Contacts of the helix formed by residues 98 - 116 (chain A) in PDB entry 2VBJ
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 LYS 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.4 20.4 - - + +
18A ASP* 3.0 38.7 + - - +
19A GLY 5.0 1.6 - - - -
21A GLY 3.2 20.9 + - - +
22A SER* 4.2 4.1 - - - +
23A ILE* 3.9 18.0 - - + +
95A LEU* 3.8 9.5 - - + +
97A LEU* 1.3 84.9 - - + +
99A GLN* 1.3 65.0 + - - +
100A LYS 3.4 2.5 - - - -
101A GLN* 3.3 23.1 + - + +
102A ALA* 3.0 23.4 + - - +
136A ASN* 4.8 4.0 + - - -
15C A 4.3 3.4 + - - -
16C G 2.9 33.9 + - - -
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 2.8 48.9 + - + +
93A PRO* 3.4 15.8 + - - +
95A LEU* 3.3 34.3 + - + +
96A LYS* 4.7 4.5 - - - +
97A LEU 3.5 2.2 - - - -
98A LYS* 1.3 77.8 - - - +
100A LYS* 1.3 66.1 + - + +
102A ALA* 3.3 3.1 + - - +
103A ASN* 2.9 32.4 + - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU 5.2 0.6 + - - -
98A LYS 3.4 0.6 - - - -
99A GLN* 1.3 78.9 - - + +
101A GLN* 1.3 61.8 + - - +
103A ASN* 3.3 6.6 + - - +
104A LEU* 2.9 34.3 + - + +
135A LEU* 3.6 37.8 - - + +
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Residues in contact with GLN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.0 21.5 - - + -
97A LEU 3.4 13.2 + - - +
98A LYS* 3.3 34.9 - - - +
99A GLN 3.3 0.2 - - - -
100A LYS* 1.3 74.9 + - - +
102A ALA* 1.3 67.2 + - - +
104A LEU* 3.2 3.5 + - - +
105A VAL* 3.0 26.3 + - - +
132A ILE* 3.9 21.9 - - + +
135A LEU* 3.6 40.9 + - + +
136A ASN* 2.8 29.9 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.9 13.6 - - + +
88A LEU* 4.2 17.7 - - + +
92A GLN* 4.3 14.8 - - + -
95A LEU* 3.8 20.4 - - + -
98A LYS 3.0 14.6 + - - +
99A GLN 3.5 8.1 - - - +
101A GLN* 1.3 76.3 - - - +
103A ASN* 1.3 62.9 + - - +
105A VAL* 3.2 4.9 + - - +
106A LEU* 3.1 25.9 + - - +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLN* 2.7 44.7 + - - +
99A GLN* 2.9 26.8 + - - +
100A LYS* 3.9 5.9 - - - +
102A ALA* 1.3 75.0 - - - +
104A LEU* 1.3 57.1 + - - +
106A LEU* 3.3 16.2 + - - +
107A LYS* 2.9 28.6 + - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 2.9 20.0 + - + +
101A GLN 3.2 2.4 + - - +
103A ASN* 1.3 73.5 - - - +
105A VAL* 1.3 59.2 + - - +
107A LYS* 3.2 20.1 + - + +
108A ILE* 2.9 36.0 + - + +
128A TRP* 4.1 21.1 - - + +
131A GLN* 3.9 37.0 - - + +
132A ILE* 3.4 31.2 - - + +
135A LEU* 3.8 21.1 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.4 31.0 - - + -
24A ILE 5.1 2.7 - - - +
25A ALA* 5.1 2.9 - - + -
41A LEU* 4.1 21.8 - - + -
42A THR 6.2 0.2 - - - +
84A LEU* 4.4 13.2 - - + -
85A ARG* 6.5 0.7 - - - -
88A LEU* 3.6 21.5 - - + -
101A GLN 3.0 10.0 + - - +
102A ALA 3.2 7.4 + - - +
104A LEU* 1.3 74.8 - - - +
106A LEU* 1.3 58.6 + - + +
108A ILE* 3.2 9.1 + - - +
109A THR* 2.9 42.8 + - - +
132A ILE* 3.7 14.4 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.6 30.6 - - + +
88A LEU* 3.9 16.6 - - + +
89A THR* 3.5 44.4 - - + +
92A GLN* 4.6 3.8 - - + +
102A ALA 3.1 15.6 + - - +
103A ASN* 3.6 28.5 - - - +
104A LEU 3.2 0.2 - - - -
105A VAL* 1.3 76.4 - - + +
107A LYS* 1.3 64.2 + - - +
109A THR* 3.3 6.7 + - - +
110A GLU* 3.0 25.6 + - - +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN 2.9 17.5 + - - +
104A LEU* 3.5 19.2 - - + +
106A LEU* 1.3 77.9 - - - +
108A ILE* 1.3 61.1 + - - +
110A GLU* 3.3 18.4 + - - +
111A GLN* 3.3 23.7 + - + +
128A TRP* 3.2 55.1 - - + +
131A GLN* 5.3 2.2 + - - -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.5 4.7 - - + -
41A LEU* 3.9 22.7 - - + -
104A LEU 2.9 21.9 + - - +
105A VAL* 3.5 6.1 - - - +
107A LYS* 1.3 72.3 - - - +
109A THR* 1.3 66.9 + - - +
111A GLN* 2.9 13.9 + - - +
112A LEU* 3.0 27.6 + - + +
125A VAL* 3.7 19.4 - - + +
128A TRP* 3.8 28.0 - - + -
129A VAL* 3.9 27.1 - - + +
132A ILE* 3.7 25.1 - - + -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.0 12.8 - - - +
81A ILE* 3.8 28.3 + - + +
84A LEU* 5.4 1.9 - - - +
85A ARG* 3.6 38.3 + - + +
105A VAL* 2.9 28.0 + - - +
106A LEU* 3.3 9.5 + - - +
108A ILE* 1.3 75.1 - - - +
110A GLU* 1.3 63.0 + - - +
112A LEU* 3.2 28.5 + - - +
113A PRO* 3.6 4.5 - - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 5.6 9.0 - - - +
106A LEU 3.0 15.4 + - - +
107A LYS* 3.6 18.4 - - - +
108A ILE 3.2 0.2 - - - -
109A THR* 1.3 78.7 - - - +
111A GLN* 1.3 79.8 + - - +
113A PRO* 3.6 10.0 - - - +
114A SER* 5.2 0.9 + - - -
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.3 6.7 + - + +
108A ILE 2.9 8.0 + - - +
110A GLU* 1.3 99.2 + - - +
112A LEU* 1.3 70.4 + - - +
113A PRO* 3.1 5.0 - - - -
114A SER* 3.1 18.7 + - - -
115A ALA* 3.0 17.0 + - - +
121A LYS* 3.1 30.3 + - - +
125A VAL* 4.3 7.0 - - + -
128A TRP* 3.5 35.8 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.8 33.7 - - + -
41A LEU* 4.5 5.8 - - + -
81A ILE* 4.3 31.4 - - + -
108A ILE* 3.0 23.6 + - + +
109A THR* 3.2 18.8 + - - +
111A GLN* 1.3 73.6 - - - +
113A PRO* 1.3 68.9 - - + +
115A ALA* 2.7 35.1 + - + +
116A LYS* 3.3 6.2 + - - +
125A VAL* 4.9 0.7 - - + -
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR 3.6 5.2 - - - +
110A GLU 3.6 12.6 - - - +
111A GLN 3.2 4.3 - - - -
112A LEU* 1.3 97.6 - - + +
114A SER* 1.3 59.3 + - - +
115A ALA 3.2 0.2 + - - -
116A LYS* 3.4 16.5 + - + +
117A GLU* 4.5 3.3 - - - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU 5.2 0.7 + - - -
111A GLN* 3.1 27.3 + - - -
113A PRO* 1.3 77.0 - - - +
115A ALA* 1.3 62.2 + - - +
116A LYS 3.3 0.2 - - - -
117A GLU* 3.8 17.2 + - - +
118A SER* 3.9 6.4 + - - -
121A LYS* 3.8 19.7 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.7 1.9 - - - -
39A LEU* 5.4 0.7 - - + -
111A GLN 3.0 10.1 + - - +
112A LEU* 2.7 31.7 + - + +
114A SER* 1.3 69.2 - - - +
116A LYS* 1.3 54.8 + - + +
117A GLU 2.9 11.1 + - - -
118A SER 3.5 16.1 + - - +
121A LYS* 4.1 10.8 - - - -
122A PHE* 3.7 26.1 - - + +
125A VAL* 4.1 22.0 - - + -
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 3.2 21.3 + - + +
35A PHE* 4.6 7.9 - - - -
112A LEU 3.3 5.6 + - - +
113A PRO* 3.4 9.6 + - + +
114A SER 3.3 0.8 - - - -
115A ALA* 1.3 77.9 - - + +
117A GLU* 1.3 58.0 + - - +
122A PHE* 5.6 1.3 - - - -
2E T 5.0 11.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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