Contacts of the strand formed by residues 74 - 82 (chain A) in PDB entry 3F61
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA* 4.6 12.3 - - + +
64A ALA 3.5 24.9 - - - +
65A ALA* 4.0 25.0 - - + +
66A LEU 5.0 0.2 + - - -
72A VAL* 3.8 5.8 + - + +
73A ALA* 1.3 78.3 - - - +
75A TYR* 1.3 65.4 + - - +
76A ASP* 4.2 8.3 - - - +
77A THR* 5.0 2.7 - - + -
90A ILE* 3.5 37.9 - - + -
91A VAL 3.8 3.1 - - - +
92A MET* 4.2 7.2 - - + -
156A ASP* 6.3 1.6 - - - +
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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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11A TYR* 5.9 0.4 - - - +
35A ARG* 4.1 25.5 + - - -
36A ASP 5.5 0.2 - - - -
37A VAL* 3.9 23.1 - - + -
73A ALA* 3.5 20.5 - - + +
74A VAL* 1.3 78.4 - - - +
76A ASP* 1.3 66.9 + - + +
91A VAL* 2.8 17.4 + - + +
92A MET* 3.6 16.8 - - - -
93A GLU* 3.5 39.0 + - - +
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Residues in contact with ASP 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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10A ARG* 4.5 9.2 + - - +
11A TYR* 4.1 16.3 + - - +
74A VAL* 3.7 4.2 - - - +
75A TYR* 1.3 84.8 - - + +
77A THR* 1.3 88.5 + - - +
89A TYR* 6.0 0.7 - - - -
90A ILE* 3.5 3.6 - - - +
91A VAL* 2.8 41.4 + - + -
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Residues in contact with THR 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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60A ALA* 3.9 29.6 - - + +
74A VAL* 5.0 4.3 - - + -
76A ASP* 1.3 98.4 + - - +
78A GLY* 1.3 60.1 + - - +
89A TYR* 3.4 12.6 - - - -
90A ILE* 4.0 20.4 - - + +
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Residues in contact with GLY 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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57A ARG* 4.6 4.4 + - - -
77A THR* 1.3 77.2 - - - +
79A GLU* 1.3 63.0 + - - +
88A PRO* 3.5 2.9 - - - +
89A TYR* 2.9 49.4 + - - +
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Residues in contact with GLU 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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8A SER* 4.2 5.4 + - - -
53A TYR* 2.6 39.4 + - - -
57A ARG* 3.0 24.8 + - - +
78A GLY* 1.3 75.1 - - - +
80A ALA* 1.3 63.4 + - - +
81A GLU* 4.0 3.9 + - + +
86A PRO* 3.4 16.5 - - + +
87A LEU 3.5 20.6 - - - +
88A PRO* 3.6 5.2 - - + +
89A TYR* 3.3 7.6 + - - -
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Residues in contact with ALA 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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4A PRO* 5.1 1.3 - - + -
6A HIS 5.2 0.7 - - - +
7A LEU* 3.6 31.6 - - + -
8A SER* 4.5 13.7 - - - +
79A GLU* 1.3 74.2 - - - +
81A GLU* 1.3 63.7 + - - +
82A THR* 3.6 8.3 + - + -
86A PRO* 3.4 3.6 - - - +
87A LEU* 2.8 40.4 + - + +
89A TYR* 3.8 4.8 - - + -
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Residues in contact with GLU 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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79A GLU* 4.0 4.3 + - + +
80A ALA* 1.3 74.2 - - - +
82A THR* 1.3 74.4 + - - +
85A GLY* 3.7 9.5 - - - -
86A PRO* 3.6 29.6 - - + +
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Residues in contact with THR 82 (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 PRO* 4.3 20.0 - - + -
80A ALA* 4.1 4.3 - - + +
81A GLU* 1.3 85.4 - - - +
83A PRO* 1.3 70.0 - - - +
84A ALA* 3.1 17.0 + - - +
85A GLY 2.7 39.4 + - - +
87A LEU* 3.8 33.2 - - + +
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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