Contacts of the strand formed by residues 115 - 121 (chain B) in PDB entry 6SQ2
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 GLU 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B MET 3.1 15.7 + - - +
83B GLY* 3.2 0.9 - - - -
84B ILE 2.8 31.2 + - - -
113B ASP 3.5 0.8 + - - -
114B VAL* 1.3 74.8 - - - +
116B LYS* 1.3 60.9 + - - +
165B LEU* 3.8 19.4 - - + +
168B ASP* 3.8 24.6 - - + +
169B ILE* 3.7 27.1 - - + +
172B LYS* 2.5 34.4 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE* 3.4 7.2 - - + +
86B LEU* 4.0 12.6 - - + -
103B ILE* 5.3 11.9 - - + -
106B ILE* 3.9 36.8 - - + -
107B GLU* 6.4 2.0 - - + -
112B ALA 5.3 4.9 + - - -
114B VAL* 3.6 24.5 + - + +
115B GLU* 1.3 84.1 + - - +
117B MET* 1.3 63.8 + - - +
143B TYR* 5.2 7.9 + - - -
145B ILE* 3.4 47.6 - - + +
146B LYS* 4.0 4.5 + - - +
165B LEU* 4.7 3.7 - - - +
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Residues in contact with MET 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE 3.1 5.8 + - - +
85B MET* 3.4 25.0 - - - +
86B LEU* 2.8 27.4 + - - +
116B LYS* 1.3 76.6 - - - +
118B ILE* 1.3 71.9 + - - +
119B LEU* 3.9 13.6 + - + -
145B ILE* 4.6 0.9 - - - -
146B LYS* 3.5 29.8 - - + +
147B PHE* 4.6 1.3 - - - +
148B MET* 4.4 9.4 - - + +
161B ALA* 3.6 32.1 - - - +
164B THR* 3.9 16.8 - - + -
165B LEU* 3.7 26.7 - - + +
168B ASP* 4.9 1.6 - - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.3 21.8 - - + +
88B TYR* 3.7 30.1 - - + -
99B ILE* 4.2 11.9 - - + -
103B ILE* 4.7 1.1 - - + -
117B MET* 1.3 74.5 - - - +
119B LEU* 1.3 64.7 + - - +
120B GLY 4.1 0.2 - - - -
136B GLY 5.2 0.9 - - - +
139B LEU* 4.1 21.8 - - + -
140B ALA* 4.0 23.3 - - + +
143B TYR* 4.7 4.7 - - + -
145B ILE* 3.7 26.7 - - + -
146B LYS 2.9 11.3 + - - +
147B PHE* 3.3 15.8 - - + -
148B MET 3.1 24.6 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 6.0 0.2 - - + -
24B VAL* 4.5 20.6 - - + -
85B MET* 3.9 33.2 - - + -
86B LEU 2.8 10.7 + - - +
87B VAL* 3.4 18.1 - - + -
88B TYR* 3.0 32.8 + - - +
117B MET* 3.9 15.5 - - + -
118B ILE* 1.3 80.3 - - - +
120B GLY* 1.3 59.8 + - - +
121B ASN 3.5 0.3 + - - -
148B MET* 3.3 9.4 - - + +
150B THR* 4.0 24.7 - - + +
158B VAL* 6.6 0.2 - - - -
161B ALA* 3.8 27.6 - - + -
162B PHE* 5.7 0.2 - - + -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.6 31.6 - - - -
90B ILE* 3.7 9.4 - - - +
119B LEU* 1.3 70.1 - - - +
121B ASN* 1.3 61.1 + - - -
123B CYS* 4.4 0.7 - - - +
147B PHE* 3.9 7.8 - - - -
148B MET 2.9 12.0 + - - -
149B GLU* 3.2 10.3 - - - +
150B THR 2.9 22.3 + - - +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 3.0 22.7 + - - +
20B GLY* 3.6 7.5 - - - -
24B VAL* 3.6 14.7 - - - +
87B VAL* 3.9 11.7 - - + -
88B TYR 2.8 17.1 + - - +
89B ASP* 3.7 0.7 - - - -
90B ILE* 3.0 22.9 + - - +
119B LEU 3.5 0.6 + - - +
120B GLY* 1.3 72.5 - - - +
122B LYS* 1.3 81.8 + - - +
123B CYS 3.4 0.9 - - - -
150B THR* 2.8 29.1 + - - +
152B ALA 3.4 16.1 + - - -
900B GTP 3.2 25.5 + - - -
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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