Contacts of the strand formed by residues 1139 - 1144 (chain A) in PDB entry 4YOC
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 LEU1139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1137A PRO 3.7 1.5 + - - +
1138A LYS* 1.3 71.4 - - - +
1140A ARG* 1.3 64.6 + - - +
1141A THR* 3.0 7.5 + - - +
1160A ILE* 2.6 20.7 + - + +
1161A SER* 3.4 0.4 - - - -
1162A ASP* 2.9 23.3 + - - -
1218A GLU* 3.5 19.3 - - + +
1219A MET* 4.1 33.0 - - + -
1261A ARG* 3.3 35.7 - - - +
1262A PHE* 3.8 27.1 - - + -
1592A ILE* 4.9 1.6 - - + -
1596A MET* 3.9 23.6 - - + -
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Residues in contact with ARG1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138A LYS 3.5 5.0 + - - +
1139A LEU* 1.3 68.2 - - - +
1141A THR* 1.3 59.0 + - - +
1162A ASP* 3.5 7.9 - - + -
1164A LEU* 3.6 23.3 - - + -
1165A TRP* 3.8 14.1 - - + -
1215A GLY 2.9 23.4 + - - -
1216A ASP* 2.8 31.9 + - - +
1217A VAL 3.9 0.9 - - - -
1218A GLU* 2.9 65.8 + - - +
1219A MET 2.9 7.1 + - - +
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Residues in contact with THR1141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139A LEU 3.0 13.3 + - - -
1140A ARG* 1.3 73.9 - - - +
1142A LEU* 1.3 63.6 + - - +
1143A ASP 4.5 0.2 - - - +
1155A PHE* 5.1 2.2 - - + -
1161A SER* 3.1 17.3 - - - -
1162A ASP 2.9 7.5 + - - -
1163A THR* 3.3 26.3 - - - +
1164A LEU 3.0 23.0 + - - -
1165A TRP* 3.4 12.3 + - - +
1219A MET* 3.3 32.6 - - + +
1221A CYS* 3.7 24.7 - - - -
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Residues in contact with LEU1142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140A ARG 4.2 0.2 + - - -
1141A THR* 1.3 74.4 - - - +
1143A ASP* 1.3 60.2 + - - +
1144A VAL* 4.1 4.5 - - + -
1165A TRP* 3.4 34.3 - - + +
1166A ALA 4.4 1.1 - - - +
1167A ILE* 4.4 20.9 - - + -
1187A PHE* 5.8 0.4 - - + -
1212A PRO* 4.6 8.1 - - + -
1217A VAL* 3.9 35.9 - - + -
1219A MET 2.9 7.9 + - - +
1220A LEU* 3.6 24.0 - - + +
1221A CYS* 3.0 27.4 + - - +
1254A TYR* 4.1 23.1 - - + -
1258A TYR* 4.3 8.3 - - + -
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Residues in contact with ASP1143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141A THR 4.0 0.4 - - - -
1142A LEU* 1.3 73.1 - - - +
1144A VAL* 1.3 67.9 + - - +
1145A PHE 4.4 0.5 - - - +
1146A SER* 3.7 29.4 - - - +
1149A GLY* 5.1 0.5 - - - -
1151A LEU* 4.2 9.4 - - - +
1152A SER* 2.4 40.3 + - - +
1163A THR* 3.9 10.5 - - + -
1165A TRP 3.0 9.4 + - - +
1166A ALA* 3.3 2.5 - - + -
1167A ILE 2.9 24.3 + - - -
1177A PHE* 4.2 0.7 - - - -
1221A CYS* 3.3 27.0 - - - +
1222A GLY* 4.2 2.6 - - - -
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Residues in contact with VAL1144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142A LEU* 4.1 11.0 - - + -
1143A ASP* 1.3 73.4 - - - +
1145A PHE* 1.3 106.3 + - + +
1167A ILE* 4.1 27.4 - - + -
1191A CYS* 4.6 5.6 - - + -
1220A LEU* 3.8 16.6 - - + -
1221A CYS 2.9 5.3 + - - -
1222A GLY* 3.2 19.4 - - - -
1251A PHE* 3.7 31.0 - - + -
1254A TYR* 4.8 10.3 - - + -
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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