Contacts of the strand formed by residues 1143 - 1147 (chain O) 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 TYR1143 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082O PRO* 4.2 6.6 - - - +
1083O LEU* 3.7 41.3 + - + -
1103O ILE* 4.3 23.6 - - + -
1141O HIS* 3.8 30.9 + + - -
1142O LEU* 1.3 77.3 - - - +
1144O LEU* 1.3 61.0 + - - +
1145O VAL* 3.8 7.4 + - + +
1155O GLN 3.6 0.3 - - - +
1156O TRP* 3.2 6.3 - - - -
1157O LEU 2.6 43.1 + - - +
1159O ARG* 3.9 36.9 - - + +
1162O LEU* 3.8 21.8 - - + -
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Residues in contact with LEU1144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103O ILE* 3.4 6.3 - - - +
1104O ILE* 2.8 47.2 + - + +
1106O PRO* 4.0 8.5 - - + +
1123O PRO* 3.8 34.1 - - + -
1127O VAL* 3.9 10.8 - - + -
1128O LEU* 4.3 0.7 - - + -
1142O LEU 4.1 0.2 + - - -
1143O TYR* 1.3 72.4 - - - +
1145O VAL* 1.3 57.1 + - - +
1154O TRP* 3.6 29.8 - - + -
1155O GLN 3.1 20.4 - - - +
1156O TRP* 3.6 47.4 - - + +
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Residues in contact with VAL1145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089O VAL* 4.5 3.1 - - + -
1091O ALA* 4.2 17.7 - - + -
1101O ALA* 3.9 12.3 - - + -
1102O LEU 3.2 9.2 - - - +
1103O ILE* 4.4 14.6 - - + -
1143O TYR* 4.2 13.0 - - + +
1144O LEU* 1.3 79.7 - - - +
1146O LEU* 1.3 61.1 + - - +
1147O PHE* 4.3 7.4 - - + -
1153O THR 3.9 0.2 - - - +
1154O TRP* 3.3 10.4 - - - -
1155O GLN* 2.9 54.5 + - + +
1157O LEU* 4.3 5.4 - - + -
1162O LEU* 4.2 22.9 - - + -
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Residues in contact with LEU1146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101O ALA* 3.3 2.1 - - - -
1102O LEU* 2.7 40.2 + - + +
1104O ILE* 4.0 16.6 - - + -
1121O PRO* 3.6 37.0 - - + -
1145O VAL* 1.3 75.0 - - - +
1147O PHE* 1.3 66.5 + - - +
1148O PHE* 3.8 1.6 + - - -
1152O ARG* 3.5 51.2 + - + +
1153O THR 3.5 9.0 - - - +
1154O TRP* 3.7 26.9 - - + -
32P THR* 3.9 4.7 - - + -
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Residues in contact with PHE1147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091O ALA* 3.7 30.7 - - + -
1093O CYS* 4.1 16.6 - - - -
1099O TYR* 3.4 34.8 - + + -
1100O PRO 3.6 7.6 - - - +
1101O ALA* 3.9 3.8 - - + -
1145O VAL* 4.3 8.1 - - + -
1146O LEU* 1.3 74.1 - - - +
1148O PHE* 1.3 58.3 + - - +
1149O ASP* 3.0 30.6 + - - +
1152O ARG* 3.1 21.7 + - - -
1153O THR* 2.9 35.8 + - - +
1154O TRP 4.7 0.2 - - - -
1155O GLN* 3.9 24.5 - - + -
1157O LEU* 4.8 0.2 - - + -
36P M3L 3.6 28.7 - - + -
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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