Contacts of the strand formed by residues 92 - 100 (chain R) in PDB entry 3DLQ
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 TYR 92 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R PHE* 5.2 0.7 - - + -
57R TYR* 5.4 5.2 - + + -
58R LYS 3.3 17.0 - - - +
59R THR* 3.6 19.7 - - - -
60R TYR 4.1 1.6 - - - +
84R GLU 3.2 21.1 + - - -
85R THR* 3.4 46.9 - - + -
86R GLY 3.7 0.7 + - - -
87R ASN* 3.1 38.8 + - - +
90R GLU* 3.8 25.5 - - + +
91R LEU* 1.3 80.7 - - - +
93R TYR* 1.3 75.1 + - - +
112R ARG* 3.7 0.9 - - - +
113R PHE* 2.8 48.8 + + + +
115R SER* 6.0 2.7 - - - -
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Residues in contact with TYR 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I SER* 5.1 2.1 + - - -
67I ASP 4.4 8.1 + - - -
69I ASN 5.3 0.3 + - - -
70I THR* 3.6 30.8 - - + +
30R PHE* 4.6 4.4 - - - -
57R TYR* 3.3 5.7 - - - +
58R LYS* 2.9 36.1 + - + +
60R TYR* 3.7 31.4 - + + -
65R TRP* 3.8 18.6 - - + -
92R TYR* 1.3 78.8 - - - +
94R ALA* 1.3 60.4 + - - +
109R MET* 3.8 21.8 - - + -
110R THR* 3.6 21.1 - - - -
111R ASP* 4.0 6.1 - - - -
112R ARG* 2.8 55.7 + - + +
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Residues in contact with ALA 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R PHE* 3.8 21.7 - - + -
39R LEU* 3.7 30.1 - - + -
56R GLU 3.3 12.3 - - - +
57R TYR* 4.2 0.2 - - - +
65R TRP* 3.8 3.8 - - - -
81R LEU* 4.1 7.4 - - + -
93R TYR* 1.3 74.2 - - - +
95R ARG* 1.3 61.9 + - - +
109R MET* 3.3 7.4 - - - +
110R THR* 2.9 30.7 + - + -
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Residues in contact with ARG 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R VAL* 5.5 0.4 - - - -
54R SER 3.7 0.7 - - - +
55R ILE* 3.4 7.3 - - - +
56R GLU* 2.7 74.5 + - + +
65R TRP* 3.4 60.4 - - + +
94R ALA* 1.3 75.2 - - - +
96R VAL* 1.3 65.2 + - - +
97R THR* 5.4 0.7 - - - +
107R THR* 4.1 21.1 - - + +
108R LYS 3.4 11.9 - - - +
109R MET* 4.0 8.1 - - + -
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Residues in contact with VAL 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R LEU* 3.3 32.5 - - + +
28R VAL* 4.0 14.1 - - + -
39R LEU* 3.8 15.0 - - + -
41R TRP* 3.7 36.6 - - + -
53R TYR* 3.9 22.4 - - + -
54R SER 3.6 3.1 - - - -
55R ILE* 4.1 4.3 - - + -
95R ARG* 1.3 79.0 - - - +
97R THR* 1.3 64.9 + - - +
107R THR* 3.3 2.9 - - - +
108R LYS 3.0 34.2 + - - +
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Residues in contact with THR 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R VAL 3.6 0.9 - - - +
53R TYR* 3.3 3.5 - - - -
54R SER* 3.0 43.4 + - - -
56R GLU* 4.5 10.4 + - - -
95R ARG* 5.3 0.3 - - - +
96R VAL* 1.3 75.3 - - - +
98R ALA* 1.3 62.1 + - - +
99R VAL* 4.2 10.5 - - + +
105R SER* 3.8 18.4 - - - +
106R ALA 3.3 2.9 - - - -
107R THR* 2.7 31.3 + - - +
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Residues in contact with ALA 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R LEU* 4.5 16.8 - - + +
25R LEU* 4.1 14.8 - - + +
51R THR* 3.9 8.3 - - + -
52R VAL 3.4 4.5 - - - -
53R TYR* 3.6 27.1 - - + -
96R VAL 4.0 1.2 + - - -
97R THR* 1.3 73.2 - - - +
99R VAL* 1.3 60.9 + - - +
100R SER 4.3 0.4 - - - -
105R SER* 3.0 21.9 + - - -
106R ALA 2.7 24.0 + - - +
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Residues in contact with VAL 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R ASP 3.9 0.7 - - - +
51R THR* 3.4 4.7 - - - +
52R VAL* 2.9 46.4 + - + +
73R ARG* 4.6 15.9 - - - +
97R THR* 4.2 13.5 - - + +
98R ALA* 1.3 80.0 - - - +
100R SER* 1.3 72.4 + - - +
103R GLY* 4.8 8.1 - - - +
104R ARG 3.5 6.7 - - - +
105R SER* 3.6 15.3 - - - +
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Residues in contact with SER 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R LEU* 5.3 4.2 - - - +
48R THR* 3.5 31.2 - - - -
50R ASP* 3.4 7.8 + - - -
51R THR* 4.0 4.6 - - - +
98R ALA 4.3 0.2 - - - -
99R VAL* 1.3 79.3 - - - +
101R ALA* 1.3 56.1 + - - +
102R GLY* 3.3 9.4 + - - -
103R GLY* 2.7 28.2 + - - -
104R ARG* 2.8 35.8 + - - +
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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