Contacts of the strand formed by residues 1192 - 1197 (chain B) in PDB entry 3CQZ
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 ILE1192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA* 3.9 15.5 - - + -
10A PRO* 3.5 23.2 - - - +
1161B HIS* 4.9 2.5 - - + -
1162B ILE 3.8 12.6 - - - +
1163B CYS* 4.5 3.4 - - + -
1171B VAL* 3.9 33.7 - - + -
1181B PHE* 4.1 41.7 - - + +
1182B GLU* 4.4 8.3 - - - -
1183B CYS* 4.5 3.6 - - + +
1188B ASN* 4.4 11.9 - - + +
1189B LYS 4.6 7.9 - - - +
1190B ILE 3.8 1.2 - - - -
1191B ASP* 1.3 80.1 - - - +
1193B TYR* 1.3 79.6 + - - +
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Residues in contact with TYR1193 (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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9A ALA* 3.8 4.1 - - - +
10A PRO* 3.6 22.7 - - + +
12A ARG* 3.2 49.6 + - + -
1161B HIS* 3.5 7.1 - - - +
1162B ILE* 3.3 45.2 + - + -
1164B GLY* 4.2 15.7 - - - -
1191B ASP* 3.5 27.0 + - - -
1192B ILE* 1.3 88.3 - - - +
1194B GLN* 1.3 62.3 + - - +
1219B THR* 3.8 19.7 - - + -
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Residues in contact with GLN1194 (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* 3.4 23.5 + - - +
9A ALA* 2.8 27.1 - - + +
10A PRO 2.9 11.3 + - - +
11A LEU* 3.2 12.7 + - - +
12A ARG 3.0 24.4 + - - -
1159B ARG* 3.3 48.2 - - + +
1160B VAL 3.6 6.5 - - - +
1161B HIS* 4.5 2.0 - - + +
1193B TYR* 1.3 77.4 - - - +
1195B ILE* 1.3 61.5 + - - +
1196B HIS* 3.5 16.8 - - + -
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Residues in contact with ILE1195 (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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11A LEU* 4.3 0.2 - - - -
12A ARG* 3.4 30.1 - - + +
13A THR* 5.4 0.7 - - - -
14A VAL* 3.9 15.7 - - + -
1432A GLN* 6.1 0.4 - - - +
1158B PHE 3.8 0.3 - - - +
1159B ARG* 3.7 2.3 - - - +
1160B VAL* 3.2 34.5 + - + +
1162B ILE* 3.7 33.4 - - + -
1169B MET* 6.3 0.4 - - - -
1194B GLN* 1.3 78.5 - - - +
1196B HIS* 1.3 65.2 + - - +
1197B ILE* 3.5 31.1 + - + -
1217B LEU* 3.6 28.3 - - + -
1219B THR* 4.5 2.0 - - + -
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Residues in contact with HIS1196 (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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11A LEU* 3.4 35.3 - - + +
12A ARG 4.5 1.9 + - - +
1430A LEU 3.8 7.3 - - - +
1431A GLY* 5.6 1.0 - - - +
1432A GLN* 4.7 5.7 - - - +
1157B ALA* 3.6 27.4 - - + +
1158B PHE 3.4 3.8 - - - -
1159B ARG* 3.5 20.7 - - + +
1194B GLN* 3.5 28.9 - - + -
1195B ILE* 1.3 73.9 - - - +
1197B ILE* 1.3 67.7 + - - +
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Residues in contact with ILE1197 (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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14A VAL* 4.9 2.5 - - + -
1430A LEU* 3.9 26.5 - - + +
1432A GLN* 5.4 0.4 - - - +
1157B ALA* 4.3 3.8 - - - -
1158B PHE* 2.8 39.2 + - - +
1160B VAL* 4.3 16.6 - - + -
1169B MET* 4.6 4.5 - - - -
1195B ILE* 3.5 25.8 - - + -
1196B HIS* 1.3 81.0 - - - +
1198B PRO* 1.3 75.5 - - + +
1201B ALA* 3.9 6.7 - - + -
1202B LYS* 3.5 36.8 - - + +
1205B PHE* 4.1 12.6 - - + -
1217B LEU* 5.0 0.9 - - + -
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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