Contacts of the helix formed by residues 79 - 97 (chain A) in PDB entry 2VRB
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 ASP 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 3.0 25.0 - - + +
78A TYR* 1.3 75.2 - - - +
80A ASN* 1.3 56.9 + - - +
81A THR* 3.1 12.5 + - - -
82A LEU* 3.1 30.3 + - + +
83A LEU* 2.9 27.4 + - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS 4.6 3.1 - - - +
78A TYR 3.2 10.8 + - - +
79A ASP* 1.3 73.7 + - - +
81A THR* 1.3 62.3 + - - +
83A LEU* 3.3 9.6 + - - +
84A ILE* 3.1 27.8 + - - +
116A PRO* 3.9 28.0 - - + +
117A LEU* 3.5 32.6 - - - +
120A VAL* 3.5 18.6 - - + +
247A ILE* 6.3 1.6 - - - +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 3.1 9.4 + - - -
80A ASN* 1.3 74.6 - - - +
82A LEU* 1.3 65.9 + - - +
84A ILE* 3.3 17.9 + - + +
85A VAL* 3.5 15.8 + - + +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 4.4 8.1 - - - +
77A HIS* 3.6 40.2 - - + +
79A ASP* 3.1 28.6 + - + +
81A THR* 1.3 74.7 - - - +
83A LEU* 1.3 66.2 + - - +
85A VAL* 3.0 26.5 + - + +
86A GLN* 3.0 31.3 + - + +
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Residues in contact with LEU 83 (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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74A SER* 4.3 4.5 - - - +
75A GLY* 3.5 42.6 - - - +
77A HIS* 4.0 21.5 - - + +
79A ASP 2.9 13.5 + - - +
80A ASN* 3.4 13.0 - - - +
82A LEU* 1.3 77.4 - - - +
84A ILE* 1.3 56.6 + - - +
86A GLN* 3.3 23.0 + - - +
87A HIS* 2.9 49.4 + - + +
117A LEU* 3.9 28.0 - - + -
120A VAL* 4.0 9.0 - - + -
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Residues in contact with ILE 84 (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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80A ASN 3.1 15.8 + - - +
81A THR* 3.6 11.0 - - + +
82A LEU 3.2 0.8 - - - -
83A LEU* 1.3 75.6 - - - +
85A VAL* 1.3 59.8 + - + +
87A HIS* 3.9 5.1 - - - +
88A ALA* 2.9 32.3 + - + +
119A HIS* 4.5 3.4 - - + +
120A VAL* 3.9 24.9 - - + +
123A ALA* 3.6 32.1 - - + -
124A THR* 5.5 0.7 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.8 14.4 - - + +
82A LEU* 3.0 18.0 + - + +
84A ILE* 1.3 79.8 - - + +
86A GLN* 1.3 61.7 + - + +
88A ALA* 3.2 7.7 + - + +
89A ASN* 3.0 37.4 + - - +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.8 36.9 - - + +
55A ASN* 2.8 38.5 + - - +
75A GLY* 4.9 1.0 - - - -
76A PRO* 5.9 0.2 - - - +
77A HIS* 4.4 12.4 + - - +
82A LEU* 3.0 38.7 + - + +
83A LEU* 3.3 28.8 + - - +
85A VAL* 1.3 74.1 - - + +
87A HIS* 1.3 62.5 + - + +
89A ASN* 3.1 7.3 - - - +
90A VAL* 2.9 32.9 + - - +
1286A NAP 4.4 7.1 + - - -
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 5.1 3.1 - + - -
72A PHE* 3.6 22.0 - + + -
74A SER* 3.0 26.1 + - - -
75A GLY* 3.0 24.4 + - - -
83A LEU* 2.9 39.4 + - + +
84A ILE* 4.0 3.6 - - - +
86A GLN* 1.3 79.3 - - + +
88A ALA* 1.3 58.4 + - - +
90A VAL* 3.1 3.1 + - - +
91A VAL* 2.9 34.1 + - - +
104A TYR* 3.1 18.4 + + - -
120A VAL* 4.1 8.1 - - + +
124A THR* 2.9 32.7 + - + +
127A ALA* 6.0 0.2 - - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 2.9 23.5 + - + +
85A VAL* 3.2 7.4 + - - +
87A HIS* 1.3 77.5 - - - +
89A ASN* 1.3 56.2 + - - +
91A VAL* 3.4 7.5 + - - +
92A LYS* 2.9 30.5 + - - +
127A ALA* 5.3 9.0 - - + -
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR 3.0 24.5 + - - +
55A ASN* 4.4 5.1 + - - +
57A PRO* 4.1 30.8 - - + +
60A LEU* 4.0 8.7 - - + +
85A VAL* 3.0 30.1 + - - +
86A GLN* 3.1 10.8 - - - +
88A ALA* 1.3 73.0 - - - +
90A VAL* 1.3 67.2 + - - +
92A LYS* 3.3 5.0 + - - +
93A ALA* 3.0 24.8 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 5.5 0.4 - - + -
54A TYR* 3.3 37.9 - - + -
60A LEU* 3.8 14.8 - - + -
64A PHE* 3.7 21.0 - - + -
70A LEU* 4.9 3.4 - - + -
72A PHE* 3.7 41.1 - - + -
86A GLN 2.9 19.0 + - - +
87A HIS 3.4 7.2 - - - +
89A ASN* 1.3 76.3 - - - +
91A VAL* 1.3 64.4 + - - +
93A ALA* 3.2 4.2 + - - +
94A ALA* 3.0 20.1 + - + +
102A ILE* 5.7 0.2 - - + -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.1 13.7 - - + -
87A HIS 2.9 21.7 + - - +
88A ALA 3.9 4.3 - - - +
90A VAL* 1.3 77.5 - - - +
92A LYS* 1.3 64.3 + - - +
94A ALA* 3.4 6.3 + - + +
95A ARG* 3.1 21.7 + - - +
102A ILE* 5.5 4.0 - - + -
124A THR* 4.5 2.9 - - + -
127A ALA* 3.6 32.1 - - + +
128A ILE* 3.7 25.6 - - + +
130A THR* 5.1 0.2 - - - +
131A THR* 3.2 28.3 - - + +
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Residues in contact with LYS 92 (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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88A ALA 2.9 19.1 + - - +
89A ASN* 3.9 5.2 - - - +
90A VAL 3.2 0.2 - - - -
91A VAL* 1.3 78.1 - - - +
93A ALA* 1.3 58.9 + - - +
95A ARG* 3.4 25.2 + - - +
96A ASP* 2.8 59.9 + - - +
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Residues in contact with ALA 93 (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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57A PRO* 4.7 4.3 - - + +
60A LEU* 3.5 36.0 - - + +
61A GLN* 4.2 9.4 - - + +
64A PHE* 3.7 9.3 - - + -
89A ASN 3.0 17.7 + - - +
90A VAL 3.2 4.2 + - - +
92A LYS* 1.3 77.8 - - - +
94A ALA* 1.3 52.8 + - - +
96A ASP* 3.3 8.4 + - - +
97A ALA* 2.8 35.5 + - - +
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Residues in contact with ALA 94 (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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64A PHE* 3.6 8.4 - - + -
70A LEU* 4.0 20.0 - - + -
90A VAL 3.0 14.6 + - - +
91A VAL* 3.8 4.9 - - + +
92A LYS 3.3 0.2 - - - -
93A ALA* 1.3 72.3 - - - +
95A ARG* 1.3 65.7 + - - +
97A ALA 3.4 0.3 + - - -
98A GLY 3.2 2.9 + - - -
99A VAL* 3.0 48.5 + - + +
102A ILE* 4.6 10.8 - - + -
133A ILE* 4.0 7.0 - - + +
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Residues in contact with ARG 95 (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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91A VAL 3.1 17.0 + - - +
92A LYS* 3.7 28.6 - - - +
93A ALA 3.4 0.2 - - - -
94A ALA* 1.3 77.8 - - - +
96A ASP* 1.3 89.9 + - - +
98A GLY* 3.1 13.7 + - - -
131A THR* 3.9 35.9 - - + +
133A ILE* 3.8 12.4 - - + +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 5.6 10.5 - - + +
92A LYS* 2.8 46.5 + - - +
93A ALA* 3.8 7.7 - - - +
95A ARG* 1.3 107.5 + - - +
97A ALA* 1.3 61.0 + - - +
98A GLY 3.1 1.4 + - - -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 4.6 7.0 - - - +
64A PHE* 3.5 41.7 - - + +
65A ALA* 4.3 4.2 - - - +
66A GLY* 4.5 9.9 + - - -
67A VAL 5.4 0.5 - - - +
93A ALA 2.8 18.2 + - - +
94A ALA 3.9 4.0 - - - +
95A ARG 3.2 0.4 - - - -
96A ASP* 1.3 77.3 - - - +
98A GLY* 1.3 62.1 + - - +
99A VAL* 3.5 2.4 + - + -
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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
------------------------------------------------------------
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