A SER* 2.9 25.4 + - - +
92A ILE* 3.4 11.4 - - + +
94A SER* 1.3 75.0 - - - +
96A LEU* 1.3 57.3 + - - +
98A ILE* 3.3 12.4 + - + +
99A ALA* 2.9 27.5 + - - +
193A MET* 3.7 18.4 - - + +
197A TYR* 4.7 1.4 + - - -
235A LEU 5.1 1.6 - - - +
238A ILE* 3.7 21.8 - - + -
239A VAL* 3.9 21.5 - - + +
242A PHE* 3.8 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 2.9 18.2 + - + +
93A PHE* 3.6 16.8 - - + +
95A LEU* 1.3 74.9 - - - +
97A ALA* 1.3 65.0 + - - +
99A ALA* 3.2 3.4 + - + +
100A ILE* 2.9 48.0 + - + +
189A PRO* 4.0 12.6 - - + +
192A LEU* 3.2 36.1 - - + -
193A MET* 3.5 26.2 - - + -
196A VAL* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.7 38.2 - - + -
93A PHE 2.9 14.1 + - - +
94A SER* 2.9 9.8 + - - +
96A LEU* 1.3 76.4 - - - +
98A ILE* 1.3 58.2 + - - +
100A ILE* 3.5 8.6 + - - +
101A ASP* 2.9 27.9 + - - +
124A ILE* 5.2 8.7 - - + -
128A CYS* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.1 9.4 - - + +
44A PHE* 3.5 23.1 - - + +
45A VAL* 3.6 38.1 - - + +
48A LEU* 4.8 11.7 - - + -
94A SER 2.9 14.9 + - - +
95A LEU* 3.4 12.3 - - + +
97A ALA* 1.3 74.5 - - - +
99A ALA* 1.3 66.2 + - - +
101A ASP* 3.1 6.8 + - - +
102A ARG* 2.9 25.3 + - + +
197A TYR* 3.8 9.4 - - - +
235A LEU* 3.8 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU 2.9 12.8 + - - +
96A LEU* 3.6 8.3 - - + +
98A ILE* 1.3 76.0 - - - +
100A ILE* 1.3 58.5 + - - +
102A ARG* 3.5 2.6 + - - +
103A TYR* 2.9 27.4 + - - +
193A MET* 3.7 9.6 - - + -
196A VAL* 3.7 25.2 - - + +
197A TYR* 3.5 36.6 - - + -
200A ILE* 4.1 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 2.9 43.0 + - + +
97A ALA* 3.7 7.2 - - - +
99A ALA* 1.3 75.2 - - + +
101A ASP* 1.3 60.9 + - - +
103A TYR* 3.0 7.7 + - + +
104A ILE* 2.8 52.0 + - + +
196A VAL* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.5 2.5 - - + +
41A THR* 2.6 35.2 + - - +
44A PHE* 4.7 9.2 - - + -
97A ALA 2.9 18.8 + - - +
98A ILE* 3.1 6.9 + - - +
100A ILE* 1.3 77.5 - - - +
102A ARG* 1.3 73.6 + - - +
104A ILE* 3.4 4.6 + - - -
105A ALA* 2.9 27.9 + - - +
112A TYR* 2.5 34.2 + - - -
116A VAL* 3.8 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.5 11.9 + - - +
98A ILE* 2.9 21.9 + - + +
99A ALA 3.7 4.7 - - - +
101A ASP* 1.3 99.5 + - - +
103A TYR* 1.3 57.6 + - - +
105A ALA* 3.3 34.2 - - - +
106A ILE* 2.9 54.1 + - + +
112A TYR* 3.6 10.7 + - - -
197A TYR* 4.5 8.5 - - + +
200A ILE* 3.9 9.6 - - + -
228A GLU* 4.7 6.2 + - - +
232A ALA* 4.6 11.7 - - + +
235A LEU* 3.7 29.6 - - + -
103C TYR* 3.4 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA 2.9 15.1 + - - +
100A ILE* 3.0 12.1 + - + +
102A ARG* 1.3 73.8 - - - +
104A ILE* 1.3 71.5 + - + +
107A ARG* 2.9 67.7 + - + +
108A ILE* 5.2 9.0 - - + -
196A VAL* 3.5 26.7 - - + -
199A ARG* 3.0 45.0 + - + -
200A ILE* 3.5 19.1 - - + -
402A STE 3.2 22.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 2.8 51.7 + - + +
101A ASP* 3.8 6.5 - - - +
103A TYR* 1.3 82.0 - - + +
105A ALA* 1.3 64.7 + - - +
108A ILE* 2.9 55.9 + - + -
112A TYR* 3.2 38.4 - - + +
115A LEU* 4.3 16.8 - - + -
116A VAL* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP 2.9 11.3 + - - +
102A ARG* 3.3 42.2 - - - +
104A ILE* 1.3 80.3 - - - +
106A ILE* 1.3 59.6 + - + +
109A PRO* 3.3 25.8 - - - +
112A TYR* 3.4 19.5 - - + -
228A GLU* 4.6 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 2.9 36.7 + - + +
105A ALA* 1.3 77.3 - - + +
107A ARG* 1.3 71.8 + - - +
109A PRO* 3.8 2.0 - - - +
200A ILE* 3.9 26.7 - - + +
204A ALA* 4.7 5.2 - - + -
207A GLN* 5.2 0.9 - - - +
220A ARG* 2.9 25.9 + - - +
225A LEU* 4.0 22.9 - - + -
228A GLU* 3.8 43.1 - - + +
229A VAL* 4.2 6.7 - - + -
232A ALA* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.9 63.1 + - + +
106A ILE* 1.3 84.5 + - - +
108A ILE* 1.3 65.6 + - + +
109A PRO* 3.4 5.7 - - - +
199A ARG* 4.9 7.2 - - - +
200A ILE* 4.9 6.7 + - + +
203A ALA* 3.5 35.4 + - - +
206A ARG* 4.1 14.8 - - - +
207A GLN* 2.6 39.4 + - - +
220A ARG* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.6 10.1 - - + +
104A ILE* 2.9 47.9 + - + +
107A ARG* 1.3 87.0 - - + +
109A PRO* 1.3 66.1 - - - +
110A LEU 3.2 4.7 + - - -
111A ARG* 3.3 24.3 + - + +
112A TYR 3.5 6.9 + - - -
115A LEU* 4.7 10.8 - - + -
----------------------------------------------------------
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