Contacts of the strand formed by residues 1171 - 1181 (chain B) in PDB entry 3E0D
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 GLU1171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025B ALA 4.6 0.5 - - - +
1026B SER 2.4 38.6 - - - +
1027B CYS* 4.1 2.3 - - - -
1031B GLU* 5.0 14.3 - - - +
1035B PHE* 2.1 51.4 - - + +
1164B ARG* 3.5 36.1 + - + +
1165B VAL 3.9 7.9 - - - +
1166B LEU* 3.8 30.5 - - + +
1167B GLY 4.5 0.4 - - - +
1170B GLY* 1.3 68.8 - - - -
1172B ALA* 1.3 61.1 + - - +
1173B LEU* 5.0 2.1 - - - +
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Residues in contact with ALA1172 (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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1035B PHE* 2.8 13.0 - - + -
1039B LEU* 5.3 9.4 - - + -
1163B LEU 3.6 1.4 - - - +
1164B ARG* 3.7 4.2 - - - -
1165B VAL* 3.2 37.4 + - + +
1170B GLY 4.0 1.8 + - - -
1171B GLU* 1.3 76.9 - - - +
1173B LEU* 1.3 61.6 + - - +
1174B PHE* 3.8 30.1 - - + -
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Residues in contact with LEU1173 (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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1024B VAL 5.1 0.9 - - - +
1026B SER* 3.8 22.2 - - - +
1035B PHE* 4.6 4.9 - - + -
1132B GLU* 4.0 11.4 - - - +
1162B TYR* 5.0 10.6 - - + -
1163B LEU 3.6 5.6 - - - +
1164B ARG* 3.5 44.9 - - + +
1171B GLU 4.1 2.9 + - - +
1172B ALA* 1.3 76.7 - - - +
1174B PHE* 1.3 63.9 + - - +
1175B ALA* 3.5 3.9 + - - +
1202B ARG* 3.5 43.9 + - - +
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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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1162B TYR* 3.6 1.0 - - - -
1163B LEU* 2.8 53.7 + - + +
1165B VAL* 3.7 23.1 - - + -
1172B ALA* 3.8 23.3 - - + -
1173B LEU* 1.3 71.9 - - - +
1175B ALA* 1.3 64.3 + - - +
1176B LEU 3.7 0.9 + - - -
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Residues in contact with ALA1175 (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 PRO* 6.1 2.0 - - + -
1161B VAL 3.5 7.2 - - - +
1162B TYR* 3.8 31.7 - - + +
1173B LEU 3.5 6.0 + - - +
1174B PHE* 1.3 76.3 - - - +
1176B LEU* 1.3 71.2 + - - +
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Residues in contact with LEU1176 (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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1148B LEU* 5.8 4.5 - - + -
1152B LEU* 3.6 23.1 - - + -
1161B VAL* 2.7 37.1 + - + +
1163B LEU* 3.7 29.8 - - + -
1174B PHE 3.7 1.2 + - - -
1175B ALA* 1.3 79.6 - - - +
1177B ARG* 1.3 76.3 + - + +
1179B VAL* 3.5 38.8 - - + +
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Residues in contact with ARG1177 (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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1149B LYS* 5.6 5.1 - - - +
1176B LEU* 1.3 90.4 - - + +
1178B GLU* 1.3 80.9 + - + +
1179B VAL* 4.7 3.4 + - + +
1180B ARG* 5.2 6.6 + - - -
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Residues in contact with GLU1178 (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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1177B ARG* 1.3 96.0 + - + +
1179B VAL* 1.3 71.6 + - + +
1180B ARG* 3.4 15.6 + - - +
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Residues in contact with VAL1179 (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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1149B LYS* 5.0 5.6 - - + +
1152B LEU* 3.3 47.1 - - + +
1153B ASP* 4.0 20.0 - - - +
1159B LEU 4.5 0.9 - - - +
1160B PRO* 4.9 1.0 - - - +
1161B VAL* 4.4 9.9 + - + +
1176B LEU* 3.5 30.2 - - + +
1177B ARG* 3.6 3.9 + - + +
1178B GLU* 1.3 83.1 + - + +
1180B ARG* 1.3 70.7 + - - +
1181B VAL* 4.2 4.5 - - + -
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Residues in contact with ARG1180 (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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1152B LEU 5.6 0.2 - - - +
1156B PRO* 3.5 6.2 - - - +
1157B GLY 2.9 30.3 + - - +
1158B SER* 3.4 34.4 + - - +
1159B LEU 3.3 9.4 - - - +
1160B PRO* 3.4 37.0 - - - +
1177B ARG 5.2 6.2 + - - +
1178B GLU 3.4 17.0 + - - +
1179B VAL* 1.3 78.5 + - - +
1181B VAL* 1.3 62.3 + - - +
1201B ASP* 5.3 0.4 + - - -
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Residues in contact with VAL1181 (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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1131B LEU* 4.3 15.0 - - + -
1152B LEU* 3.7 39.0 - - + -
1155B HIS* 3.6 9.6 - - + +
1157B GLY* 4.0 0.7 - - - -
1158B SER 3.2 2.8 + - - -
1159B LEU* 2.8 39.3 + - + +
1161B VAL* 3.8 19.2 - - + +
1179B VAL* 4.2 2.0 - - + -
1180B ARG* 1.3 73.0 - - - +
1182B GLY* 1.3 62.7 + - - +
1183B GLU* 3.4 12.1 - - - +
1185B ALA* 3.3 32.1 - - + -
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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