Contacts of the helix formed by residues 2 - 18 (chain B) in PDB entry 1RVA
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 SER 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B LEU* 1.3 64.2 + - - +
4B ARG* 3.6 8.8 + - - +
5B SER* 2.8 37.0 + - - -
6B ASP* 3.0 29.9 + - - +
59B HIS* 3.6 13.2 - - - -
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Residues in contact with LEU 3 (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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2B SER* 1.3 73.8 - - - +
4B ARG* 1.3 59.7 + - - +
6B ASP* 3.7 1.4 - - - +
7B LEU* 2.9 35.7 + - + +
55B ILE* 3.9 18.8 - - + -
56B ALA* 4.1 16.8 - - - +
59B HIS* 3.6 29.5 + - + +
61B TYR* 3.6 25.4 - - + +
77B LEU* 4.1 18.2 - - + -
87B ILE* 3.5 32.3 - - + -
132B TRP* 4.1 12.3 - - + -
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Residues in contact with ARG 4 (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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2B SER* 3.3 8.1 + - - +
3B LEU* 1.3 80.8 - - - +
5B SER* 1.3 57.0 - - - +
7B LEU* 3.4 3.0 + - - +
8B ILE* 3.0 44.8 + - + +
132B TRP* 3.4 49.3 - - + +
170B LEU* 4.1 20.1 + - + +
171B GLN* 3.4 24.7 + - - +
172B ASP* 2.8 34.7 + - - +
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Residues in contact with SER 5 (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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2B SER* 2.8 38.3 + - - -
4B ARG* 1.3 76.5 - - - +
6B ASP* 1.3 67.7 + - - +
8B ILE* 3.5 8.7 + - - +
9B ASN* 3.1 36.6 + - - +
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Residues in contact with ASP 6 (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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2B SER 3.0 19.5 + - - +
3B LEU 3.7 3.1 - - - +
5B SER* 1.3 78.8 + - - +
7B LEU* 1.3 61.3 + - - +
9B ASN* 3.4 11.3 + - - +
10B ALA* 2.9 30.5 + - - +
55B ILE* 3.8 16.6 - - + +
58B LYS* 2.9 25.1 + - - -
59B HIS* 2.7 31.2 + - - +
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Residues in contact with LEU 7 (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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3B LEU* 2.9 23.1 + - + +
4B ARG* 3.7 4.7 - - - +
6B ASP* 1.3 77.4 - - - +
8B ILE* 1.3 57.1 + - - +
10B ALA* 3.3 1.4 + - - +
11B LEU* 2.9 42.0 + - + +
51B ILE* 4.4 9.2 - - + -
52B ILE* 4.1 34.5 - - + +
55B ILE* 3.8 20.6 - - + +
77B LEU* 5.5 0.9 - - + -
89B ILE* 3.9 26.7 - - + -
132B TRP* 4.2 9.0 - - + -
134B ILE* 4.6 2.5 - - + -
170B LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 8 (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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4B ARG* 3.0 41.3 + - + +
5B SER* 3.8 8.3 - - - +
7B LEU* 1.3 75.4 - - - +
9B ASN* 1.3 66.2 + - - +
11B LEU* 3.5 8.5 + - - +
12B TYR* 3.2 55.4 + - + +
170B LEU* 3.7 37.2 - - + +
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Residues in contact with ASN 9 (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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5B SER* 3.1 28.4 + - - +
6B ASP* 3.8 11.8 + - - +
7B LEU 3.3 0.2 - - - -
8B ILE* 1.3 80.8 - - - +
10B ALA* 1.3 63.9 + - - +
12B TYR* 3.3 12.0 + - - +
13B ASP* 3.1 26.2 + - - +
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Residues in contact with ALA 10 (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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6B ASP 2.9 18.4 + - - +
7B LEU 3.3 4.7 + - - +
9B ASN* 1.3 76.5 - - - +
11B LEU* 1.3 56.5 + - - +
13B ASP* 3.9 5.3 - - - +
14B GLU* 3.0 34.1 + - - +
51B ILE* 3.6 21.4 - - + +
55B ILE* 3.9 18.8 - - + -
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Residues in contact with LEU 11 (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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7B LEU* 2.9 38.4 + - + +
8B ILE* 3.8 5.8 - - - +
10B ALA* 1.3 73.5 - - - +
12B TYR* 1.3 66.8 + - + +
14B GLU* 4.2 0.7 - - - +
15B ASN* 3.2 27.2 + - - +
47B PHE* 5.7 0.2 - - - -
48B SER* 4.9 3.8 - - - +
51B ILE* 4.0 30.6 - - + +
52B ILE* 5.4 0.9 - - + -
134B ILE* 3.8 42.6 - - + -
136B TYR* 4.1 16.9 + - - +
168B VAL* 4.1 16.3 - - + +
169B PHE 5.1 0.9 - - - +
170B LEU* 4.3 14.4 - - + -
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Residues in contact with TYR 12 (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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8B ILE* 3.2 41.5 + - + +
9B ASN* 3.7 11.9 - - - +
11B LEU* 1.3 78.9 - - + +
13B ASP* 1.3 58.6 + - - +
15B ASN* 3.8 2.1 - - - +
16B GLN* 3.0 32.1 + - - +
168B VAL* 3.5 37.5 + - + -
169B PHE* 4.8 7.4 - - - -
170B LEU 5.5 0.7 + - - -
196B TYR* 4.2 7.8 + - - -
200B VAL* 4.3 18.5 - - - +
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Residues in contact with ASP 13 (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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9B ASN 3.1 15.0 + - - +
10B ALA* 3.9 5.6 - - - +
12B TYR* 1.3 78.5 - - - +
14B GLU* 1.3 64.3 + - - +
16B GLN* 3.1 10.2 + - - +
17B LYS* 2.8 64.3 + - - +
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Residues in contact with GLU 14 (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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29A LYS* 3.1 18.3 + - - -
31A TYR* 2.9 26.2 + - + -
150A THR* 4.7 1.2 - - - +
10B ALA 3.0 19.7 + - - +
11B LEU 4.2 0.7 - - - +
13B ASP* 1.3 76.6 + - - +
15B ASN* 1.3 56.7 + - - +
17B LYS* 3.3 3.1 + - - +
18B TYR* 3.0 52.2 + - - -
47B PHE* 3.6 15.6 - - + -
50B PRO* 6.0 0.2 - - - +
51B ILE* 3.5 33.8 - - + +
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Residues in contact with ASN 15 (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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11B LEU 3.2 18.5 + - - +
12B TYR 3.8 3.1 + - - +
14B GLU* 1.3 79.2 - - - +
16B GLN* 1.3 62.5 + - - +
18B TYR 3.4 15.6 + - - +
19B ASP* 4.4 5.2 - - - +
44B PHE* 5.2 2.6 - - - -
47B PHE* 4.1 17.2 - - + -
136B TYR* 3.9 13.1 - - + -
166B VAL* 3.4 46.9 + - - +
167B LYS* 4.6 0.8 - - - +
168B VAL* 4.3 19.7 - - + +
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Residues in contact with GLN 16 (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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12B TYR 3.0 18.8 + - - +
13B ASP* 3.1 8.0 + - - +
15B ASN* 1.3 77.6 - - - +
17B LYS* 1.3 81.8 + - + +
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Residues in contact with LYS 17 (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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27A GLU* 3.4 23.6 - - - +
13B ASP* 2.8 52.6 + - - +
14B GLU* 3.3 4.7 + - - +
16B GLN* 1.3 94.3 + - - +
18B TYR* 1.3 78.8 + - + +
19B ASP* 5.9 0.7 - - - -
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Residues in contact with TYR 18 (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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25A SER* 3.7 11.4 - - - -
27A GLU* 3.4 35.9 - - + +
29A LYS* 3.5 33.6 + - + +
31A TYR* 3.6 15.0 - - - +
14B GLU* 3.0 46.8 + - - +
15B ASN* 3.4 12.5 - - - +
17B LYS* 1.3 96.9 - - + +
19B ASP* 1.3 69.6 + - - +
20B VAL 4.2 1.2 + - - -
47B PHE* 3.9 17.1 - - + -
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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