Contacts of the strand formed by residues 28 - 37 (chain A) in PDB entry 2CGZ
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 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.8 2.9 - - - +
18A VAL* 2.6 53.3 + - - +
19A PRO 3.7 0.7 - - - -
20A SER* 3.3 30.4 + - - -
25A ARG* 3.9 15.3 - - + -
26A ASP 4.1 2.5 - - - +
27A ASN* 1.3 75.8 - - - +
29A ARG* 1.3 61.6 + - - +
81A TYR* 3.1 30.7 - - + +
82A THR 3.6 5.4 - - - -
83A TRP* 3.7 17.7 - - + -
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Residues in contact with ARG 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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12A ASP* 3.1 40.0 + - - -
15A TRP* 4.2 18.4 - - + +
16A ALA 3.3 14.1 - - - +
17A LYS* 4.2 19.3 - - + +
18A VAL* 4.3 1.6 - - - +
27A ASN* 3.1 25.3 + - - +
28A THR* 1.3 77.7 - - - +
30A GLU* 1.3 66.2 + - - +
81A TYR* 3.7 5.7 - - - -
82A THR* 2.9 44.0 + - - +
83A TRP* 3.4 20.2 + - - +
84A HIS 2.8 26.8 + - - -
86A THR 3.3 17.7 + - - -
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Residues in contact with GLU 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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15A TRP* 3.9 8.5 - - - +
16A ALA* 3.0 30.1 + - - +
18A VAL* 3.6 27.0 - - + +
29A ARG* 1.3 80.2 - - - +
31A LEU* 1.3 58.9 + - - +
32A ALA* 3.5 25.5 + - + +
69A TYR* 2.6 30.1 + - - -
77A LYS* 4.0 7.1 + - - -
79A SER* 3.0 21.4 + - - -
80A CYS 3.2 12.8 - - - +
81A TYR* 3.6 12.6 - - + -
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Residues in contact with LEU 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 ILE* 5.3 1.0 - - + +
8A ASN 5.2 2.2 - - - +
9A CYS* 4.0 32.7 - - + +
14A GLY 3.9 16.4 - - - +
15A TRP* 3.5 39.8 - - + +
16A ALA 5.1 0.2 - - - +
30A GLU* 1.3 69.7 - - - +
32A ALA* 1.3 70.8 + - - +
33A LYS* 3.9 33.7 + - + +
79A SER* 3.3 5.1 - - - -
80A CYS 3.0 25.4 + - - +
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Residues in contact with ALA 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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30A GLU* 3.5 22.2 + - + +
31A LEU* 1.3 79.7 - - - +
33A LYS* 1.3 72.7 + - - +
77A LYS* 3.8 25.8 - - + +
78A ALA 4.4 0.9 - - - +
79A SER* 3.6 10.3 - - - -
1101A NAG 5.0 11.0 - - - +
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Residues in contact with LYS 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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7A ILE* 4.1 26.9 - - + +
31A LEU* 3.9 27.2 - - + +
32A ALA* 1.3 83.1 - - - +
34A ASN* 1.3 65.4 + - - +
35A ILE* 3.8 18.5 + - + +
76A PHE 3.8 1.2 - - - +
77A LYS* 3.5 7.8 - - - +
78A ALA 3.0 33.8 + - - +
1101A NAG 5.1 2.5 - - - -
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Residues in contact with ASN 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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33A LYS* 1.3 75.2 - - - +
35A ILE* 1.3 71.1 + - - +
36A THR* 3.9 8.7 + - - +
75A GLY* 5.7 0.5 - - - -
76A PHE 3.8 11.1 + - - +
77A LYS* 4.4 14.1 - - - +
1101A NAG 1.5 75.3 + - - +
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Residues in contact with ILE 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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6A LYS 5.7 1.1 - - - +
7A ILE* 3.9 31.0 - - + -
33A LYS* 4.5 17.5 - - + +
34A ASN* 1.3 80.6 - - - +
36A THR* 1.3 71.6 + - - +
37A PHE* 4.2 1.1 - - + +
75A GLY* 3.2 3.3 - - - -
76A PHE* 3.0 70.6 + - + +
95A TRP* 3.7 22.0 - - + +
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Residues in contact with THR 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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34A ASN* 4.0 8.9 + - - +
35A ILE* 1.3 84.0 - - - +
37A PHE* 1.3 68.7 + - - +
38A ALA* 3.5 2.3 + - - -
74A THR* 3.5 27.8 - - + +
75A GLY* 5.0 0.2 - - - -
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Residues in contact with PHE 37 (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 GLN* 3.3 18.4 - - - +
35A ILE* 5.2 0.4 - - + -
36A THR* 1.3 76.3 - - - +
38A ALA* 1.3 64.7 + - - +
39A SER 3.9 12.1 - - - +
40A PRO* 4.2 9.8 - - + +
41A TYR* 3.6 8.1 - + - -
45A PRO* 3.4 31.6 - - + -
47A VAL* 4.4 3.1 - - + -
72A SER 3.7 5.2 - - - -
73A PRO 3.5 9.9 - - - -
74A THR 3.1 13.3 + - - +
75A GLY* 3.2 35.4 - - - -
76A PHE* 3.6 37.0 - + - -
95A TRP* 4.1 13.7 - + - -
97A SER* 3.9 19.7 - - - -
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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