Contacts of the strand formed by residues 4 - 14 (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 THR 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLN 3.8 9.8 + - - +
3A ASP* 1.3 85.7 - - - +
5A ILE* 1.3 64.5 + - - +
6A PHE* 4.5 15.3 - - - -
34A THR* 3.8 25.5 - - + +
35A LEU 3.2 15.0 - - - +
36A LYS* 4.8 3.4 - - + -
37A VAL 4.6 0.9 - - - +
39A LEU* 3.5 17.9 - - - +
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Residues in contact with ILE 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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4A THR* 1.3 79.0 - - - +
6A PHE* 1.3 70.4 + - - +
7A LEU* 5.1 3.8 - - + -
33A VAL 3.8 0.3 - - - +
34A THR* 3.4 3.1 - - - +
35A LEU* 2.9 45.8 + - + +
37A VAL* 3.9 12.8 - - + -
39A LEU* 3.7 19.5 - - + -
51A THR* 3.8 13.2 - - - +
52A VAL* 3.7 38.4 - - + +
54A TYR* 3.3 38.6 - - + -
57A VAL* 5.7 1.1 - - + -
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Residues in contact with PHE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 4.5 14.4 - - - -
5A ILE* 1.3 86.6 - - - +
7A LEU* 1.3 69.5 + - - +
8A LYS* 3.5 33.7 - - + -
33A VAL 3.3 8.7 - - - +
34A THR* 4.7 11.0 - - + +
54A TYR* 4.8 7.4 - - - -
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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
----------------------------------------------------------
5A ILE* 5.1 4.9 - - + -
6A PHE* 1.3 78.3 - - - +
8A LYS* 1.3 61.0 + - - +
10A MET* 3.7 29.8 - - + +
31A VAL 3.9 2.4 - - - +
32A ASP* 3.5 3.5 - - - -
33A VAL* 2.9 40.4 + - + +
35A LEU* 5.5 0.9 - - + -
54A TYR* 4.0 22.0 - - + +
57A VAL* 3.4 34.8 - - + -
58A PHE* 3.7 33.4 - - + -
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Residues in contact with LYS 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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6A PHE* 3.5 36.9 - - + -
7A LEU* 1.3 73.7 - - - +
9A GLY* 1.3 64.6 + - - +
10A MET* 3.3 5.9 + - - +
32A ASP* 3.3 23.8 + - + +
33A VAL 5.8 0.2 - - - +
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Residues in contact with GLY 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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8A LYS* 1.3 72.5 - - - +
10A MET* 1.3 66.7 + - - +
11A ARG* 3.0 27.0 + - - -
30A LYS* 4.0 21.8 - - - -
31A VAL 3.5 2.6 + - - -
32A ASP* 2.8 16.4 + - - -
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Residues in contact with MET 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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7A LEU* 3.7 37.5 - - + +
8A LYS 3.3 2.6 - - - +
9A GLY* 1.3 78.3 - - - +
11A ARG* 1.3 56.6 + - - +
12A PHE* 3.7 16.8 - - + -
30A LYS* 3.2 2.4 - - - -
31A VAL* 2.5 67.3 + - + +
33A VAL* 3.7 19.1 - - + -
58A PHE* 3.6 32.5 - - + -
61A VAL* 3.9 18.8 - - + -
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Residues in contact with ARG 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 GLY* 3.0 20.5 + - - +
10A MET* 1.3 76.8 - - - +
12A PHE* 1.3 73.1 + - - +
28A ILE* 4.0 25.8 - - + +
29A PHE 3.1 5.6 - - - +
30A LYS* 3.4 50.2 - - - +
58A PHE* 5.9 0.2 - - - -
66A GLU* 5.0 0.3 - - - +
101A GLU* 4.3 16.4 + - - -
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Residues in contact with PHE 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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10A MET* 3.7 23.6 - - + -
11A ARG* 1.3 83.0 - - - +
13A TYR* 1.3 60.9 + - - +
14A GLY 3.7 0.4 - - - +
27A GLN 3.5 0.7 - - - +
28A ILE* 3.2 7.1 - - - -
29A PHE* 2.6 47.8 + - + +
31A VAL* 4.3 5.2 - - + -
58A PHE* 3.7 35.2 - + - -
61A VAL* 3.7 28.9 - - + -
62A LYS* 3.8 21.1 - - + -
65A MET* 3.4 35.2 - - + -
66A GLU* 3.1 32.3 - - + +
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 1.3 73.9 - - - +
14A GLY* 1.3 58.8 + - - +
15A TYR* 4.0 23.7 - + - -
25A ILE* 3.4 27.1 + - - +
26A GLY* 3.4 10.6 + - - -
27A GLN* 3.2 32.3 - - - -
28A ILE* 3.6 25.4 - - + +
66A GLU* 4.1 17.4 + - - +
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Residues in contact with GLY 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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12A PHE 3.6 3.4 + - - -
13A TYR* 1.3 75.1 - - - +
15A TYR* 1.3 67.8 - - - -
16A HIS* 3.5 5.6 - - - -
26A GLY* 3.5 0.9 - - - -
27A GLN* 3.1 27.5 + - - +
29A PHE* 3.2 17.4 - - - -
65A MET 4.0 17.5 - - - -
66A GLU* 5.4 0.9 - - - -
67A GLY 6.0 0.4 - - - -
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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