Contacts of the strand formed by residues 71 - 79 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C CYS* 3.9 5.4 - - - -
69C CYS* 3.1 22.0 + - + +
70C CYS* 1.3 78.2 - - - +
72C PRO* 1.3 85.8 + - + +
73C THR* 3.6 2.5 - - + +
75C TYR* 4.4 10.9 + - - -
98C CYS* 3.6 0.7 - - - -
99C GLY 3.1 30.1 + - - +
41D SER* 4.5 0.8 + - - -
43D HIS* 5.4 0.2 + - - -
44D ASP* 2.7 43.4 + - - -
47D LEU* 5.1 1.8 - - - +
65D VAL* 3.3 31.5 + - - -
67D GLN 3.2 26.2 + - - +
68D PRO* 3.6 24.1 - - + +
69D CYS 5.1 0.9 - - - +
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C CYS* 3.5 13.0 - - + +
70C CYS 4.7 0.2 - - - +
71C ARG* 1.3 109.7 - - + +
73C THR* 1.3 60.4 + - - +
74C ARG 4.4 1.3 - - - +
75C TYR* 2.9 43.1 + - + +
95C ALA* 3.6 27.8 - - + -
97C ALA 3.3 8.5 - - - +
43D HIS* 4.4 14.1 - - + +
47D LEU* 6.4 0.4 - - + -
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ARG* 3.6 4.3 - - + +
72C PRO* 1.3 73.1 - - - +
74C ARG* 1.3 62.9 + - - +
75C TYR* 4.8 7.2 - - - -
97C ALA* 2.9 24.1 + - - +
98C CYS 3.5 4.3 + - - +
99C GLY* 3.4 35.0 - - - +
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C THR* 1.3 83.1 + - - +
75C TYR* 1.3 75.6 + - - +
95C ALA* 3.4 6.4 - - - +
96C THR* 2.5 65.5 + - - +
97C ALA* 3.4 21.8 + - + +
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ARG* 4.4 4.9 + - - -
72C PRO* 2.9 43.4 + - + +
73C THR 4.8 4.7 - - - -
74C ARG* 1.3 88.1 - - - +
76C GLU* 1.3 63.8 + - - +
92C ARG* 3.6 43.1 - - + +
94C SER 3.4 14.6 - - - +
95C ALA* 4.0 2.7 - - - -
96C THR* 3.5 8.3 + - - +
41D SER* 3.6 23.3 + - - -
43D HIS* 3.5 26.9 - + + +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 3.8 20.7 + - - -
75C TYR* 1.3 78.5 - - - +
77C ALA* 1.3 73.8 + - - +
92C ARG* 4.0 6.5 - - - +
93C LEU 3.5 1.7 + - - -
94C SER* 2.9 35.7 + - - +
95C ALA 5.0 1.4 - - - +
96C THR* 3.4 21.8 - - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLU* 1.3 89.7 + - - +
78C VAL* 1.3 65.7 + - - +
79C SER* 4.5 2.6 + - - +
89C THR* 3.5 16.2 - - - +
90C VAL 3.3 16.2 - - - +
91C ASP* 4.1 14.6 - - - +
92C ARG 3.9 4.9 - - - +
93C LEU 4.6 0.2 - - - +
94C SER* 4.6 0.9 - - - -
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.4 9.9 - - + -
27C VAL* 4.2 24.0 - - + -
28C ARG 4.3 10.3 - - - +
29C PHE* 4.7 6.1 - - + -
77C ALA* 1.3 81.6 - - - +
79C SER* 1.3 71.0 + - - +
80C PHE* 4.1 8.2 - - + -
89C THR* 3.2 3.3 - - - -
90C VAL* 3.1 27.4 + - - +
93C LEU* 3.7 38.8 - - + -
94C SER* 3.8 18.6 - - - -
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Residues in contact with SER 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.7 1.3 - - - +
27C VAL* 3.3 18.2 - - - +
77C ALA* 4.3 2.1 - - - +
78C VAL* 1.3 77.0 + - - +
80C PHE* 1.3 69.4 + - - +
87C TRP* 3.3 37.9 - - - -
88C ARG 3.2 6.9 + - - -
89C THR* 4.0 5.0 + - - -
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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