Contacts of the strand formed by residues 44 - 52 (chain A) in PDB entry 2CSX
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A MET* 4.7 13.9 - - + +
5A LYS 2.8 21.5 + - - +
6A LYS* 3.1 11.7 - - + +
7A PHE 3.1 16.1 + - - -
43A TYR* 1.3 68.8 - - - +
45A VAL* 1.3 59.7 + - - +
46A PHE 3.7 0.2 + - - -
247A ILE* 3.3 17.2 - - - +
248A TYR* 2.4 38.9 + - - -
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Residues in contact with VAL 45 (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 PHE* 3.2 19.5 - - + +
9A VAL* 5.0 0.4 - - + -
35A ALA* 4.0 26.2 - - + +
38A TYR* 3.5 29.2 - - + -
39A ARG* 3.0 49.0 + - + +
43A TYR* 3.0 23.3 + - + +
44A ASP* 1.3 74.0 + - - +
46A PHE* 1.3 67.8 + - - +
47A PHE* 4.6 0.2 - - + -
92A THR* 3.5 4.3 + - - +
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Residues in contact with PHE 46 (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 PHE 3.0 7.0 + - - +
8A TYR* 3.2 25.3 - + + -
9A VAL* 3.2 25.5 + - - +
44A ASP 3.7 2.8 + - - -
45A VAL* 1.3 73.0 - - - +
47A PHE* 1.3 61.1 + - - +
48A LEU* 4.1 20.6 - - + -
92A THR* 3.6 25.1 - - + -
93A LYS* 4.0 18.6 - - + -
240A ALA 4.5 10.5 - - - -
241A LEU* 3.7 22.2 - - + -
244A LYS* 3.3 32.5 - - - -
248A TYR* 3.6 42.6 - + + -
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Residues in contact with PHE 47 (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 VAL* 3.6 15.0 - - + -
11A THR* 3.8 4.7 - - + -
28A THR* 4.1 11.4 - - + -
31A ALA* 3.5 31.2 - - + -
32A ASP* 3.8 19.5 - - - -
35A ALA* 3.9 20.4 - - + -
39A ARG* 3.6 15.7 - - - +
45A VAL* 3.7 0.4 + - + -
46A PHE* 1.3 73.0 - - - +
48A LEU* 1.3 79.1 + - - +
49A THR* 4.7 2.0 - - - -
89A ILE* 3.9 14.8 - - + -
90A GLU 3.1 26.0 - - - -
91A TYR* 3.3 18.9 - - + +
92A THR* 2.7 41.0 + - - +
93A LYS 3.4 3.1 + - - -
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Residues in contact with LEU 48 (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 TYR* 3.3 33.0 - - + +
9A VAL 3.2 5.7 + - - -
10A THR* 3.5 6.0 - - + -
11A THR* 3.0 26.8 + - - +
46A PHE* 4.1 6.2 - - + -
47A PHE* 1.3 82.6 - - - +
49A THR* 1.3 74.0 + - - +
93A LYS* 3.3 27.8 - - + +
95A ILE* 3.8 8.3 - - + -
236A ASN* 3.7 25.1 - - - +
237A TYR* 4.0 12.6 - - + -
240A ALA* 3.8 27.6 - - + -
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Residues in contact with THR 49 (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 THR* 2.7 29.0 + - - +
12A PRO 4.6 0.7 - - - -
13A ILE* 4.9 0.9 - - - -
14A TYR* 3.9 8.7 - - - -
28A THR* 4.4 4.0 + - + -
47A PHE* 4.7 4.7 - - + -
48A LEU* 1.3 76.0 - - - +
50A GLY* 1.3 63.8 + - - +
84A TRP* 3.9 21.4 + - + -
91A TYR* 4.0 21.3 - - + -
93A LYS 3.1 13.3 + - - +
94A PHE* 3.8 21.1 - - + -
95A ILE* 3.0 26.4 + - - +
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Residues in contact with GLY 50 (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 PRO 3.7 6.3 + - - +
13A ILE* 3.0 20.3 - - - +
14A TYR* 3.1 13.3 + - - -
49A THR* 1.3 81.8 + - - +
51A THR* 1.3 66.9 + - - +
94A PHE* 4.2 10.7 - - - -
95A ILE* 3.1 19.9 - - - +
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Residues in contact with THR 51 (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 ILE* 3.5 6.4 - - - +
14A TYR 3.4 4.9 - - - +
16A VAL* 3.2 28.3 - - + -
50A GLY* 1.3 74.8 - - - +
52A ASP* 1.3 60.8 + - - +
53A GLU* 2.7 25.7 + - - -
77A ALA* 4.1 3.3 - - - +
80A PHE* 3.7 19.5 - - + -
94A PHE* 3.5 26.6 - - + -
95A ILE 2.8 11.3 + - - +
96A ARG* 3.7 8.8 - - - +
97A THR* 3.3 27.5 + - - +
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Residues in contact with ASP 52 (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 ILE* 3.2 37.7 - - + +
14A TYR 2.8 15.3 + - - +
15A TYR* 4.0 15.5 - - - +
16A VAL* 3.1 15.9 + - - +
51A THR* 1.3 69.5 - - - +
53A GLU* 1.3 59.0 + - - +
54A HIS 3.7 11.9 + - - +
58A ILE* 5.6 0.2 - - - +
97A THR* 4.1 2.9 + - - +
229A VAL* 6.0 1.2 - - - +
232A ASP* 4.0 15.6 - - - +
233A ALA* 4.4 12.7 - - - +
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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