Contacts of the helix formed by residues 101 - 113 (chain B) in PDB entry 4JVS
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 ASN 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 2.7 40.5 + - - +
97B GLU* 2.9 41.1 + - - +
98B SER 3.9 3.1 - - - +
99B PHE 3.1 0.6 - - - -
100B ASN* 1.3 76.1 - - - +
102B VAL* 1.3 57.7 + - - +
103B LYS 3.1 2.7 - - - -
104B GLN* 2.9 30.7 + - + +
105B TRP* 2.9 19.2 + - + +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.9 14.8 - - + -
90B VAL 5.0 1.1 - - - +
91B TYR* 3.9 19.5 - - + +
98B SER 3.5 12.5 + - - +
99B PHE* 3.1 21.1 + - + +
101B ASN* 1.3 77.9 - - - +
103B LYS* 1.3 61.9 + - - +
105B TRP* 3.2 9.1 + - + +
106B LEU* 2.9 38.8 + - + +
121B LEU* 3.5 33.0 - - + -
142B PHE* 4.1 12.8 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE 4.5 0.2 + - - -
100B ASN 3.4 14.6 + - - +
102B VAL* 1.3 80.7 - - - +
104B GLN* 1.3 61.8 + - - +
106B LEU* 3.2 16.5 + - - +
107B GLN* 3.3 12.2 + - - +
142B PHE* 4.7 18.9 - - + -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 6.1 0.4 - - - +
74B ARG* 5.1 5.8 - - - +
100B ASN 4.4 0.2 + - - -
101B ASN* 2.9 23.9 + - + +
103B LYS* 1.3 80.4 - - - +
105B TRP* 1.3 61.3 + - + +
107B GLN* 3.1 29.7 + - - +
108B GLU* 3.2 47.4 + - + +
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Residues in contact with TRP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 4.0 12.3 - - + +
18B GLY* 3.3 37.7 - - - -
19B ASP* 2.8 31.9 + - - +
68B ALA 4.8 2.5 - - - -
69B GLY* 3.4 31.4 - - - -
74B ARG* 3.7 34.5 - - - -
81B TYR* 3.9 23.6 - - - -
89B VAL* 3.8 17.9 - - + -
90B VAL 5.1 0.7 - - - -
98B SER 5.1 2.0 - - - -
101B ASN* 2.9 31.4 + - + +
102B VAL* 3.2 12.5 + - + +
104B GLN* 1.3 76.6 - - + +
106B LEU* 1.3 65.1 + - - +
107B GLN 3.1 2.2 - - - -
108B GLU* 3.3 11.3 + - + +
109B ILE* 3.1 26.0 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 4.5 9.2 - - + -
102B VAL* 2.9 27.0 + - + +
103B LYS* 3.2 6.7 + - - +
105B TRP* 1.3 77.5 - - - +
107B GLN* 1.3 56.7 + - - +
109B ILE* 3.4 14.7 - - + +
110B ASP* 2.9 31.6 + - - +
119B LYS* 3.8 30.5 - - + -
121B LEU* 5.9 1.3 - - + -
142B PHE* 3.8 20.6 - - + -
146B LEU* 3.7 28.3 - - + -
148B ILE* 4.3 8.7 - - + -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS 3.3 10.7 + - - +
104B GLN* 3.1 37.5 + - - +
106B LEU* 1.3 76.1 - - - +
108B GLU* 1.3 59.0 + - - +
109B ILE 3.2 1.3 - - - -
110B ASP* 3.1 14.2 + - + +
111B ARG* 2.9 29.7 + - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 3.0 38.3 + - - +
81B TYR* 3.4 23.0 - - + +
104B GLN* 3.2 33.3 + - + +
105B TRP* 3.3 16.6 + - + +
107B GLN* 1.3 76.7 - - - +
109B ILE* 1.3 56.3 + - - +
111B ARG* 4.2 10.4 + - - -
112B TYR* 3.1 60.5 + - + -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 4.0 8.5 - - + -
81B TYR* 3.9 7.0 - - + -
87B ILE* 3.8 31.9 - - + -
89B VAL* 3.7 28.5 - - + -
105B TRP 3.1 12.2 + - - +
106B LEU* 3.4 15.0 - - + +
107B GLN 3.2 0.2 - - - -
108B GLU* 1.3 73.9 - - - +
110B ASP* 1.3 62.3 + - - +
113B ALA* 2.9 39.5 + - + +
114B SER 4.6 2.3 - - - +
117B VAL* 4.9 5.8 - - + -
119B LYS* 3.9 37.9 - - + -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 4.6 2.8 + - - -
106B LEU 2.9 16.1 + - - +
107B GLN* 3.1 16.5 + - + +
109B ILE* 1.3 82.4 - - - +
111B ARG* 1.3 65.4 + - - +
112B TYR 3.5 0.2 + - - -
113B ALA 3.8 9.1 - - - +
114B SER 5.9 0.2 - - - -
119B LYS* 5.3 5.0 - - - -
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 4.1 8.0 + - - -
107B GLN 2.9 15.0 + - - +
108B GLU* 3.7 13.3 + - - +
110B ASP* 1.3 80.0 - - - +
112B TYR* 1.3 105.6 + - + +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 4.9 10.9 + - + +
75B THR* 5.6 2.3 + - - -
78B SER* 3.7 39.4 + - - +
81B TYR* 3.4 26.7 - + + -
82B ARG* 2.6 41.9 + - + +
108B GLU* 3.1 44.8 + - + +
111B ARG* 1.3 130.0 + - + +
113B ALA* 1.3 55.9 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.6 21.7 - - + +
82B ARG* 3.3 17.0 + - - -
87B ILE* 3.8 19.1 - - + -
109B ILE* 2.9 23.1 + - + +
110B ASP 3.8 5.9 - - - +
112B TYR* 1.3 78.4 - - - +
114B SER* 1.3 66.8 + - - +
117B VAL* 3.6 18.6 - - + -
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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