Contacts of the helix formed by residues 73 - 88 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ASP* 3.8 11.1 - - - +
71D ASN 4.6 2.6 + - - +
72D ALA* 1.3 78.3 + - - +
74D SER* 1.3 66.8 + - - +
75D ARG* 3.4 21.8 + - - +
76D GLY* 3.2 29.8 + - - +
77D LEU* 3.5 11.2 + - - +
79D ARG* 4.3 4.7 + - - -
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP* 2.7 33.4 + - - -
39D ASP* 3.6 4.0 - - - +
42D LEU* 3.8 29.2 - - - -
43D HIS* 3.1 26.0 + - - -
46D THR* 4.8 1.4 + - - -
58D ILE* 6.1 0.2 - - - -
72D ALA 3.1 3.4 + - - -
73D ASP* 1.3 69.7 - - - +
75D ARG* 1.3 55.6 + - - +
77D LEU* 2.8 14.1 + - - +
78D LEU* 2.7 34.2 + - - +
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Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.7 20.4 - - + +
73D ASP* 3.3 18.5 - - - +
74D SER* 1.3 76.1 - - - +
76D GLY* 1.3 58.6 - - - +
78D LEU* 3.1 5.9 + - - +
79D ARG* 2.8 56.2 + - - +
116D LYS* 3.2 52.9 + - - +
119D GLU* 3.2 23.4 + - - -
120D ASP* 2.6 40.1 + - - +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 5.9 2.7 - - - -
73D ASP* 3.2 15.6 + - - -
74D SER 3.1 1.2 - - - -
75D ARG* 1.3 79.2 - - - +
77D LEU* 1.3 55.4 + - - +
79D ARG* 3.2 17.4 + - - +
80D GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 6.4 0.4 - - - -
43D HIS* 4.3 13.7 - - + +
46D THR* 4.5 2.0 - - + +
58D ILE* 3.4 31.4 - - + +
61D LEU* 3.2 35.6 - - + +
62D PHE* 3.5 32.3 - - + -
71D ASN* 4.1 28.5 - - - +
72D ALA 5.2 1.1 - - - +
73D ASP 3.5 8.3 + - - +
74D SER* 2.8 12.2 + - - +
76D GLY* 1.3 74.4 - - - +
78D LEU* 1.3 58.2 + - - +
80D GLU* 3.4 2.8 + - - -
81D ALA* 2.8 26.4 + - - +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.1 26.2 - - + +
45D LEU* 4.3 15.0 - - + -
46D THR* 3.6 30.6 + - + +
49D ILE* 3.8 27.8 - - + -
74D SER 2.7 15.8 + - - +
75D ARG* 3.4 10.8 - - - +
77D LEU* 1.3 73.0 - - - +
79D ARG* 1.3 57.7 + - - +
81D ALA* 3.1 5.7 + - + +
82D PHE* 2.8 26.2 + - - +
117D ILE* 4.6 8.7 - - + -
120D ASP* 3.8 29.4 - - + +
121D LEU* 4.3 6.3 - - + -
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ASP* 4.3 4.2 + - - -
75D ARG* 2.8 78.7 + - - +
76D GLY* 3.2 13.6 - - - +
78D LEU* 1.3 71.6 - - - +
80D GLU* 1.3 53.0 + - - +
82D PHE* 2.9 4.8 + - - +
83D ARG* 2.7 36.0 + - - +
119D GLU* 6.0 0.6 - - - +
120D ASP* 3.2 43.0 + - + +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 3.5 25.5 - - + +
62D PHE* 3.9 33.0 - - + -
76D GLY 2.9 18.3 + - - +
77D LEU* 3.6 6.7 - - - +
79D ARG* 1.3 75.3 - - - +
81D ALA* 1.3 62.2 + - - +
83D ARG* 3.2 41.5 + - - +
84D GLN* 3.2 32.6 + - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 3.7 22.4 - - + +
49D ILE* 4.7 4.9 - - + -
50D LEU* 3.4 29.9 - - + +
61D LEU* 4.0 6.1 - - + -
77D LEU 2.8 18.9 + - - +
78D LEU* 3.4 5.6 - - + +
80D GLU* 1.3 78.7 - - - +
82D PHE* 1.3 54.8 + - - +
84D GLN* 3.4 5.5 + - - +
85D VAL* 2.7 34.7 + - - +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 4.7 2.0 - - - +
78D LEU* 2.8 13.5 + - - +
79D ARG* 3.4 7.0 - - - +
81D ALA* 1.3 74.8 - - - +
83D ARG* 1.3 67.3 + - - +
85D VAL* 2.9 20.9 + - + +
86D GLN* 3.0 43.0 + - + +
90D TYR 4.5 5.2 - - - -
91D LYS* 5.1 3.4 - - + -
92D ILE* 3.6 41.1 - - + -
120D ASP 3.6 23.3 - - - +
121D LEU* 3.3 30.3 - - + -
122D GLN* 3.4 35.2 - - + -
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ARG 2.7 15.3 + - - +
80D GLU* 3.2 38.5 + - - +
82D PHE* 1.3 76.1 - - - +
84D GLN* 1.3 73.5 + - - +
86D GLN* 3.1 24.8 + - + +
87D GLU* 3.1 34.5 + - + +
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Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 5.2 1.1 - - - +
55D LEU* 3.4 35.4 - - + +
60D LYS 5.1 4.8 + - - +
61D LEU* 3.4 28.5 + - - +
80D GLU* 3.2 32.8 + - - +
81D ALA* 3.8 7.0 - - - +
82D PHE 3.2 0.2 - - - -
83D ARG* 1.3 89.3 - - - +
85D VAL* 1.3 62.0 + - - +
86D GLN 3.3 0.2 - - - -
87D GLU* 3.2 33.6 - - - +
88D LYS* 3.8 8.8 + - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 3.2 30.5 - - + +
50D LEU* 4.8 0.9 - - + -
53D ALA* 4.3 4.7 - - + -
55D LEU* 4.4 10.8 - - + -
81D ALA 2.7 27.1 - - - +
82D PHE* 2.9 14.5 + - + +
84D GLN* 1.3 76.1 - - - +
86D GLN* 1.3 67.0 + - - +
88D LYS* 3.2 8.9 + - - +
89D GLY 3.5 0.2 + - - -
90D TYR* 2.9 51.3 + - + +
92D ILE* 5.2 0.2 - - + -
155D LEU* 3.6 26.7 - - + -
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PHE* 3.0 49.1 + - + +
83D ARG* 3.2 11.9 - - + +
85D VAL* 1.3 76.7 - - - +
87D GLU* 1.3 54.3 + - - +
89D GLY* 2.6 28.4 + - - -
90D TYR 3.1 22.7 + - - +
91D LYS* 4.5 0.8 - - - +
122D GLN* 3.9 13.9 + - - +
158D GLN* 3.0 37.8 + - - +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ARG* 3.1 30.7 + - + +
84D GLN* 3.2 36.7 - - - +
85D VAL 3.3 0.4 - - - -
86D GLN* 1.3 79.8 - - - +
88D LYS* 1.3 59.1 + - + +
89D GLY 3.3 2.8 + - - -
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ALA* 3.4 16.7 + - + +
54D ALA* 4.8 2.4 + - - +
55D LEU* 3.7 29.2 - - + +
84D GLN 3.9 11.0 - - - +
85D VAL* 3.2 8.3 + - - +
86D GLN 3.1 1.4 + - - -
87D GLU* 1.3 77.5 - - + +
89D GLY* 1.3 59.7 + - - +
90D TYR* 3.5 18.5 - - + -
157D ARG* 3.2 24.1 + - - +
126E GLU* 2.6 40.3 + - - +
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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