Contacts of the strand formed by residues 2 - 12 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ILE* 4.4 24.0 - - + -
0E SER* 3.3 6.6 - - - -
1E LEU* 1.3 92.1 - - + +
3E ARG* 1.3 81.7 + - - +
90E TYR* 5.5 0.2 - - - -
154E LEU* 3.4 29.4 - - + -
155E LEU 3.5 7.2 - - - +
156E ILE* 4.9 7.6 - - + -
2F ILE* 4.2 25.6 - - + -
93F GLY 5.5 1.7 - - - -
94F ASN* 4.4 0.3 - - - +
154F LEU* 3.7 24.1 - - + +
156F ILE* 5.6 4.8 - - + +
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Residues in contact with ARG 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0E SER* 3.5 20.0 + - - +
2E ILE* 1.3 93.2 - - - +
4E ILE* 1.3 58.9 + - - +
51E GLY 4.4 2.0 + - - -
52E ALA* 2.3 50.6 + - + +
53E ALA* 4.3 2.3 - - - -
54E ALA* 3.8 11.3 - - - +
90E TYR* 3.5 34.3 + - + -
153E ALA 3.7 0.5 - - - +
154E LEU* 2.9 12.3 - - - +
155E LEU* 2.8 39.8 + - + -
94F ASN* 2.7 45.9 - - - +
95F VAL 5.5 0.2 + - - -
126F GLU* 2.9 42.6 + - - -
127F GLN* 4.0 6.2 + - - +
129F ASN* 6.2 0.2 - - - +
154F LEU* 4.6 0.4 - - - -
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Residues in contact with ILE 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.4 25.8 - - + -
154D LEU* 6.3 0.2 - - + -
3E ARG* 1.3 71.9 - - - +
5E GLY* 1.3 62.4 + - - +
52E ALA* 3.2 10.4 - - - -
153E ALA 3.5 2.9 - - - -
154E LEU* 4.2 5.4 - - + -
4F ILE* 3.3 34.8 - - + -
94F ASN* 2.8 45.1 + - - +
96F ASP* 4.0 4.4 - - - +
152F VAL* 4.1 28.7 - - + +
153F ALA* 4.2 7.9 - - - +
154F LEU* 3.7 27.1 - - + +
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Residues in contact with GLY 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 1.3 78.8 - - - +
6E HIS* 1.3 61.4 + - - +
48E ALA* 3.2 23.8 - - - -
52E ALA* 3.5 3.6 - - - +
152E VAL* 3.2 8.7 - - - +
153E ALA 2.8 32.2 + - - -
96F ASP* 3.4 9.4 - - - -
152F VAL* 4.1 3.3 - - - +
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Residues in contact with HIS 6 (chain E).
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* 5.1 2.5 - + - -
150D GLU* 5.0 1.6 - - - -
5E GLY* 1.3 74.4 - - - +
7E GLY* 1.3 75.8 + - - +
8E PHE* 4.0 8.3 - - + -
48E ALA* 3.6 7.5 - - - +
150E GLU* 2.8 33.0 + - + +
151E ALA 3.2 15.5 - - - +
152E VAL* 4.3 7.0 - - + -
6F HIS* 5.2 1.8 - + - -
96F ASP* 2.8 14.9 + - - +
98F THR* 3.3 13.1 + - - +
131F LYS* 3.1 26.7 - - - -
150F GLU* 3.2 33.2 + - + +
151F ALA 5.6 0.4 - - - -
152F VAL* 3.6 33.9 - - + -
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Residues in contact with GLY 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E HIS* 1.3 88.4 + - - +
8E PHE* 1.3 60.3 + - - -
44E ALA* 3.4 23.8 - - - -
47E ASP* 4.0 6.7 - - - -
48E ALA* 3.6 5.1 - - - +
150E GLU* 3.4 3.1 - - - -
151E ALA 2.8 33.4 + - - -
98F THR* 4.8 0.7 - - - -
131F LYS* 5.0 0.4 - - - -
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Residues in contact with PHE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E HIS* 4.0 13.0 - - + -
7E GLY* 1.3 75.5 - - - +
9E ASP* 1.3 63.1 + - - +
10E VAL* 3.6 28.5 - - + -
44E ALA* 4.1 2.9 - - - +
47E ASP* 4.2 9.9 + - - +
100E ILE* 5.2 7.6 - - + -
140E PHE* 5.2 3.4 - + - -
148E ALA* 4.3 17.3 - - + -
149E CYS 3.3 14.4 - - - -
150E GLU* 4.5 15.3 - - - -
169E ACY 5.9 1.8 - - + -
98F THR* 4.4 12.5 - - + +
100F ILE* 3.4 47.1 - - + -
131F LYS* 5.5 0.2 - - - +
133F THR* 3.8 23.4 + - + +
134F THR 5.1 1.6 - - - -
135F THR* 4.2 7.2 - - + -
150F GLU* 5.5 1.8 - - + -
170F ACY 5.0 5.6 - - + -
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Residues in contact with ASP 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PHE* 1.3 77.4 - - - +
10E VAL* 1.3 75.1 + - - +
11E HIS* 5.2 0.5 - - - +
35E HIS* 6.0 1.6 - - - -
38E GLY 5.4 0.3 - - - -
40E VAL* 3.1 48.2 + - - +
43E HIS* 3.3 33.7 + - + +
44E ALA* 3.9 4.5 - - - +
47E ASP* 5.2 4.0 - - - +
58E ILE* 6.0 1.4 - - - +
148E ALA* 3.2 3.6 - - - +
149E CYS 2.9 33.4 + - - -
133F THR* 4.8 8.8 + - - -
136F GLU* 5.5 0.2 - - - +
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PHE* 3.6 30.3 - - + -
9E ASP* 1.3 90.2 + - - +
11E HIS* 1.3 72.1 + - - +
12E ALA 4.4 0.9 - - - +
40E VAL* 3.8 3.4 - - - -
140E PHE* 3.9 22.9 - - + -
147E ILE 3.4 9.6 - - - +
148E ALA* 3.7 11.2 - - + -
134F THR 4.1 6.1 + - - +
135F THR* 3.4 38.1 - - - +
136F GLU* 3.0 20.0 - - - +
138F LEU* 4.3 3.1 - - + -
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Residues in contact with HIS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ASP* 5.2 0.4 - - - +
10E VAL* 1.3 77.2 - - - +
12E ALA* 1.3 78.1 + - - +
13E PHE* 4.1 22.8 - + - -
14E GLY 5.2 2.1 + - - -
34E ALA* 5.8 10.1 - - + -
35E HIS* 6.0 0.4 + - - -
36E SER* 5.3 4.2 + - - -
37E ASP 5.4 1.3 + - - -
38E GLY* 3.7 34.9 - - - +
40E VAL* 3.6 17.4 - - + +
146E GLY* 3.2 3.1 - - - -
147E ILE* 2.9 36.8 + - + +
136F GLU* 3.5 9.6 + - - -
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 4.4 0.2 - - - +
11E HIS* 1.3 92.1 - - - +
13E PHE* 1.3 66.1 + - - +
14E GLY 3.6 0.7 + - - -
32E PHE* 4.1 18.0 - - + +
145E GLU 3.7 5.6 - - - +
136F GLU* 2.7 37.1 + - + +
138F LEU* 3.6 28.0 - - + -
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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