Contacts of the helix formed by residues 2 - 18 (chain A) in PDB entry 1RVC
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 1.3 64.6 + - - +
4A ARG* 3.6 8.9 + - - +
5A SER* 3.0 45.2 + - - -
6A ASP* 3.2 19.5 + - - -
59A HIS* 3.5 11.6 - - - -
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Residues in contact with LEU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 73.3 - - - +
4A ARG* 1.3 57.8 - - - +
6A ASP* 3.6 1.7 - - - +
7A LEU* 2.9 36.0 + - + +
55A ILE* 3.9 32.1 - - + +
56A ALA* 4.1 11.4 - - - -
59A HIS* 3.4 29.7 + - + +
61A TYR* 3.8 24.5 - - + +
77A LEU* 4.1 20.0 - - + -
87A ILE* 3.8 25.1 - - + -
132A TRP* 4.1 13.0 - - + -
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Residues in contact with ARG 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.2 9.1 - - - +
3A LEU* 1.3 81.3 - - - +
5A SER* 1.3 61.8 + - - +
7A LEU* 3.4 3.2 + - - +
8A ILE* 3.1 44.8 + - + +
132A TRP* 3.5 46.6 - - + +
170A LEU* 4.0 21.7 + - + +
171A GLN* 3.1 39.0 + - - +
172A ASP* 2.9 23.8 + - - -
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.0 35.6 + - - -
4A ARG* 1.3 76.5 - - - +
6A ASP* 1.3 62.8 + - - +
8A ILE* 3.6 9.7 + - - +
9A ASN* 3.1 36.7 + - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER 3.2 14.7 + - - +
3A LEU 3.6 3.4 - - - +
5A SER* 1.3 83.8 + - - +
7A LEU* 1.3 60.3 + - - +
9A ASN* 3.3 8.0 + - - +
10A ALA* 2.9 30.7 + - - +
55A ILE* 3.8 20.5 - - + +
58A LYS* 3.6 21.8 + - - -
59A HIS* 2.8 26.3 + - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 2.9 21.9 + - + +
4A ARG 3.7 4.7 - - - +
6A ASP* 1.3 77.1 - - - +
8A ILE* 1.3 61.8 + - - +
10A ALA* 3.3 2.1 + - - +
11A LEU* 2.9 38.8 + - + +
51A ILE* 4.5 1.6 - - + +
52A ILE* 3.9 34.8 - - + +
55A ILE* 3.8 22.6 - - + +
77A LEU* 5.7 2.0 - - + -
89A ILE* 3.8 27.8 - - + -
132A TRP* 4.2 9.2 - - + -
134A ILE* 4.5 5.8 - - + -
170A LEU* 3.5 25.6 - - + -
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.1 38.2 + - + +
5A SER* 3.8 8.3 - - - +
7A LEU* 1.3 76.5 - - - +
9A ASN* 1.3 62.7 - - - +
11A LEU* 3.4 7.9 + - - +
12A TYR* 2.9 34.5 + - + +
169A PHE* 6.1 1.8 - - - -
170A LEU* 3.8 36.3 - - + +
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Residues in contact with ASN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 3.1 20.9 + - - +
6A ASP* 3.3 9.2 + - - +
8A ILE* 1.3 85.7 - - - +
10A ALA* 1.3 58.0 + - - +
12A TYR* 3.7 6.1 - - - +
13A ASP* 2.9 31.8 + - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASP 2.9 17.2 + - - +
7A LEU 3.7 2.5 - - - +
9A ASN* 1.3 74.5 - - - +
11A LEU* 1.3 58.8 + - - +
13A ASP* 3.7 4.7 - - - +
14A GLU* 2.9 33.3 + - - +
51A ILE* 3.6 22.6 - - + +
54A LYS* 6.4 1.3 - - + -
55A ILE* 3.9 19.7 - - + -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 2.9 33.5 + - + +
8A ILE* 3.8 5.6 - - - +
10A ALA* 1.3 76.1 - - - +
12A TYR* 1.3 57.7 + - - +
14A GLU* 3.8 1.4 - - - +
15A ASN* 2.9 32.6 + - - +
47A PHE* 5.1 2.0 - - + -
48A SER* 4.3 12.6 - - - +
51A ILE* 4.0 31.2 - - + -
52A ILE* 5.1 0.9 - - + -
134A ILE* 3.5 40.8 - - + -
136A TYR* 3.8 20.6 + - - +
168A VAL* 4.3 15.4 - - + +
169A PHE 5.9 0.2 - - - -
170A LEU* 4.5 8.1 - - + -
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Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 2.9 24.5 + - + +
9A ASN* 3.7 6.7 - - - +
11A LEU* 1.3 77.5 - - - +
13A ASP* 1.3 64.3 + - + +
15A ASN* 3.7 3.0 + - - +
16A GLN* 3.1 59.9 + - + +
168A VAL* 4.2 24.3 - - + +
196A TYR* 5.1 7.9 - - - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASN 2.9 20.0 + - - +
10A ALA* 3.7 5.6 - - - +
11A LEU 3.2 0.2 - - - -
12A TYR* 1.3 78.7 - - + +
14A GLU* 1.3 69.1 + - - +
16A GLN* 3.2 15.7 + - - +
17A LYS* 3.2 53.0 + - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 2.9 21.1 + - - +
11A LEU 3.8 1.3 - - - +
13A ASP* 1.3 76.3 + - - +
15A ASN* 1.3 58.2 + - - +
17A LYS* 3.4 1.0 + - - -
18A TYR* 3.0 48.5 + - + +
47A PHE* 3.4 22.4 - - + -
51A ILE* 3.4 30.7 - - + +
29B LYS* 2.8 29.8 + - - -
31B TYR* 2.9 19.4 + - - -
150B THR* 5.5 0.2 - - - +
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 2.9 18.9 + - - +
12A TYR* 3.9 5.9 + - - +
14A GLU* 1.3 77.6 - - - +
16A GLN* 1.3 64.4 + - - +
18A TYR 3.5 13.7 - - - +
19A ASP* 4.3 4.9 - - - +
44A PHE* 5.5 1.0 - - - -
47A PHE* 4.1 15.5 - - + -
136A TYR* 4.3 8.6 - - + -
166A VAL* 3.0 50.5 + - - +
167A LYS* 4.5 1.0 - - - +
168A VAL* 4.3 20.3 - - + +
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Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.1 55.6 + - + +
13A ASP* 3.2 10.1 + - - +
15A ASN* 1.3 83.8 - - - +
17A LYS* 1.3 64.5 + - + +
18A TYR 3.5 0.7 + - - +
19A ASP* 5.1 3.6 - - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 3.2 44.8 + - - +
16A GLN* 1.3 82.5 - - + +
18A TYR* 1.3 80.0 + - + +
27B GLU* 3.5 19.4 - - - +
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.0 47.6 + - - +
15A ASN* 3.5 12.8 - - - +
16A GLN 3.5 0.6 - - - -
17A LYS* 1.3 97.8 - - + +
19A ASP* 1.3 70.9 + - - +
20A VAL 4.2 0.8 + - - -
47A PHE* 4.1 13.0 - - + -
25B SER* 3.7 11.2 - - - -
27B GLU* 3.5 33.0 - - + +
29B LYS* 3.8 28.6 + - + +
31B TYR* 3.7 15.9 - - - +
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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