Contacts of the strand formed by residues 1154 - 1158 (chain G) 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 TRP1154 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104G ILE* 3.8 24.5 - - + -
1121G PRO* 3.9 13.9 - - + -
1122G VAL 3.7 7.9 - - - -
1123G PRO* 3.5 27.8 - - + -
1124G PRO* 3.6 9.1 - - + +
1127G VAL* 3.9 28.7 - - + -
1144G LEU* 3.6 31.6 - - + -
1145G VAL 3.4 14.8 - - - -
1146G LEU* 3.7 18.6 - - + -
1147G PHE* 4.5 2.0 - - - -
1152G ARG 4.3 0.2 - - - -
1153G THR* 1.3 75.1 - - - +
1155G GLN* 1.3 67.0 + - - +
32H THR* 3.2 35.4 + - + -
33H GLY 3.3 17.7 + - - -
34H GLY 3.0 17.2 + - - +
35H VAL* 3.5 5.9 - - + +
36H M3L 2.9 23.4 + - - +
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Residues in contact with GLN1155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093G CYS* 3.9 23.1 - - - -
1130G LEU* 5.6 0.8 - - - +
1134G MET* 4.1 14.9 - - - +
1144G LEU* 3.6 4.5 - - - +
1145G VAL* 2.9 40.2 + - + +
1147G PHE* 3.8 14.4 - - + -
1154G TRP* 1.3 79.3 - - - +
1156G TRP* 1.3 94.4 + - - +
1157G LEU* 4.1 8.0 - - + +
35H VAL* 3.6 13.8 - - - +
36H M3L 3.2 30.8 + - + -
38H PRO* 5.8 3.6 - - - +
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Residues in contact with TRP1156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106G PRO* 3.7 33.0 - - + -
1127G VAL* 2.9 34.2 + - + +
1128G LEU* 4.0 15.0 - - + -
1130G LEU* 4.5 8.1 - - + -
1131G GLY* 3.2 34.8 - - - -
1134G MET* 3.8 32.0 - - - +
1135G THR* 5.0 2.5 - - - -
1142G LEU* 3.6 42.5 - - + +
1143G TYR 3.2 4.0 - - - -
1144G LEU* 3.7 35.9 - - + -
1154G TRP 5.9 0.2 - - - -
1155G GLN* 1.3 87.8 + - - +
1157G LEU* 1.3 71.2 + - - +
1158G PRO* 4.6 1.2 - - - +
35H VAL* 5.7 1.3 - - + -
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Residues in contact with LEU1157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091G ALA* 3.7 31.0 - - + -
1092G LYS 3.9 27.6 - - - +
1093G CYS* 4.4 19.1 - - + -
1142G LEU* 3.8 6.0 - - - +
1143G TYR* 2.8 41.0 + - - +
1145G VAL* 4.2 11.2 - - + -
1155G GLN* 4.4 10.5 - - + +
1156G TRP* 1.3 83.3 - - - +
1158G PRO* 1.4 77.1 - - + +
1161G LYS* 4.3 4.3 - - + -
1162G LEU* 3.9 17.9 - - + +
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Residues in contact with PRO1158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140G GLU* 3.4 40.4 - - + +
1141G HIS 3.6 10.1 - - - +
1142G LEU* 3.6 10.5 - - + -
1143G TYR* 4.3 1.1 - - - -
1156G TRP 4.6 0.9 - - - +
1157G LEU* 1.4 95.0 - - + +
1159G ARG* 1.3 67.9 + - - +
1160G THR* 3.6 17.5 - - - +
1161G LYS* 2.9 33.3 + - + +
1162G LEU* 3.7 5.4 - - - +
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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