Contacts of the strand formed by residues 1158 - 1163 (chain B) in PDB entry 3GTO
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 PHE1158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLN* 3.9 16.8 - - - +
75A ASN 5.0 2.2 - - - -
76A GLU* 3.7 33.0 - - - -
77A CYS 4.6 1.8 - - - -
78A PRO* 4.4 11.4 - - + -
1116B ARG* 5.6 6.5 - - - -
1152B MET* 5.1 0.2 - - - +
1157B ALA* 1.3 77.2 - - - +
1159B ARG* 1.3 81.1 + - - +
1160B VAL* 3.6 29.8 + - + +
1194B ILE 3.7 2.6 - - - +
1195B HIS* 3.9 6.8 + - - +
1196B ILE* 2.9 31.4 + - + +
1198B TYR* 3.2 48.2 - + + -
1201B LYS* 3.6 23.8 - - + -
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Residues in contact with ARG1159 (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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4A GLN* 2.9 45.5 + - + +
5A GLN 2.9 37.8 + - - +
7A SER* 4.1 3.0 - - - -
76A GLU* 2.4 35.6 + - - +
78A PRO* 5.6 0.5 - - - +
1158B PHE* 1.3 87.0 - - - +
1160B VAL* 1.3 61.3 + - - +
1161B HIS* 3.8 21.3 + - - -
1175B LEU* 3.7 13.3 - - - +
1193B GLN* 2.9 48.6 - - + +
1194B ILE 3.7 4.3 - - - +
1195B HIS* 3.8 21.8 - - + -
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Residues in contact with VAL1160 (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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78A PRO* 4.4 18.2 - - + -
1158B PHE* 3.6 32.8 - - + +
1159B ARG* 1.3 79.1 - - - +
1161B HIS* 1.3 82.4 + - - +
1169B MET* 3.7 35.4 - - + -
1193B GLN* 4.0 0.7 - - - -
1194B ILE* 3.4 42.9 + - + +
1196B ILE* 3.8 20.4 - - + -
1201B LYS* 4.5 4.9 - - + -
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Residues in contact with HIS1161 (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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7A SER* 3.3 26.3 + - - -
9A ALA* 5.4 1.9 - - + +
76A GLU* 4.5 1.3 + - - -
78A PRO* 5.2 6.4 - - + +
1159B ARG* 3.8 36.3 + - - -
1160B VAL* 1.3 86.4 + - - +
1162B ILE* 1.3 63.6 + - - +
1169B MET* 3.8 16.6 - - - +
1171B VAL* 3.6 37.6 - - + +
1173B ALA* 3.6 30.7 - - + +
1175B LEU* 4.9 3.8 - - - +
1180B PHE* 4.7 12.7 - + - -
1191B ILE* 4.9 8.2 - - + +
1192B TYR 4.0 3.6 + - - -
1193B GLN* 4.0 13.8 - - + -
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Residues in contact with ILE1162 (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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1160B VAL* 5.5 0.2 - - + -
1161B HIS* 1.3 79.7 - - - +
1163B CYS* 1.3 74.0 + - - +
1167B GLY 4.1 2.7 - - - +
1168B LEU 3.3 21.1 - - - +
1169B MET* 4.1 6.5 - - + -
1171B VAL* 3.5 5.6 - - - -
1191B ILE* 3.2 9.5 - - - +
1192B TYR* 3.1 46.9 + - + +
1194B ILE* 3.8 30.7 - - + -
1216B LEU* 3.5 53.2 - - + +
1218B THR* 5.7 4.5 - - + -
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Residues in contact with CYS1163 (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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1162B ILE* 1.3 87.5 - - - +
1164B GLY* 1.3 64.6 + - - +
1165B ILE* 3.2 24.1 + - - +
1166B CYS* 3.2 13.5 - - - +
1167B GLY* 3.7 13.0 - - - -
1168B LEU 3.3 9.0 + - - +
1170B THR 5.8 0.7 - - - +
1171B VAL* 3.5 7.2 - - + +
1182B CYS* 3.5 18.2 - - - -
1185B CYS* 4.4 1.8 - - - -
1187B ASN* 4.6 2.2 - - - -
1190B ASP 4.3 3.8 - - - -
1191B ILE* 3.9 6.1 - - - -
1192B TYR* 5.3 0.2 - - - -
1216B LEU 4.7 0.9 - - - +
1217B TYR* 5.9 0.2 - - - -
1307B ZN 2.5 36.1 - - - -
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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