Contacts of the strand formed by residues 1168 - 1176 (chain B) in PDB entry 1Q6P
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 THR1168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1100B TRP* 4.4 0.2 - - - -
1159B GLU* 3.9 25.6 + - - +
1160B LEU 3.3 8.5 - - - -
1161B GLU* 3.5 30.7 - - + +
1166B GLN 4.0 4.5 - - - +
1167B GLU* 1.3 82.7 - - - +
1169B ARG* 1.3 68.5 + - - +
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Residues in contact with ARG1169 (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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1099B VAL 4.5 0.8 + - - -
1100B TRP* 2.8 84.0 + - + +
1103B LYS* 3.9 35.5 - - - +
1104B SER 5.4 3.8 + - - -
1159B GLU* 3.4 7.9 - - - +
1160B LEU* 2.9 34.2 + - + +
1167B GLU* 4.1 9.8 + - + -
1168B THR* 1.3 78.7 - - - +
1170B GLU* 1.3 62.8 + - - +
1171B ILE* 3.8 17.2 + - + -
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Residues in contact with GLU1170 (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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1105B ARG* 2.6 59.1 + - - +
1157B GLN* 2.5 43.1 + - + +
1158B LEU 3.4 9.6 - - - +
1159B GLU* 4.8 1.3 - - - +
1169B ARG* 1.3 75.2 - - - +
1171B ILE* 1.3 66.5 + - - +
1172B LEU* 4.0 12.8 - - + +
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Residues in contact with ILE1171 (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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1096B TRP* 4.2 13.5 - - + -
1099B VAL* 3.9 16.4 - - + -
1104B SER 3.5 23.6 - - - +
1105B ARG 3.5 10.5 - - - +
1107B VAL* 4.0 26.5 - - + -
1157B GLN* 3.9 1.0 - - - -
1158B LEU* 2.9 45.5 + - + +
1160B LEU* 3.9 27.6 - - + +
1169B ARG* 4.3 15.3 - - + +
1170B GLU* 1.3 81.8 - - - +
1172B LEU* 1.3 68.2 + - - +
1173B HIS* 3.8 1.1 + - + -
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Residues in contact with LEU1172 (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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1105B ARG* 2.9 37.7 + - - +
1106B GLY* 3.2 2.3 - - - -
1107B VAL 2.8 32.4 + - - +
1155B VAL* 5.5 5.8 - - + -
1156B ARG 3.5 9.0 - - - +
1157B GLN* 4.5 10.5 - - + +
1170B GLU* 4.0 25.1 - - - +
1171B ILE* 1.3 78.7 - - - +
1173B HIS* 1.3 55.1 + - - +
1174B PHE* 3.4 20.0 - - + -
1201B SER* 3.7 23.1 - - - +
1203B SER* 3.7 15.5 - - - +
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Residues in contact with HIS1173 (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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1096B TRP* 5.0 0.4 - + - -
1107B VAL* 3.5 23.6 - - + -
1109B MET* 3.1 24.1 - - + +
1124B TYR* 2.8 33.8 + + - -
1125B TRP* 4.1 15.1 - + - -
1154B THR 3.5 2.3 - - - +
1155B VAL* 3.3 6.1 - - - +
1156B ARG* 2.8 81.4 + - + +
1158B LEU* 4.1 23.1 - - + -
1171B ILE* 3.8 0.4 + - + -
1172B LEU* 1.3 71.4 - - - +
1174B PHE* 1.3 61.1 + - - +
1175B HIS* 4.1 8.9 - - + +
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Residues in contact with PHE1174 (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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1106B GLY* 4.7 0.4 - - - -
1107B VAL 2.8 20.6 + - - +
1108B VAL* 3.2 8.2 - - + -
1109B MET 2.7 33.0 + - - +
1153B TYR* 6.0 0.2 - + - -
1154B THR 3.8 3.4 - - - -
1155B VAL* 3.9 28.3 - - + -
1172B LEU* 3.4 28.7 - - + -
1173B HIS* 1.3 73.0 - - - +
1175B HIS* 1.3 54.6 - - - +
1194B PHE* 3.6 24.3 - + + -
1197B LYS* 4.1 13.2 - - + -
1198B VAL* 3.9 31.9 - - + -
1201B SER* 3.3 33.4 - - - -
1203B SER* 3.4 21.3 - - - -
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Residues in contact with HIS1175 (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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1109B MET* 3.3 32.5 - - + -
1111B ASN 2.6 28.9 + - - -
1112B ARG* 4.3 12.6 - - - -
1113B VAL* 5.2 2.0 - - + -
1125B TRP* 4.1 10.7 - + - -
1153B TYR* 3.0 5.2 - - - -
1154B THR 2.9 35.0 + - - +
1156B ARG* 3.4 39.1 + - - +
1173B HIS* 3.8 4.9 + - + -
1174B PHE* 1.3 73.2 - - - +
1176B TYR* 1.3 70.0 + - - +
1177B THR* 3.5 19.0 + - + +
1194B PHE* 3.8 3.3 - - - -
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Residues in contact with TYR1176 (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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1109B MET 2.8 8.3 + - - -
1110B LEU* 3.6 39.3 - - + +
1111B ASN 3.9 1.4 - - - +
1152B TYR* 3.8 14.6 - + - -
1153B TYR* 3.8 2.5 - - + -
1175B HIS* 1.3 78.8 - - - +
1177B THR* 1.3 59.7 + - - +
1178B THR* 3.1 36.3 + - - -
1179B TRP* 3.8 23.3 + + + -
1185B PRO* 3.5 11.7 - - + +
1186B GLU* 3.4 18.5 + - - +
1190B SER* 3.2 46.0 + - - -
1191B PHE* 4.2 7.2 - + - -
1194B PHE* 3.6 33.1 - + + -
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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