Contacts of the helix formed by residues 73 - 88 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ASP* 3.7 8.5 - - - +
71B ASN 4.2 6.7 + - - +
72B ALA* 1.3 76.9 + - - +
74B SER* 1.3 62.9 + - - +
75B ARG* 2.8 22.1 + - - +
76B GLY* 2.8 37.9 + - - +
77B LEU* 3.5 12.9 + - - +
79B ARG* 4.8 1.9 + - - -
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Residues in contact with SER 74 (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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37B ASP* 2.6 34.8 + - - -
39B ASP* 3.5 13.9 - - - +
42B LEU* 3.9 15.2 - - - +
43B HIS* 2.7 31.2 + - - -
46B THR* 4.7 1.0 + - - -
72B ALA 3.1 0.9 + - - -
73B ASP* 1.3 70.4 - - - +
75B ARG* 1.3 59.5 + - - +
77B LEU* 3.2 12.7 + - - +
78B LEU* 2.9 28.8 + - - +
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Residues in contact with ARG 75 (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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42B LEU* 3.6 20.4 - - + -
73B ASP* 2.8 17.3 + - - +
74B SER* 1.3 77.5 - - - +
76B GLY* 1.3 61.5 + - - +
78B LEU* 3.3 6.4 + - - +
79B ARG* 3.0 50.4 + - - +
116B LYS* 3.6 55.8 + - - +
119B GLU* 4.2 12.9 + - - +
120B ASP* 2.9 36.6 + - - +
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Residues in contact with GLY 76 (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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62B PHE* 5.2 5.4 - - - -
73B ASP* 2.8 17.6 + - - -
74B SER 3.2 0.4 - - - -
75B ARG* 1.3 77.1 - - - +
77B LEU* 1.3 56.4 + - - +
79B ARG* 3.4 18.3 + - - +
80B GLU* 3.0 28.6 + - - +
83B ARG* 4.6 2.3 + - - -
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Residues in contact with LEU 77 (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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36B SER* 5.8 1.1 - - - -
43B HIS* 4.4 13.9 - - + +
46B THR* 4.4 2.5 - - - +
58B ILE* 3.7 30.5 - - + +
61B LEU* 3.8 18.6 - - + +
62B PHE* 3.6 33.9 - - + -
71B ASN* 3.8 25.8 - - - +
72B ALA 5.0 1.1 - - - +
73B ASP 3.5 7.4 + - - +
74B SER* 3.2 19.9 + - - +
76B GLY* 1.3 77.3 - - - +
78B LEU* 1.3 57.8 + - - +
80B GLU* 3.2 5.5 + - - +
81B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 78 (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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42B LEU* 3.9 28.9 - - + +
45B LEU* 4.0 26.9 - - + -
46B THR* 3.6 24.4 + - + +
49B ILE* 4.1 7.2 - - + -
74B SER 2.9 16.4 + - - +
75B ARG 3.6 5.4 - - - +
77B LEU* 1.3 77.1 - - - +
79B ARG* 1.3 57.3 + - - +
81B ALA* 3.3 3.3 + - + +
82B PHE* 3.0 25.6 + - - +
117B ILE* 4.7 6.3 - - + -
120B ASP* 4.0 24.9 - - + +
121B LEU* 3.8 24.2 - - + -
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Residues in contact with ARG 79 (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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73B ASP* 4.8 1.8 + - - -
75B ARG* 3.0 45.6 + - - +
76B GLY* 3.7 25.5 - - - +
78B LEU* 1.3 73.0 - - - +
80B GLU* 1.3 61.6 + - - +
82B PHE* 3.8 6.6 - - - +
83B ARG* 2.9 54.1 + - + +
119B GLU* 5.0 2.2 + - - -
120B ASP* 2.8 43.6 + - + +
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Residues in contact with GLU 80 (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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61B LEU* 4.0 12.3 - - + -
62B PHE* 4.0 32.0 - - + -
76B GLY 3.0 14.5 + - - +
77B LEU* 3.2 12.3 + - - +
79B ARG* 1.3 77.4 - - - +
81B ALA* 1.3 62.3 + - - +
83B ARG* 2.7 35.5 + - - +
84B GLN* 3.1 54.1 + - - +
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Residues in contact with ALA 81 (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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46B THR* 3.6 24.7 - - + +
49B ILE* 4.7 6.3 - - + -
50B LEU* 3.5 29.3 - - + +
61B LEU* 4.6 3.8 - - + +
77B LEU 2.9 12.9 + - - +
78B LEU* 3.5 8.5 - - + +
80B GLU* 1.3 77.9 - - - +
82B PHE* 1.3 62.9 + - - +
84B GLN* 3.3 4.2 + - - +
85B VAL* 3.0 28.6 + - - +
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Residues in contact with PHE 82 (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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49B ILE* 4.8 4.0 - - + +
78B LEU 3.0 16.1 + - - +
79B ARG* 3.8 4.0 - - - +
81B ALA* 1.3 76.3 - - - +
83B ARG* 1.3 63.9 + - + +
85B VAL* 3.0 11.4 + - + +
86B GLN* 2.8 60.4 + - + +
90B TYR 4.5 1.6 - - - -
91B LYS* 4.3 17.7 - - + -
92B ILE* 3.3 36.3 - - + -
120B ASP 4.0 12.3 - - - +
121B LEU* 3.5 30.5 - - + +
122B GLN* 3.4 38.4 - - + -
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Residues in contact with ARG 83 (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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62B PHE* 5.6 0.6 - - - -
76B GLY 4.6 2.2 + - - -
79B ARG* 2.9 46.4 + - + +
80B GLU* 2.7 45.9 + - - +
82B PHE* 1.3 82.4 - - + +
84B GLN* 1.3 56.1 - - - +
86B GLN* 2.9 16.4 + - - +
87B GLU* 2.8 32.9 + - + +
122B GLN* 5.4 4.0 - - - +
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Residues in contact with GLN 84 (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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50B LEU* 5.0 2.0 - - + +
55B LEU* 3.8 31.4 - - + +
60B LYS 5.0 4.2 + - - +
61B LEU* 3.5 34.4 + - - +
80B GLU* 3.1 36.8 + - - +
81B ALA* 3.7 5.4 - - - +
83B ARG* 1.3 76.5 - - + +
85B VAL* 1.3 61.1 + - - +
87B GLU* 3.4 13.6 + - + +
88B LYS* 3.4 18.9 + - - +
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Residues in contact with VAL 85 (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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49B ILE* 3.3 34.3 - - + +
50B LEU* 4.7 1.8 - - - +
53B ALA* 4.1 9.9 - - + -
55B LEU* 4.2 8.5 - - + -
81B ALA 3.0 14.4 - - - +
82B PHE* 3.0 12.2 + - + +
84B GLN* 1.3 77.3 - - - +
86B GLN* 1.3 61.2 + - - +
88B LYS* 3.4 6.6 + - - +
89B GLY 3.4 3.8 + - - -
90B TYR* 3.0 40.3 + - + +
155B LEU* 3.2 35.4 - - + -
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Residues in contact with GLN 86 (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 PHE* 2.8 52.4 + - + +
83B ARG* 2.9 16.9 + - - +
85B VAL* 1.3 74.0 - - - +
87B GLU* 1.3 58.8 + - + +
88B LYS 2.9 1.8 - - - -
89B GLY* 2.5 28.6 + - - -
90B TYR 3.6 12.5 + - - +
122B GLN* 3.6 16.8 + - - +
158B GLN* 4.6 21.5 + - - +
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Residues in contact with GLU 87 (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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83B ARG* 2.8 20.9 + - + +
84B GLN* 3.6 16.2 - - + +
86B GLN* 1.3 74.7 - - - +
88B LYS* 1.3 62.2 + - + +
89B GLY* 3.4 0.5 + - - -
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Residues in contact with LYS 88 (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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53B ALA* 3.2 29.2 + - + -
54B ALA* 5.6 0.4 - - - +
55B LEU* 3.5 36.7 - - + +
84B GLN 3.4 7.2 + - - +
85B VAL 3.8 8.5 - - - +
86B GLN 2.9 1.2 - - - -
87B GLU* 1.3 79.5 - - + +
89B GLY* 1.3 59.6 + - - +
90B TYR* 3.7 18.9 - - + -
157B ARG* 3.8 19.1 + - - -
126C GLU* 3.5 27.8 + - - +
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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