Contacts of the helix formed by residues 110 - 129 (chain A) in PDB entry 1VYH
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 THR 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 1.3 73.9 - - - +
111A ALA* 1.3 65.0 + - - +
112A GLU* 3.5 15.3 + - - +
113A GLU* 2.7 42.4 + - + +
114A VAL* 3.0 10.6 + - - +
152A LYS* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN 3.7 1.4 + - - -
110A THR* 1.3 70.7 - - - +
112A GLU* 1.3 71.0 + - - +
114A VAL* 3.1 6.7 + - - +
115A ALA* 2.9 22.0 + - - +
152A LYS* 3.7 40.6 - - + +
155A LYS* 3.8 21.5 - - + +
156A VAL* 3.7 15.2 - - + +
159A LEU* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.6 11.9 + - - +
111A ALA* 1.3 87.2 + - - +
113A GLU* 1.3 62.7 + - - +
115A ALA* 3.2 4.5 + - - +
116A GLY* 3.1 17.5 + - - -
155A LYS* 4.7 14.0 - - - +
159A LEU* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 3.5 34.2 + - + +
8A PRO* 3.1 30.1 - - + +
9A ALA* 3.6 4.0 - - + +
108A GLU 3.9 2.8 - - - +
109A ASN* 2.8 22.4 - - + +
110A THR* 2.7 48.4 + - - +
112A GLU* 1.3 77.1 - - - +
114A VAL* 1.3 59.3 + - - +
116A GLY* 3.0 6.5 + - - -
117A GLY 2.8 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.4 5.8 - - - -
78A THR* 4.3 2.9 - - + +
103A GLY* 4.1 28.9 - - - +
106A ASN* 3.8 19.5 - - + +
109A ASN* 3.5 25.8 - - + +
110A THR 3.0 14.7 + - - +
111A ALA* 3.1 8.5 + - - +
113A GLU* 1.3 75.5 - - - +
115A ALA* 1.3 62.9 + - - +
117A GLY* 2.9 12.1 + - - +
118A ILE* 3.1 20.7 + - + +
139A LEU* 4.7 0.7 - - + -
152A LYS* 4.5 5.8 - - - -
156A VAL* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA 2.9 11.2 + - - +
112A GLU 3.3 9.9 - - - +
114A VAL* 1.3 76.5 - - - +
116A GLY* 1.3 64.2 + - - +
117A GLY 3.3 0.2 + - - -
118A ILE* 3.3 8.3 + - - +
119A GLU* 2.9 38.6 + - - +
156A VAL* 4.4 7.5 - - + +
159A LEU* 3.8 30.3 - - + -
160A LEU* 4.1 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.2 13.0 - - - -
10A ALA* 4.3 1.0 - - - +
112A GLU 3.1 7.0 + - - -
113A GLU* 3.0 9.8 + - - -
115A ALA* 1.3 76.2 - - - +
117A GLY* 1.3 56.8 + - - +
119A GLU* 3.3 15.1 + - - +
120A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.0 21.5 - - - -
10A ALA* 4.1 8.4 - - - +
78A THR* 3.9 12.8 - - - -
82A LEU* 5.1 0.7 - - - +
113A GLU 2.8 12.9 + - - -
114A VAL 2.9 6.4 + - - -
116A GLY* 1.3 71.3 - - - +
118A ILE* 1.3 65.3 + - - -
120A ALA* 3.0 6.9 + - - +
121A ILE* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.8 9.2 - - + +
100A VAL* 4.5 13.5 - - + -
102A VAL* 3.5 26.2 - - + +
114A VAL* 3.1 18.4 + - + +
115A ALA 3.6 4.3 - - - +
117A GLY* 1.3 71.3 - - - +
119A GLU* 1.3 66.8 + - - +
121A ILE* 2.9 13.8 + - - +
122A VAL* 2.8 22.6 + - + +
136A VAL* 4.3 31.4 - - + -
137A LEU 6.0 0.2 - - - +
139A LEU* 4.5 4.3 - - + -
156A VAL* 3.9 15.7 - - + -
160A LEU* 3.5 31.2 - - + -
164A LEU* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 2.9 32.5 + - - +
116A GLY* 3.5 12.3 - - - +
118A ILE* 1.3 75.2 - - - +
120A ALA* 1.3 56.8 + - - +
122A VAL* 3.1 10.1 + - - +
123A GLN* 2.8 40.4 + - - +
159A LEU* 4.5 1.7 - - - +
160A LEU* 3.9 12.0 - - + +
163A SER* 2.6 39.2 + - - +
164A LEU* 4.9 3.6 - - + -
167A LEU* 4.4 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 3.8 23.8 - - + +
82A LEU* 4.5 14.1 - - + +
116A GLY 2.9 12.7 + - - +
117A GLY 3.1 9.9 - - - +
119A GLU* 1.3 76.3 - - - +
121A ILE* 1.3 62.1 + - - +
123A GLN* 3.2 14.4 + - - +
124A LEU* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 4.0 20.2 - - + +
81A VAL* 3.5 26.7 - - + -
82A LEU* 4.1 20.4 - - + +
85A LEU* 3.7 24.2 - - + -
100A VAL* 4.5 14.6 - - + -
102A VAL* 3.8 20.4 - - + -
117A GLY 2.9 13.3 + - - +
118A ILE* 2.9 9.9 + - - +
120A ALA* 1.3 72.8 - - - +
122A VAL* 1.3 67.2 + - - +
124A LEU* 3.1 8.2 + - - +
125A ILE* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL* 5.5 3.6 - - + -
118A ILE* 2.8 18.9 + - + +
119A GLU* 3.4 8.1 - - - +
121A ILE* 1.3 71.1 - - + +
123A GLN* 1.3 65.6 + - - +
125A ILE* 3.0 10.2 + - - +
126A ASN* 3.0 31.6 + - - +
134A ILE* 4.3 8.8 - - + +
136A VAL* 3.9 21.1 - - + -
164A LEU* 4.0 8.1 - - + -
167A LEU* 3.5 24.7 - - + -
170A VAL* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 2.8 39.4 + - - +
120A ALA* 3.3 12.8 - - - +
122A VAL* 1.3 73.9 - - - +
124A LEU* 1.3 63.5 + - - +
126A ASN* 3.4 13.3 + - - +
127A THR* 3.1 26.5 + - - +
167A LEU* 4.3 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.4 12.1 - - + -
85A LEU* 3.5 38.8 - - + +
86A LYS* 4.0 32.1 - - + +
90A LEU* 4.5 6.5 - - + -
120A ALA 3.0 12.7 + - - +
121A ILE* 3.4 8.5 - - - +
123A GLN* 1.3 76.4 - - - +
125A ILE* 1.3 66.1 + - - +
127A THR* 2.9 17.7 + - + -
128A ARG* 3.0 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.9 1.6 - - + -
85A LEU* 4.0 19.5 - - + -
90A LEU* 4.1 15.3 - - + -
98A ILE* 3.4 38.1 - - + -
100A VAL* 3.7 30.3 - - + -
121A ILE* 2.9 31.4 + - + +
122A VAL* 3.0 6.7 + - - +
124A LEU* 1.3 76.9 - - - +
126A ASN* 1.3 58.8 + - - +
127A THR 2.9 0.3 + - - -
128A ARG 3.3 0.2 + - - -
129A GLN* 2.6 37.4 + - + +
134A ILE* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.0 30.6 + - - +
123A GLN* 3.5 12.4 + - - +
125A ILE* 1.3 76.0 - - - +
127A THR* 1.3 62.8 + - - +
129A GLN 4.1 12.3 - - - +
130A PRO* 3.8 18.0 - - + +
132A ALA 5.3 2.9 - - - +
134A ILE* 4.0 14.3 - - + +
167A LEU* 4.9 3.1 - - - +
168A ALA* 3.4 35.2 + - + +
169A ASN* 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 3.1 12.7 + - - +
124A LEU* 2.9 16.3 + - + -
126A ASN* 1.3 81.7 + - - +
128A ARG* 1.3 74.1 + - - +
129A GLN 3.3 0.7 + - - -
130A PRO* 3.6 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 5.0 5.7 + - - -
86A LYS* 3.1 44.0 + - - +
90A LEU* 4.0 33.8 - - + +
91A GLU* 5.0 13.1 + - - +
94A LYS* 3.9 8.5 + - - -
124A LEU* 3.0 37.5 + - - +
127A THR* 1.3 84.4 - - - +
129A GLN* 1.3 69.0 + - + +
130A PRO* 3.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.3 38.5 + - + +
93A ILE* 2.9 36.1 + - - +
94A LYS* 3.0 19.2 + - - +
95A PRO* 3.9 9.4 - - - +
98A ILE* 4.4 5.6 - - + -
125A ILE* 2.6 30.4 + - + +
126A ASN* 4.2 3.0 - - - -
128A ARG* 1.3 81.6 - - + +
130A PRO* 1.3 59.0 - - - +
131A GLN* 3.0 19.3 + - - +
132A ALA* 2.9 33.0 + - + +
----------------------------------------------------------
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