Contacts of the strand formed by residues 1154 - 1158 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104I ILE* 3.8 23.6 - - + -
1121I PRO* 3.8 13.2 - - + -
1122I VAL 3.9 4.5 - - - -
1123I PRO* 3.6 28.3 - - + -
1124I PRO* 3.5 11.9 - - + +
1127I VAL* 4.0 28.9 - - + -
1144I LEU* 3.7 31.2 - - + -
1145I VAL 3.3 13.9 - - - -
1146I LEU* 3.7 17.7 - - + -
1147I PHE* 4.4 2.0 - - - -
1152I ARG 4.3 1.3 - - - -
1153I THR* 1.3 76.3 - - - +
1155I GLN* 1.3 66.1 + - - +
32J THR* 3.0 40.4 + - + -
34J GLY* 2.9 33.7 + - - +
35J VAL* 3.5 5.7 - - + +
36J M3L 2.7 28.4 + - - +
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Residues in contact with GLN1155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093I CYS* 3.6 25.9 - - - -
1130I LEU* 5.5 0.6 - - - +
1134I MET* 3.8 15.6 - - - +
1143I TYR 3.6 0.2 - - - +
1144I LEU* 3.5 5.6 - - - +
1145I VAL* 2.8 41.0 + - + +
1147I PHE* 3.7 18.4 - - + -
1154I TRP* 1.3 77.7 - - - +
1156I TRP* 1.3 86.7 + - - +
1157I LEU* 4.2 8.0 - - + +
35J VAL* 3.6 14.6 - - - +
36J M3L 3.2 26.8 + - + -
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Residues in contact with TRP1156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106I PRO* 3.8 33.2 - - + -
1127I VAL* 2.8 37.7 + - + +
1128I LEU* 3.9 16.2 - - + -
1130I LEU* 4.1 19.1 - - + -
1131I GLY* 3.2 30.8 - - - -
1134I MET* 3.5 23.4 - - + +
1135I THR* 5.1 2.2 - - - -
1142I LEU* 3.8 37.0 - - + +
1143I TYR 3.2 5.2 - - - -
1144I LEU* 3.6 39.7 - - + -
1155I GLN* 1.3 85.5 + - - +
1157I LEU* 1.3 69.8 + - - +
1158I PRO* 4.6 1.6 - - - +
35J VAL* 5.6 0.4 - - + -
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Residues in contact with LEU1157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091I ALA* 3.6 32.3 - - + -
1092I LYS 3.6 28.3 - - - +
1093I CYS* 4.4 18.8 - - - -
1142I LEU* 3.7 4.2 - - - +
1143I TYR* 2.7 41.6 + - - +
1145I VAL* 4.3 10.8 - - + -
1155I GLN* 4.4 10.1 - - + +
1156I TRP* 1.3 82.8 - - - +
1158I PRO* 1.4 75.2 - - + +
1161I LYS* 4.4 4.7 - - + +
1162I LEU* 4.0 17.4 - - + +
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Residues in contact with PRO1158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140I GLU* 3.4 36.1 - - - +
1141I HIS 3.7 11.7 - - - +
1142I LEU* 3.4 14.8 - - + -
1143I TYR* 4.4 1.1 - - - -
1156I TRP 4.6 0.9 - - - +
1157I LEU* 1.4 92.9 - - + +
1159I ARG* 1.3 66.7 + - - +
1160I THR* 3.6 16.6 - - - +
1161I LYS* 2.9 29.2 + - + +
1162I LEU* 3.6 8.5 - - - +
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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