Contacts of the strand formed by residues 6 - 14 (chain A) in PDB entry 1RFV
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 ARG 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU* 4.0 12.9 + - - +
5A CYS* 1.3 72.8 - - - +
7A VAL* 1.3 63.2 + - - +
34A GLU* 3.3 38.2 + - + +
36A ASP* 2.8 30.6 + - - +
74A VAL 5.3 0.7 - - - -
76A GLN 3.6 23.1 + - - +
77A TYR* 3.6 23.6 - - + -
78A ASP* 2.8 40.7 + - - +
79A TYR 3.2 7.4 + - - +
16B ARG* 3.4 39.1 - - - +
17B GLY 5.1 1.4 - - - +
290B GLU* 6.2 1.4 - - - +
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Residues in contact with VAL 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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6A ARG* 1.3 75.5 - - - +
8A LEU* 1.3 68.1 + - - +
9A SER* 3.7 6.5 + - - +
28A LEU* 4.3 14.8 - - + -
33A PHE* 3.9 33.7 - - + -
34A GLU 2.8 12.0 + - - +
35A VAL* 3.6 5.7 - - + +
36A ASP* 2.7 34.8 + - - +
77A TYR* 3.9 3.3 - - - -
79A TYR* 3.4 28.3 - - + +
81A LEU* 4.2 16.6 - - + -
242A LEU* 4.3 11.9 - - + -
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Residues in contact with LEU 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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7A VAL* 1.3 71.4 - - - +
9A SER* 1.3 58.8 + - - +
10A ILE* 4.0 20.5 + - + -
36A ASP* 3.5 14.1 - - + +
38A VAL* 3.9 25.8 - - + -
66A TYR* 5.1 6.5 - - + -
69A LEU* 4.9 3.8 - - + -
77A TYR* 3.6 38.5 - - + +
79A TYR 2.8 13.4 + - - +
80A VAL* 3.2 11.6 - - + +
81A LEU 2.8 24.6 + - - +
97A ILE* 4.6 9.0 - - + -
101A LEU* 4.0 25.1 - - + -
15B VAL* 4.4 2.7 - - + -
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Residues in contact with SER 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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7A VAL* 3.7 3.3 + - - -
8A LEU* 1.3 73.7 - - - +
10A ILE* 1.3 59.6 + - - +
11A GLN* 3.0 18.1 + - - -
21A ASN* 2.5 34.1 + - - +
24A ALA* 4.6 2.2 - - - +
28A LEU* 5.7 0.9 - - - -
35A VAL* 4.3 16.2 - - - -
36A ASP 2.9 11.0 + - - -
37A ALA* 3.5 1.7 - - - -
38A VAL 2.9 25.5 + - - -
81A LEU* 3.3 17.6 - - - +
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Residues in contact with ILE 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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8A LEU* 4.2 24.9 - - + +
9A SER* 1.3 74.8 + - - +
11A GLN* 1.3 67.3 + - - +
38A VAL* 3.4 31.9 - - + +
40A SER* 4.8 2.0 - - - -
62A LEU* 4.2 14.4 - - + -
80A VAL* 5.1 4.7 - - + -
81A LEU 3.0 8.3 + - - -
82A THR* 3.8 25.3 - - + -
83A GLY 4.2 1.4 + - - -
84A TYR 5.3 1.9 - - - +
85A THR* 5.8 0.5 + - - -
90A PHE* 3.9 33.4 - - + -
94A VAL* 4.7 17.3 - - + -
97A ILE* 5.0 11.9 - - + -
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Residues in contact with GLN 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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9A SER* 3.0 21.8 + - - +
10A ILE* 1.3 81.8 - - - +
12A SER* 1.3 66.2 + - - +
20A GLY* 3.6 13.5 - - - +
21A ASN* 3.5 24.5 + - - +
24A ALA* 3.8 7.9 - - - +
38A VAL 3.2 8.2 + - - +
39A ASN* 3.3 4.0 - - - -
40A SER* 3.0 25.8 + - - -
81A LEU* 3.6 27.0 - - - +
82A THR 4.4 1.3 - - - -
83A GLY* 3.8 22.8 + - - +
84A TYR 5.1 7.1 + - - +
235A ASP* 3.5 25.3 + - - +
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Residues in contact with SER 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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11A GLN* 1.3 77.8 - - - +
13A HIS* 1.3 59.0 + - - +
19A VAL* 3.9 5.4 - - - +
20A GLY* 3.7 16.5 + - - -
21A ASN* 2.8 32.1 + - - +
40A SER* 3.2 10.1 + - - -
41A VAL* 3.3 24.0 - - - -
84A TYR* 5.3 2.5 + - - +
122A GLY* 3.6 22.1 + - - -
123A GLU* 3.7 16.0 + - - -
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Residues in contact with HIS 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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12A SER* 1.3 75.7 - - - +
14A VAL* 1.3 82.8 + - - +
21A ASN* 5.0 1.8 - - + +
22A ARG* 3.7 24.6 + - - +
39A ASN* 3.4 23.5 + - - +
41A VAL 3.0 15.6 + - - +
42A GLN* 3.3 21.6 - - + -
43A PHE 2.9 23.2 + - - -
122A GLY 4.4 1.6 - - - +
37B ALA* 3.0 34.4 + - + -
39B ASN* 3.4 27.8 + - - -
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Residues in contact with VAL 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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13A HIS* 1.3 93.0 + - - +
15A VAL* 1.3 67.8 + - - +
16A ARG 3.2 21.3 - - - +
17A GLY 3.7 16.4 - - - +
19A VAL* 3.6 32.5 - - + -
22A ARG* 3.5 18.8 - - + +
43A PHE* 3.1 6.5 - - + +
45A ASN* 3.5 31.6 - - - +
46A HIS* 5.1 0.9 - - + +
122A GLY* 4.1 11.9 - - - +
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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