Contacts of the strand formed by residues 1147 - 1152 (chain A) in PDB entry 1LJM
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 THR1147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106A MET 3.5 2.3 - - - +
1107A ALA* 4.0 0.8 - - - -
1108A GLY 2.8 33.8 + - - -
1109A ASN* 5.6 1.6 - - - +
1146A PHE* 1.3 71.6 + - - +
1148A LEU* 1.3 61.8 + - - +
1149A THR* 3.5 14.8 + - - +
1161A THR* 3.5 27.6 - - + -
1162A TYR 5.6 0.2 - - - +
1164A ARG 5.4 0.9 - - - -
1165A ALA* 4.9 8.5 - - - +
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Residues in contact with LEU1148 (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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1075A LEU* 4.3 17.0 - - + -
1089A PHE* 4.4 7.9 - - + -
1105A VAL* 3.3 39.0 - - + -
1106A MET 3.4 7.2 - - - +
1107A ALA* 4.1 6.5 - - + -
1136A PHE* 3.9 29.2 - - + -
1146A PHE* 3.9 3.2 + - - +
1147A THR* 1.3 69.8 - - - +
1149A THR* 1.3 61.5 + - - +
1150A ILE* 3.6 26.7 - - + -
1161A THR* 3.4 6.4 - - - +
1162A TYR* 2.9 50.2 + - + +
1164A ARG 5.1 2.2 + - - +
1166A ILE* 5.1 6.7 - - + +
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Residues in contact with THR1149 (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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1104A THR* 3.8 1.2 + - - +
1105A VAL* 3.7 2.1 - - - -
1106A MET* 2.7 52.0 + - + +
1147A THR* 3.8 16.5 + - - +
1148A LEU* 1.3 74.3 + - - +
1150A ILE* 1.3 61.8 + - - +
1151A THR* 3.9 8.9 + - - +
1159A VAL* 3.7 26.2 - - + -
1160A ALA 3.7 3.1 - - - +
1161A THR* 4.5 6.6 + - - +
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Residues in contact with ILE1150 (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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1065A THR* 4.5 14.1 - - + -
1070A PHE* 6.3 0.4 - - + -
1072A CYS* 4.4 14.6 - - + -
1089A PHE* 4.0 14.8 - - + -
1091A VAL* 3.8 33.0 - - + -
1103A VAL* 3.8 24.0 - - + -
1104A THR 3.5 5.4 - - - +
1105A VAL* 4.6 5.2 - - + +
1148A LEU* 3.6 21.8 - - + +
1149A THR* 1.3 72.9 - - - +
1151A THR* 1.3 61.0 + - - +
1152A VAL* 4.1 7.1 - - + +
1158A GLN 4.1 0.5 - - - +
1159A VAL* 3.4 6.8 - - - +
1160A ALA* 2.7 50.9 + - + +
1162A TYR* 5.1 4.5 - - + +
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Residues in contact with THR1151 (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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1103A VAL* 3.3 4.1 - - - -
1104A THR* 2.9 45.0 + - - -
1106A MET* 6.1 0.7 - - - +
1149A THR* 4.4 11.6 + - - +
1150A ILE* 1.3 76.0 + - - +
1152A VAL* 1.3 63.2 + - - +
1153A PHE* 3.4 35.1 - - + -
1157A PRO* 4.8 6.5 - - + -
1158A GLN 3.8 3.1 - - - +
1159A VAL* 4.2 20.5 - - + +
2110B ASP* 4.9 7.2 - - + +
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Residues in contact with VAL1152 (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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1070A PHE* 3.5 39.7 - - + -
1091A VAL* 4.9 0.9 - - + -
1097A VAL* 3.9 17.7 - - + -
1101A THR* 3.7 20.6 - - + -
1102A LEU 3.8 3.6 - - - -
1103A VAL* 4.3 21.8 - - + -
1124A MET* 4.8 2.2 - - + -
1150A ILE* 4.6 9.6 - - + -
1151A THR* 1.3 72.2 - - - +
1153A PHE* 1.3 61.1 + - - +
1154A THR* 2.9 16.2 + - + +
1157A PRO* 3.5 1.6 - - - +
1158A GLN* 2.9 33.9 + - + +
1160A ALA* 6.1 1.3 - - + -
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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