Contacts of the helix formed by residues 73 - 88 (chain A) in PDB entry 1VHA
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASP* 4.0 3.2 - - - +
70A LYS 3.7 14.2 + - - +
71A ASN 3.1 2.2 - - - -
72A ALA* 1.3 78.9 - - + +
74A SER* 1.3 65.7 + - - +
75A ARG* 3.4 21.3 + - - +
76A GLY* 3.5 21.8 + - - -
77A LEU* 3.5 15.8 + - - +
79A ARG* 4.3 8.1 + - - -
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Residues in contact with SER 74 (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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37A ASP* 2.7 37.7 + - - -
39A ASP* 3.6 13.3 - - - +
42A LEU* 3.8 20.2 - - - +
43A HIS* 3.1 26.0 + - - -
46A THR* 4.7 0.9 + - - -
71A ASN 4.9 0.7 + - - -
73A ASP* 1.3 70.3 + - - +
75A ARG* 1.3 60.0 + - - +
76A GLY 3.2 1.6 - - - -
77A LEU* 3.7 10.2 - - - +
78A LEU* 3.0 26.3 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.6 21.3 - - + -
73A ASP* 3.4 11.7 + - - +
74A SER* 1.3 77.0 - - - +
76A GLY* 1.3 61.9 + - - +
78A LEU* 3.6 5.3 - - - +
79A ARG* 2.9 56.3 + - - +
116A LYS* 3.4 56.5 + - - +
119A GLU* 3.6 24.9 + - - -
120A ASP* 2.8 35.7 + - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.6 5.5 - - - -
70A LYS 5.5 2.2 - - - -
73A ASP* 3.5 15.9 + - - -
74A SER 3.2 0.2 - - - -
75A ARG* 1.3 81.0 - - - +
77A LEU* 1.3 62.5 + - - +
79A ARG* 3.1 21.0 - - - +
80A GLU* 3.1 24.3 + - - +
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Residues in contact with LEU 77 (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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36A SER* 5.8 0.7 - - - -
43A HIS* 4.2 12.1 - - + -
46A THR* 4.5 1.6 - - + +
58A ILE* 3.7 31.0 - - + +
61A LEU* 3.2 29.1 - - + +
62A PHE* 3.9 20.6 - - + -
70A LYS 4.1 7.0 - - - +
71A ASN* 3.1 47.8 - - - +
73A ASP 3.5 12.0 + - - +
74A SER* 3.5 7.1 + - - +
75A ARG 3.3 0.4 - - - -
76A GLY* 1.3 74.4 - - - +
78A LEU* 1.3 65.0 + - - +
80A GLU* 3.3 3.2 + - - +
81A ALA* 3.0 19.4 + - - +
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Residues in contact with LEU 78 (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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42A LEU* 3.9 27.6 - - + +
45A LEU* 4.0 26.2 - - + -
46A THR* 3.3 28.0 + - + +
49A ILE* 4.5 4.3 - - + -
74A SER 3.0 18.1 + - - +
75A ARG 3.6 4.7 - - - +
77A LEU* 1.3 76.6 - - - +
79A ARG* 1.3 63.6 + - - +
81A ALA* 3.1 7.3 + - + +
82A PHE* 3.0 20.1 + - - +
117A ILE* 4.7 6.7 - - + -
120A ASP* 4.0 24.9 - - + +
121A LEU* 4.0 22.7 - - + -
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Residues in contact with ARG 79 (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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73A ASP* 4.3 7.5 + - - -
75A ARG* 2.9 51.4 + - - +
76A GLY* 3.1 31.9 - - - +
78A LEU* 1.3 76.2 - - - +
80A GLU* 1.3 54.0 + - - +
82A PHE* 3.0 5.0 + - - +
83A ARG* 2.7 35.9 + - - +
120A ASP* 3.1 42.5 + - + +
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Residues in contact with GLU 80 (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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61A LEU* 3.8 19.9 - - + +
62A PHE* 3.7 34.9 - - + -
76A GLY 3.1 15.5 + - - +
77A LEU* 3.6 5.4 - - - +
78A LEU 3.3 0.2 - - - -
79A ARG* 1.3 79.0 - - - +
81A ALA* 1.3 62.4 + - - +
83A ARG* 2.7 48.0 + - - -
84A GLN* 2.7 39.3 + - - +
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Residues in contact with ALA 81 (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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46A THR* 3.9 17.3 - - + +
49A ILE* 4.9 6.3 - - + -
50A LEU* 3.6 34.0 - - + +
61A LEU* 4.1 5.6 - - + +
77A LEU 3.0 13.2 + - - +
78A LEU* 3.1 10.7 + - + +
80A GLU* 1.3 76.4 - - - +
82A PHE* 1.3 59.4 + - - +
84A GLN* 3.3 5.0 + - - +
85A VAL* 2.9 32.3 + - - +
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Residues in contact with PHE 82 (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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49A ILE* 5.0 3.5 - - + +
78A LEU 3.0 12.5 + - - +
79A ARG* 3.0 6.9 + - - +
81A ALA* 1.3 74.5 - - - +
83A ARG* 1.3 68.4 + - - +
85A VAL* 3.2 8.9 + - + -
86A GLN* 3.0 56.6 + - + +
90A TYR 4.8 0.9 - - - -
91A LYS* 4.5 6.7 - - + -
92A ILE* 3.2 40.6 - - + -
120A ASP 3.8 20.9 - - - +
121A LEU* 3.1 29.6 - - + -
122A GLN* 3.3 36.1 - - + -
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Residues in contact with ARG 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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79A ARG 2.7 16.7 + - - +
80A GLU* 2.7 48.6 + - - +
81A ALA 3.2 0.2 - - - -
82A PHE* 1.3 77.3 - - - +
84A GLN* 1.3 73.5 + - - +
86A GLN* 3.2 8.5 + - - +
87A GLU* 3.1 60.6 + - + +
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Residues in contact with GLN 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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50A LEU* 4.9 1.4 - - - +
55A LEU* 3.8 28.0 - - + +
60A LYS 4.8 4.6 + - - +
61A LEU* 4.1 23.6 + - - +
80A GLU* 2.7 40.7 + - - +
81A ALA* 3.6 8.5 - - - +
83A ARG* 1.3 88.0 - - - +
85A VAL* 1.3 63.9 + - - +
87A GLU* 3.2 28.0 + - - +
88A LYS* 3.4 13.0 + - - +
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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
----------------------------------------------------------
49A ILE* 3.2 42.4 - - + +
50A LEU* 4.8 1.1 - - - +
53A ALA* 4.0 12.8 - - + -
55A LEU* 4.5 9.0 - - + -
81A ALA 2.9 15.9 + - - +
82A PHE* 3.2 13.4 + - + +
84A GLN* 1.3 75.5 - - - +
86A GLN* 1.3 62.4 + - - +
88A LYS* 3.1 16.1 + - - +
89A GLY 3.5 0.2 + - - -
90A TYR* 3.1 42.6 + - + +
91A LYS* 5.2 0.4 - - - -
155A LEU* 3.7 16.6 - - + -
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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
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82A PHE* 3.0 48.2 + - + +
83A ARG* 3.2 11.0 + - - +
85A VAL* 1.3 74.2 - - - +
87A GLU* 1.3 58.1 + - + +
88A LYS 3.0 2.0 - - - -
89A GLY* 2.7 24.6 + - - -
90A TYR 3.4 16.4 - - - +
91A LYS* 5.0 1.4 - - - +
122A GLN* 4.0 15.5 + - - +
158A GLN* 3.0 32.0 + - - +
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Residues in contact with GLU 87 (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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83A ARG* 3.1 46.9 + - + +
84A GLN* 3.2 20.6 + - - +
86A GLN* 1.3 76.2 - - + +
88A LYS* 1.3 61.0 + - + +
89A GLY 3.2 1.0 + - - -
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Residues in contact with LYS 88 (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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53A ALA* 2.8 29.7 + - + +
54A ALA* 4.5 2.2 + - - +
55A LEU* 4.1 23.1 - - + +
84A GLN 3.4 8.2 + - - +
85A VAL* 3.1 11.3 + - - +
86A GLN 3.0 1.2 - - - -
87A GLU* 1.3 78.7 - - + +
89A GLY* 1.3 57.9 + - - +
90A TYR* 3.6 17.0 - - + -
157A ARG* 3.4 27.2 + - - +
126B GLU* 2.8 35.2 + - - +
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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