Contacts of the strand formed by residues 1142 - 1147 (chain A) in PDB entry 2X4Y
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 LEU1142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106A PRO* 5.7 1.4 - - - +
1131A GLY 4.5 0.7 - - - +
1134A MET* 3.6 43.7 - - + +
1135A THR* 3.7 18.9 + - - +
1138A ALA* 5.0 4.7 - - + -
1140A GLU* 3.4 19.4 + - + +
1141A HIS* 1.3 97.3 + - - +
1143A TYR* 1.3 62.8 - - - +
1144A LEU 3.9 0.2 + - - -
1156A TRP* 3.6 34.4 - - + +
1157A LEU* 3.6 9.2 - - - +
1158A PRO* 3.5 32.3 - - + -
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Residues in contact with TYR1143 (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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1082A PRO* 3.4 14.4 - - - +
1083A LEU* 2.9 48.2 + - + -
1103A ILE* 4.1 20.4 - - + -
1141A HIS* 3.7 30.1 + + - -
1142A LEU* 1.3 72.6 - - - +
1144A LEU* 1.3 61.6 + - - +
1145A VAL* 3.7 8.3 + - + +
1155A GLN 3.6 0.5 - - - +
1156A TRP* 3.2 7.2 - - - -
1157A LEU 2.7 40.3 + - - +
1159A ARG* 4.0 32.1 - - + +
1162A LEU* 3.6 26.0 - - + -
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Residues in contact with LEU1144 (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 ILE* 3.6 6.1 - - - +
1104A ILE* 2.9 44.8 + - + +
1106A PRO* 4.3 11.8 - - + +
1123A PRO* 3.6 38.4 - - + -
1127A VAL* 3.8 10.5 - - + -
1128A LEU* 4.4 0.4 - - + -
1143A TYR* 1.3 73.5 - - - +
1145A VAL* 1.3 61.6 + - - +
1154A TRP* 3.7 28.9 - - + -
1155A GLN 3.5 17.0 - - - +
1156A TRP* 3.6 46.7 - - + +
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Residues in contact with VAL1145 (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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1089A VAL* 4.4 4.7 - - + -
1091A ALA* 4.2 9.4 - - + -
1101A ALA* 4.0 10.1 - - + -
1102A LEU 3.4 6.5 - - - +
1103A ILE* 4.3 17.7 - - + -
1143A TYR* 4.3 7.4 - - + +
1144A LEU* 1.3 79.3 - - - +
1146A LEU* 1.3 59.9 + - - +
1147A PHE* 4.1 17.7 - - + -
1153A THR 4.0 0.2 - - - +
1154A TRP* 3.3 11.9 - - - -
1155A GLN* 2.8 55.6 + - + +
1157A LEU* 4.2 5.2 - - + -
1162A LEU* 4.1 28.0 - - + -
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Residues in contact with LEU1146 (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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1101A ALA* 3.9 2.0 - - - -
1102A LEU* 2.9 34.4 + - + +
1104A ILE* 3.9 20.6 - - + -
1121A PRO* 3.5 33.0 - - + -
1145A VAL* 1.3 72.9 - - - +
1147A PHE* 1.3 67.2 + - - +
1148A PHE* 4.6 1.2 - - - -
1152A ARG* 3.3 56.2 + - + +
1153A THR 3.5 8.7 - - - +
1154A TRP* 3.8 25.6 - - + -
32B THR* 3.8 5.6 - - + -
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Residues in contact with PHE1147 (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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1091A ALA* 3.7 26.9 - - + -
1093A CYS* 3.4 23.6 - - - -
1099A TYR* 3.7 31.4 - + + -
1100A PRO 3.6 8.5 - - - +
1101A ALA* 3.8 5.8 - - + -
1145A VAL* 4.1 12.3 - - + -
1146A LEU* 1.3 74.1 - - - +
1148A PHE* 1.3 58.7 + - - +
1149A ASP* 3.1 27.9 + - - +
1152A ARG* 3.0 25.1 + - - -
1153A THR* 2.8 37.5 + - - +
1154A TRP 4.6 0.7 - - - -
1155A GLN* 3.7 24.2 - - + -
1157A LEU* 4.7 0.4 - - + -
36B M3L 3.7 23.3 - - + -
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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