Contacts of the strand formed by residues 27 - 36 (chain A) in PDB entry 1RS2
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 GLN 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.2 19.5 - - - -
14A GLY 3.1 28.0 + - - +
16A HIS 4.0 8.5 + - - -
22A GLU* 3.5 34.3 + - - +
26A GLY* 1.3 78.5 + - - +
28A ILE* 1.3 65.7 + - - +
29A PHE* 3.5 17.5 - - + -
100A LYS* 3.0 39.1 - - - +
102A ASN* 4.0 25.9 + - + +
103A PRO* 4.3 2.0 - - - +
104A PRO* 5.3 0.4 - - - +
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Residues in contact with ILE 28 (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 ARG* 4.0 32.1 - - + +
12A PHE* 3.2 26.0 - - - +
13A TYR* 3.6 24.8 - - + +
27A GLN* 1.3 81.9 - - - +
29A PHE* 1.3 65.9 + - - +
30A LYS* 4.2 1.2 + - + +
99A THR 4.3 4.0 - - - +
100A LYS* 4.7 2.3 - - - -
101A GLU* 4.7 13.4 + - + +
102A ASN* 5.5 1.9 + - - +
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Residues in contact with PHE 29 (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 MET 3.7 0.2 - - - +
11A ARG* 3.1 3.8 - - - -
12A PHE* 2.6 46.4 + - + +
14A GLY* 3.2 35.4 - - - -
16A HIS* 3.6 43.7 - + + -
27A GLN* 3.5 21.8 - - + -
28A ILE* 1.3 75.9 - - - +
30A LYS* 1.3 60.3 + - - +
31A VAL* 4.0 0.4 + - - -
65A MET* 3.3 28.5 - - + -
73A LEU* 3.9 22.7 - - + -
76A LEU* 4.6 0.7 - - + -
98A ILE* 4.3 5.4 - - + -
99A THR 3.7 4.5 - - - +
100A LYS* 3.6 29.8 - - + -
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Residues in contact with LYS 30 (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 GLY* 4.0 16.8 - - - +
10A MET 3.2 7.6 - - - +
11A ARG* 3.4 48.4 - - - +
28A ILE* 4.2 1.7 - - + +
29A PHE* 1.3 72.6 - - - +
31A VAL* 1.3 62.7 + - - +
32A ASP* 4.4 15.5 - - - +
97A ARG 3.7 0.7 - - - +
98A ILE* 3.3 4.5 - - - +
99A THR* 2.8 55.2 + - - +
101A GLU* 4.0 20.3 + - + +
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Residues in contact with VAL 31 (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 3.9 0.2 - - - +
9A GLY* 3.5 3.4 + - - -
10A MET* 2.5 68.4 + - + +
12A PHE* 4.3 8.7 - - + -
30A LYS* 1.3 80.7 - - - +
32A ASP* 1.3 66.7 + - - +
33A VAL* 3.9 13.9 - - + -
61A VAL* 4.1 7.6 - - + -
65A MET* 3.5 39.7 - - + -
80A ILE* 4.6 1.3 - - + -
96A VAL* 4.3 10.5 - - + -
97A ARG 3.3 9.0 - - - +
98A ILE* 3.9 10.5 - - + -
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Residues in contact with ASP 32 (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 3.5 3.1 - - - +
8A LYS* 3.3 24.6 + - + +
9A GLY* 2.8 31.2 + - - -
30A LYS* 4.4 16.4 + - - +
31A VAL* 1.3 74.0 - - - +
33A VAL* 1.3 66.7 + - - +
34A THR* 5.2 3.4 - - - +
95A LYS 3.7 2.9 - - - +
97A ARG* 2.9 60.0 + - + +
99A THR* 5.4 0.5 + - - -
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Residues in contact with VAL 33 (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 ILE 3.8 0.2 - - - +
6A PHE* 3.3 5.2 - - - +
7A LEU* 2.9 40.8 + - + +
10A MET* 3.7 23.3 - - + +
31A VAL* 3.9 9.9 - - + -
32A ASP* 1.3 79.2 - - - +
34A THR* 1.3 64.8 + - - +
35A LEU* 3.9 28.3 - - + -
57A VAL* 4.4 9.0 - - + -
61A VAL* 4.2 12.8 - - + -
80A ILE* 4.5 5.6 - - + -
84A ILE* 4.3 11.2 - - + -
94A THR* 4.7 1.1 - - + -
95A LYS 3.5 5.6 - - - +
96A VAL* 4.3 12.6 - - + -
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Residues in contact with THR 34 (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 THR* 3.8 32.8 - - + +
5A ILE 3.4 4.7 - - - +
6A PHE* 4.7 8.1 - - + +
32A ASP* 4.3 3.3 - - - +
33A VAL* 1.3 75.4 + - - +
35A LEU* 1.3 64.6 + - - +
36A LYS 4.2 0.2 + - - -
93A GLU* 4.0 0.9 - - - +
94A THR* 3.7 1.0 - - - -
95A LYS* 2.9 57.0 + - + +
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Residues in contact with LEU 35 (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 THR* 3.2 10.5 - - - -
5A ILE* 2.9 43.4 + - + +
7A LEU* 5.5 0.9 - - + -
33A VAL* 3.9 12.8 - - + -
34A THR* 1.3 76.5 - - - +
36A LYS* 1.3 60.9 + - - +
37A VAL* 3.4 13.8 + - + +
52A VAL* 4.5 5.6 - - + -
57A VAL* 4.1 31.9 - - + -
84A ILE* 3.6 13.2 - - + -
91A VAL* 3.9 18.2 - - + -
93A GLU 3.5 0.9 - - - -
94A THR* 3.0 44.6 - - + +
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Residues in contact with LYS 36 (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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1A MET* 3.5 41.6 + - + +
3A ASP 4.0 7.0 - - - +
4A THR* 4.8 3.8 - - + +
34A THR 4.2 0.4 + - - -
35A LEU* 1.3 67.8 - - - +
37A VAL* 1.3 64.7 + - - +
91A VAL* 3.2 0.7 - - - -
92A MET* 2.7 71.3 + - + +
93A GLU* 2.7 45.0 + - + +
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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