Contacts of the strand formed by residues 2 - 12 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ILE* 3.6 15.7 - - + -
93D GLY 5.7 0.5 - - - -
94D ASN* 4.2 0.3 - - - +
154D LEU* 3.4 29.3 - - + +
2E ILE* 4.2 23.6 - - + -
0F SER* 3.5 19.4 + - - +
1F LEU* 1.3 111.6 - - + +
3F ARG* 1.3 63.6 + - - +
154F LEU* 3.2 31.0 - - + -
155F LEU 3.3 5.4 - - - +
156F ILE* 4.8 15.0 - - + -
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Residues in contact with ARG 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY 4.5 2.5 + - - -
94D ASN* 3.3 34.0 - - - +
126D GLU* 2.7 51.9 + - - -
127D GLN* 4.0 9.9 - - - +
0F SER* 4.0 15.6 - - - +
2F ILE* 1.3 80.3 - - - +
4F ILE* 1.3 60.1 + - - +
52F ALA* 2.9 32.8 + - - +
53F ALA* 3.9 12.6 - - - +
54F ALA* 4.1 3.2 - - - +
90F TYR* 3.5 34.3 + - + +
153F ALA 3.6 0.7 - - - +
154F LEU* 3.0 9.9 - - - +
155F LEU* 2.7 53.0 + - + +
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Residues in contact with ILE 4 (chain F).
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* 3.5 32.8 - - + -
94D ASN* 2.9 40.7 + - - +
95D VAL* 5.3 0.2 - - - -
96D ASP* 4.0 4.5 - - - +
152D VAL* 3.9 31.4 - - + +
153D ALA 4.1 7.0 - - - +
154D LEU* 3.7 26.2 - - + +
4E ILE* 3.3 25.1 - - + -
3F ARG* 1.3 74.5 - - - +
5F GLY* 1.3 63.3 + - - +
52F ALA* 3.2 8.8 - - - -
153F ALA 3.4 2.7 - - - -
154F LEU* 4.4 2.9 - - + -
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Residues in contact with GLY 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASP* 3.3 10.8 - - - -
152D VAL* 4.2 3.5 - - - +
4F ILE* 1.3 78.4 - - - +
6F HIS* 1.3 62.3 + - - +
48F ALA* 3.3 20.2 - - - -
52F ALA* 3.5 4.0 - - - +
152F VAL* 3.2 8.1 - - - +
153F ALA 2.8 36.2 + - - -
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Residues in contact with HIS 6 (chain F).
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* 5.5 0.7 - + - -
96D ASP* 2.6 14.8 + - - +
98D THR* 3.0 26.9 + - - -
131D LYS* 2.7 33.1 + - - -
150D GLU* 3.2 42.0 + - + +
152D VAL* 3.5 33.2 - - + -
6E HIS* 5.2 2.0 - + - -
5F GLY* 1.3 75.2 - - - +
7F GLY* 1.3 65.3 + - - +
8F PHE* 4.0 4.3 - - + -
48F ALA* 3.5 7.5 - - - +
150F GLU* 2.5 34.3 + - + -
151F ALA 3.4 14.1 - - - +
152F VAL* 4.5 7.9 - - + -
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Residues in contact with GLY 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR* 4.6 1.6 - - - -
6F HIS* 1.3 79.8 - - - +
8F PHE* 1.3 60.7 + - - -
44F ALA* 3.4 25.6 - - - -
47F ASP* 3.9 6.7 - - - -
48F ALA* 3.5 4.9 - - - +
150F GLU* 3.3 7.6 - - - +
151F ALA 2.8 34.3 + - - -
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Residues in contact with PHE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR* 4.3 11.1 - - + +
100D ILE* 3.4 37.5 - - + -
131D LYS* 5.5 0.6 - - - +
133D THR* 3.7 21.5 + - + +
134D THR 5.3 0.4 - - - -
135D THR* 4.2 13.5 - - + -
150D GLU* 5.1 1.1 - - - +
171D ACY 5.0 7.4 - - + -
6F HIS* 4.0 9.8 + - + -
7F GLY* 1.3 73.3 - - - -
9F ASP* 1.3 84.7 + - - +
10F VAL* 3.6 28.7 - - + -
44F ALA* 4.4 0.2 - - - -
47F ASP* 4.2 3.3 - - - +
100F ILE* 5.3 7.2 - - + -
140F PHE* 5.3 3.1 - + - -
148F ALA* 4.3 11.9 - - + -
149F CYS 3.4 18.8 - - - -
150F GLU* 3.5 26.0 - - - +
170F ACY 6.0 2.2 - - + -
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Residues in contact with ASP 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D THR* 3.4 16.1 + - - -
134D THR 5.3 0.2 - - - -
8F PHE* 1.3 86.8 - - - +
10F VAL* 1.3 70.5 + - - +
40F VAL* 4.2 11.6 - - - +
43F HIS* 3.1 26.2 - - + +
44F ALA* 2.9 28.2 + - - +
47F ASP* 2.9 24.9 - - - +
58F ILE* 5.5 2.9 - - - +
148F ALA* 3.4 1.7 - - - +
149F CYS 3.1 31.4 + - - -
169F MN 4.1 8.3 + - - -
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Residues in contact with VAL 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D THR 4.2 3.1 + - - +
135D THR* 3.6 44.9 - - + +
136D GLU* 3.1 8.5 - - - +
138D LEU* 4.4 2.2 - - + -
8F PHE* 3.6 27.4 - - + -
9F ASP* 1.3 82.9 - - - +
11F HIS* 1.3 71.3 + - - +
12F ALA 4.3 1.3 - - - +
40F VAL* 3.7 4.8 - - - +
43F HIS* 5.7 1.0 - - - -
140F PHE* 3.7 24.7 - - + -
147F ILE 3.5 11.2 - - - +
148F ALA* 4.0 3.4 - - + -
169F MN 3.0 25.6 + - - -
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Residues in contact with HIS 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLU* 3.2 8.6 + - - -
10F VAL* 1.3 78.9 - - - +
12F ALA* 1.3 76.6 + - - +
13F PHE* 4.0 25.0 - + - -
14F GLY 5.2 1.5 + - - -
32F PHE* 6.3 1.1 - + - -
34F ALA* 5.8 9.2 - - + -
35F HIS* 5.7 4.2 + + - -
36F SER* 5.3 3.7 + - - -
37F ASP 5.4 1.3 + - - -
38F GLY* 3.7 34.1 - - - +
40F VAL* 3.4 19.9 - - + +
43F HIS* 6.3 0.4 - - + -
146F GLY* 3.2 4.0 - - - -
147F ILE* 2.9 35.9 + - + -
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Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLU* 2.6 38.3 + - + +
138D LEU* 3.6 32.1 - - + -
10F VAL* 4.1 0.8 - - - +
11F HIS* 1.3 88.2 - - - +
13F PHE* 1.3 66.5 + - - +
14F GLY 3.7 0.7 + - - -
32F PHE* 3.9 19.4 - - + +
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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
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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