Contacts of the strand formed by residues 71 - 81 (chain A) in PDB entry 2GYR
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A CYS* 3.6 5.6 - - - -
69A CYS* 3.0 23.3 + - + +
70A CYS* 1.3 76.0 - - - +
72A PRO* 1.3 83.5 - - + +
73A THR* 3.3 3.3 + - - +
75A TYR* 4.5 7.7 + - - -
99A GLY 3.1 27.4 + - - +
41B SER* 4.4 3.8 + - - -
43B HIS* 5.6 0.2 + - - -
44B ASP* 2.7 36.9 + - - -
47B LEU* 5.3 1.8 - - - +
65B VAL* 3.3 31.7 + - - -
67B GLN 3.1 35.4 + - - +
68B PRO* 3.7 22.0 - - + +
69B CYS 5.4 0.7 - - - +
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Residues in contact with PRO 72 (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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32A CYS* 3.3 20.1 - - + -
70A CYS 4.8 0.2 - - - +
71A ARG* 1.3 109.2 - - + +
73A THR* 1.3 60.5 + - - +
74A ARG 4.1 1.3 - - - +
75A TYR* 2.7 51.5 + - + +
95A ALA* 3.6 20.2 - - + -
97A ALA 3.4 1.6 - - - +
43B HIS* 4.2 14.6 - - + +
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Residues in contact with THR 73 (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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71A ARG 3.7 6.5 - - - +
72A PRO* 1.3 73.4 - - - +
74A ARG* 1.3 70.2 + - - +
75A TYR* 4.9 5.2 - - - -
97A ALA* 3.0 23.6 + - - +
98A CYS 3.6 25.5 + - - +
99A GLY* 3.8 7.9 - - - +
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Residues in contact with ARG 74 (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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72A PRO* 4.1 1.6 - - - +
73A THR* 1.3 87.5 + - - +
75A TYR* 1.3 79.4 + - - +
92A ARG* 6.1 0.2 - - - +
95A ALA* 3.6 3.6 - - - +
96A THR* 3.0 53.4 + - - +
97A ALA* 3.5 20.5 + - + +
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Residues in contact with TYR 75 (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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71A ARG* 4.5 4.9 + - - -
72A PRO* 2.7 49.5 + - + +
73A THR 4.9 2.9 - - - -
74A ARG* 1.3 84.8 - - - +
76A GLU* 1.3 65.9 + - - +
92A ARG* 3.6 66.5 + - + +
94A SER 3.4 15.9 - - - +
95A ALA* 4.0 2.9 - - - -
96A THR* 3.7 7.8 + - - +
41B SER* 3.9 20.6 + - - -
43B HIS* 3.7 21.3 - + + -
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Residues in contact with GLU 76 (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 ARG* 4.0 19.4 + - - -
75A TYR* 1.3 79.1 - - - +
77A ALA* 1.3 72.4 + - - +
92A ARG* 4.0 6.7 - - - +
93A LEU 3.2 2.8 + - - -
94A SER* 2.8 39.7 + - - +
95A ALA 5.0 0.7 - - - +
96A THR* 3.4 21.8 - - + +
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Residues in contact with ALA 77 (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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76A GLU* 1.3 90.3 - - - +
78A VAL* 1.3 66.1 + - - +
79A SER* 4.2 3.8 - - - +
89A THR* 3.7 16.8 - - - +
90A VAL 3.4 14.8 - - - +
91A ASP* 3.9 20.8 + - - +
92A ARG 4.1 1.6 - - - +
94A SER* 4.6 0.7 - - - -
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Residues in contact with VAL 78 (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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17A LEU* 4.4 8.1 - - + -
27A VAL* 4.1 22.2 - - + -
28A ARG 4.0 11.7 - - - +
29A PHE* 4.8 4.9 - - + -
77A ALA* 1.3 81.5 - - - +
79A SER* 1.3 71.5 + - - +
80A PHE* 4.1 10.1 - - + -
89A THR* 3.6 1.7 - - - -
90A VAL* 3.0 26.3 + - - +
93A LEU* 3.6 39.0 - - + -
94A SER* 3.7 20.6 - - - -
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Residues in contact with SER 79 (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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27A VAL* 3.5 15.1 - - - +
77A ALA* 4.2 3.0 - - - +
78A VAL* 1.3 80.1 + - - +
80A PHE* 1.3 66.9 + - - +
87A TRP* 3.1 37.7 - - - -
88A ARG 3.3 9.6 - - - -
89A THR* 4.0 5.1 + - - +
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Residues in contact with PHE 80 (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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14A VAL* 3.9 28.5 - - + -
19A LEU* 4.8 3.8 - - + -
21A HIS* 3.2 41.1 - + + -
23A SER* 4.3 4.5 - - - -
25A GLU* 3.2 16.6 - - + +
27A VAL* 3.7 11.2 - - + -
78A VAL* 4.1 17.9 - - + -
79A SER* 1.3 83.3 - - - +
81A MET* 1.3 76.8 + - - +
82A ASP* 4.1 17.9 - - + -
86A THR 3.7 0.2 - - - +
87A TRP* 3.4 3.9 - - - +
88A ARG* 3.1 48.7 + - + -
90A VAL* 4.6 13.5 - - + -
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Residues in contact with MET 81 (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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23A SER* 2.9 18.4 + - - -
24A ASP 4.8 0.3 - - - +
25A GLU* 2.8 35.4 + - + +
80A PHE* 1.3 74.6 - - - +
82A ASP* 1.3 65.6 + - - +
85A SER* 4.2 20.6 - - - +
86A THR 3.6 1.1 - - - -
87A TRP* 3.2 61.0 - - + -
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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