Contacts of the strand formed by residues 2 - 12 (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 ILE 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0D SER* 3.6 4.4 - - - -
1D LEU* 1.3 83.4 - - + +
3D ARG* 1.3 72.7 + - - +
154D LEU* 3.6 24.7 - - + -
155D LEU 3.3 10.1 - - - +
156D ILE* 4.5 8.1 - - + -
2E ILE* 4.4 25.4 - - + -
93E GLY 5.2 3.3 - - - +
94E ASN* 4.2 1.7 - - - +
154E LEU* 3.9 21.6 - - + +
156E ILE* 4.8 15.5 - - + +
2F ILE* 3.6 35.4 - - + -
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Residues in contact with ARG 3 (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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0D SER* 3.4 24.6 + - - -
2D ILE* 1.3 78.1 - - - +
4D ILE* 1.3 58.9 + - - +
51D GLY 5.2 0.2 + - - -
52D ALA* 2.9 34.0 + - - +
53D ALA* 4.0 2.0 - - - +
54D ALA* 3.5 15.4 - - - +
90D TYR* 3.2 42.5 + - + +
153D ALA 3.7 0.3 - - - +
154D LEU* 3.3 9.5 - - - +
155D LEU* 2.6 51.1 + - + +
93E GLY 4.9 0.2 - - - -
94E ASN* 3.2 30.8 - - - +
95E VAL 5.9 0.2 + - - -
126E GLU* 2.8 32.3 + - - -
127E GLN* 3.5 20.8 - - - +
154E LEU* 4.4 0.2 - - - -
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Residues in contact with ILE 4 (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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3D ARG* 1.3 73.5 - - - +
5D GLY* 1.3 62.9 + - - +
52D ALA* 3.4 8.8 - - - -
153D ALA 3.5 2.2 - - - -
154D LEU* 4.2 4.0 - - + -
4E ILE* 3.4 39.9 - - + -
94E ASN* 2.9 44.3 + - - +
95E VAL* 5.3 0.4 - - - -
96E ASP* 4.2 5.4 - - - +
152E VAL* 3.8 31.0 - - + +
153E ALA 4.3 7.0 - - - +
154E LEU* 3.6 26.6 - - + +
4F ILE* 3.5 19.1 - - + -
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Residues in contact with GLY 5 (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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4D ILE* 1.3 77.9 - - - +
6D HIS* 1.3 60.3 + - - +
48D ALA* 3.4 22.0 - - - -
52D ALA* 3.5 5.1 - - - +
152D VAL* 3.0 9.9 - - - +
153D ALA 2.8 39.2 + - - +
96E ASP* 3.7 7.9 - - - -
152E VAL* 4.2 3.6 - - - -
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Residues in contact with HIS 6 (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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5D GLY* 1.3 74.4 - - - +
7D GLY* 1.3 76.3 + - - +
8D PHE* 3.7 13.7 - - + -
48D ALA* 3.6 8.8 - - - +
150D GLU* 2.7 33.5 + - + +
151D ALA 3.2 11.7 - - - +
152D VAL* 4.4 5.4 - - + -
6E HIS* 5.1 2.7 - + - -
96E ASP* 3.1 12.6 + - - +
98E THR* 3.0 22.7 + - - +
131E LYS* 2.9 30.3 + - - -
150E GLU* 3.2 27.1 + - + +
152E VAL* 3.7 32.1 - - + +
6F HIS* 5.5 0.7 - + - -
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Residues in contact with GLY 7 (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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6D HIS* 1.3 81.0 + - - +
8D PHE* 1.3 61.0 + - - +
44D ALA* 3.4 26.0 - - - +
47D ASP* 3.9 9.6 - - - -
48D ALA* 3.7 1.6 - - - +
150D GLU* 3.5 4.2 - - - -
151D ALA 2.7 39.1 + - - +
98E THR* 4.9 0.9 - - - -
131E LYS* 4.9 0.7 - - - -
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Residues in contact with PHE 8 (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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6D HIS* 3.7 16.0 - - + -
7D GLY* 1.3 75.5 - - - +
9D ASP* 1.3 63.9 + - - +
10D VAL* 3.9 26.7 - - + -
44D ALA* 4.2 1.9 - - - +
47D ASP* 4.2 8.8 + - - +
100D ILE* 5.0 6.7 - - + -
140D PHE* 5.3 2.7 - + - -
148D ALA* 4.1 16.6 - - + -
149D CYS 3.4 20.4 - - - -
150D GLU* 4.2 18.8 - - - -
98E THR* 4.2 12.0 - - + +
100E ILE* 3.7 42.2 - - + -
131E LYS* 5.6 0.9 - - - +
133E THR* 3.5 28.4 + - + +
134E THR 5.5 0.4 - - - -
135E THR* 4.4 4.5 - - + -
150E GLU* 4.6 4.3 - - - +
169E ACY 5.0 9.4 - - + -
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Residues in contact with ASP 9 (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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8D PHE* 1.3 78.9 - - - +
10D VAL* 1.3 84.2 + - - +
11D HIS* 5.4 0.7 - - - +
38D GLY 6.1 0.2 - - - -
39D ASP 5.0 0.2 - - - -
40D VAL* 3.2 39.4 - - + +
43D HIS* 3.5 31.1 - - + +
44D ALA* 4.1 4.9 - - - +
47D ASP* 4.9 4.4 - - - +
58D ILE* 6.2 0.2 - - - +
148D ALA* 3.6 0.7 - - - +
149D CYS 3.2 20.1 + - - -
169D MN 2.4 31.7 + - - -
133E THR* 4.0 10.2 + - - -
134E THR 5.2 0.4 - - - -
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Residues in contact with VAL 10 (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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8D PHE* 3.9 19.1 - - + -
9D ASP* 1.3 96.4 + - - +
11D HIS* 1.3 72.7 + - - +
12D ALA 4.3 1.6 - - - +
40D VAL* 3.8 1.1 - - - -
140D PHE* 4.0 23.3 - - + -
147D ILE 3.5 9.0 - - - +
148D ALA* 3.8 15.9 - - + -
169D MN 3.6 4.4 + - - -
134E THR 4.1 4.0 + - - +
135E THR* 3.6 39.5 - - - +
136E GLU* 3.1 20.1 - - + +
138E LEU* 4.3 2.9 - - + -
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Residues in contact with HIS 11 (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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9D ASP* 5.4 0.7 - - - +
10D VAL* 1.3 77.4 - - - +
12D ALA* 1.3 78.5 + - - +
13D PHE* 4.0 24.6 - + - -
14D GLY 4.9 2.8 + - - -
32D PHE* 6.5 0.4 - + - -
34D ALA* 6.1 6.3 - - + -
35D HIS* 6.0 2.2 + - - -
36D SER* 5.3 1.6 + - - -
37D ASP 5.6 0.2 - - - -
38D GLY* 3.7 41.6 - - - +
40D VAL* 4.3 3.8 - - + +
146D GLY* 3.3 4.2 - - - -
147D ILE* 3.0 43.8 + - + -
136E GLU* 3.4 8.2 + - - -
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Residues in contact with ALA 12 (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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10D VAL* 4.1 0.8 - - - +
11D HIS* 1.3 90.5 - - - +
13D PHE* 1.3 67.4 + - - +
14D GLY 3.6 0.2 + - - -
32D PHE* 3.9 18.2 - - + +
145D GLU 4.3 0.2 - - - +
136E GLU* 2.7 36.7 + - + +
138E LEU* 3.6 31.9 - - + -
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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