Contacts of the strand formed by residues 1154 - 1158 (chain B) in PDB entry 2VE7
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 LEU1154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146B ILE* 5.8 2.7 - - + -
1147B ARG 3.8 7.0 - - - +
1148B LYS* 3.7 39.0 - - + +
1153B LYS* 1.3 76.9 - - - +
1155B GLN* 1.3 61.8 + - - +
1156B PHE* 4.4 8.5 - - + -
1173B SER* 3.4 11.3 - - - -
1174B LEU* 2.9 55.1 + - + +
1175B HIS* 6.4 0.4 - - - -
1176B LEU* 6.2 4.3 - - + -
1207B PHE* 5.4 4.0 - - + -
1138D TYR* 3.8 30.1 - - + +
1139D VAL* 5.1 3.1 - - + -
1142D LEU* 4.5 16.4 - - + -
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Residues in contact with GLN1155 (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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1145B GLU 3.5 0.5 - - - +
1146B ILE* 3.2 7.4 - - - +
1147B ARG* 2.9 79.2 + - + +
1149B ILE* 5.8 0.9 - - + +
1150B TYR* 6.3 1.6 - - + -
1153B LYS* 5.3 4.0 - - - +
1154B LEU* 1.3 75.4 - - - +
1156B PHE* 1.3 63.2 + - - +
1157B ILE* 3.7 16.9 - - + +
1171B MET* 3.4 37.8 - - - +
1172B PHE 4.0 2.5 - - - +
1173B SER* 3.3 24.3 + - - +
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Residues in contact with PHE1156 (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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1144B LEU* 4.3 6.5 - - + -
1145B GLU 3.4 4.7 - - - -
1146B ILE* 3.2 33.7 - - + -
1154B LEU* 4.4 9.6 - - + -
1155B GLN* 1.3 76.7 - - - +
1157B ILE* 1.3 62.2 + - - +
1158B PHE* 4.2 1.5 - - + -
1170B PHE 3.8 1.0 - - - +
1171B MET* 3.2 23.4 - - - +
1172B PHE* 3.2 52.4 + + + +
1174B LEU* 3.3 31.2 - - + -
1207B PHE* 4.2 21.1 - + - -
1211B LEU* 3.4 29.2 - - + -
1142D LEU* 4.3 19.1 - - + -
1146D VAL* 5.1 4.0 - - + -
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Residues in contact with ILE1157 (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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1144B LEU* 3.4 6.3 - - - +
1145B GLU* 2.7 52.8 + - + +
1147B ARG* 3.7 31.0 - - + +
1155B GLN* 3.7 31.9 - - + +
1156B PHE* 1.3 77.2 - - - +
1158B PHE* 1.3 65.3 - - - +
1159B THR* 3.8 10.0 - - + +
1169B PRO* 3.6 30.3 - - + -
1170B PHE 3.5 2.9 - - - +
1171B MET* 3.6 19.3 - - + -
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Residues in contact with PHE1158 (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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1143B GLY 3.4 10.8 - - - -
1144B LEU* 3.8 22.0 - - + -
1156B PHE* 5.2 1.3 - - + -
1157B ILE* 1.3 74.1 - - - +
1159B THR* 1.3 60.5 + - - +
1161B ILE* 3.8 20.2 - - + -
1168B SER 3.9 0.2 - - - +
1169B PRO* 3.4 6.1 - - - +
1170B PHE* 2.7 41.8 + - + +
1172B PHE* 4.5 10.5 - + - -
1211B LEU* 3.9 19.5 - - + -
1214B VAL* 3.9 22.2 - - + -
1215B ARG* 3.5 47.3 - - + -
1218B PHE* 3.8 18.8 - + + -
1190D TRP* 3.8 18.2 - + - -
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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