Contacts of the strand formed by residues 1142 - 1147 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106E PRO* 5.8 0.7 - - - +
1131E GLY 4.6 0.4 - - - +
1134E MET* 3.6 40.6 - - + +
1135E THR* 3.5 22.5 + - - +
1138E ALA* 4.7 6.5 - - + -
1140E GLU* 3.4 17.9 + - + +
1141E HIS* 1.3 92.3 + - - +
1143E TYR* 1.3 63.4 + - - +
1156E TRP* 3.6 35.5 - - + +
1157E LEU* 3.5 10.3 - - - +
1158E PRO* 3.5 32.3 - - + -
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Residues in contact with TYR1143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139C ARG* 3.1 35.8 + - + +
1082E PRO* 3.7 4.5 - - - +
1083E LEU* 3.4 42.1 + - + -
1084E ASP 5.9 0.2 - - - -
1103E ILE* 4.1 22.7 - - + -
1141E HIS* 3.8 15.7 - + - -
1142E LEU* 1.3 73.4 - - - +
1144E LEU* 1.3 64.4 + - - +
1145E VAL* 3.7 6.0 + - + +
1155E GLN 3.7 0.2 - - - +
1156E TRP* 3.2 7.3 - - - -
1157E LEU 2.8 39.4 + - - +
1159E ARG* 4.0 34.2 - - + +
1162E LEU* 3.6 27.1 - - + -
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Residues in contact with LEU1144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103E ILE* 3.4 7.5 - - - +
1104E ILE* 2.9 41.9 + - + +
1106E PRO* 4.2 13.4 - - + +
1123E PRO* 3.7 35.9 - - + -
1127E VAL* 3.6 16.8 - - + -
1128E LEU* 4.5 0.4 - - + -
1143E TYR* 1.3 72.4 - - - +
1145E VAL* 1.3 61.5 + - - +
1154E TRP* 3.8 20.4 - - + -
1155E GLN 3.7 12.3 - - - +
1156E TRP* 3.5 48.2 - - + +
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Residues in contact with VAL1145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089E VAL* 4.4 11.2 - - + -
1091E ALA* 4.2 0.7 - - + -
1101E ALA* 3.8 15.7 - - + -
1102E LEU 3.3 5.2 - - - +
1103E ILE* 4.6 4.9 - - + -
1104E ILE* 4.8 0.4 - - - -
1143E TYR* 4.3 13.9 - - + +
1144E LEU* 1.3 79.7 - - - +
1146E LEU* 1.3 61.9 + - - +
1147E PHE* 4.0 27.6 - - + -
1153E THR 3.9 0.2 - - - +
1154E TRP* 3.3 10.8 - - - -
1155E GLN 2.8 44.2 + - - +
1157E LEU* 4.2 12.8 - - + -
1162E LEU* 3.9 25.8 - - + -
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Residues in contact with LEU1146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101E ALA* 3.2 2.1 - - - -
1102E LEU* 2.9 36.5 + - + +
1104E ILE* 3.8 21.8 - - + -
1121E PRO* 3.7 31.4 - - + -
1145E VAL* 1.3 74.8 - - - +
1147E PHE* 1.3 65.6 + - - +
1148E PHE* 4.6 1.0 - - - -
1152E ARG* 3.3 56.1 + - + +
1153E THR 3.5 7.9 - - - +
1154E TRP* 3.7 26.2 - - + -
32F THR* 3.8 5.6 - - + -
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Residues in contact with PHE1147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091E ALA* 3.7 26.0 - - + -
1093E CYS* 3.6 25.1 - - - -
1099E TYR* 3.7 32.8 - + + -
1100E PRO 3.6 8.3 - - - +
1101E ALA* 3.8 4.3 - - + -
1145E VAL* 4.0 13.7 - - + -
1146E LEU* 1.3 73.0 - - - +
1148E PHE* 1.3 58.8 + - - +
1149E ASP* 3.0 30.6 + - - +
1152E ARG* 3.1 23.4 + - - -
1153E THR* 2.9 36.1 + - - +
1155E GLN* 3.7 22.0 - - + -
36F M3L 3.6 26.7 - - + -
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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