Contacts of the strand formed by residues 1099 - 1104 (chain M) 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 TYR1099 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090M TRP* 4.0 2.7 - - - -
1091M ALA* 2.9 37.9 + - - +
1097M PRO* 3.8 9.9 - - + +
1098M SER* 1.3 75.5 - - - +
1100M PRO* 1.3 88.0 - - + +
1101M ALA 3.4 0.5 + - - -
1147M PHE* 3.7 17.7 - + + -
1149M ASP* 3.2 44.5 - - + +
1150M ASN 4.7 0.2 + - - -
1184M ILE 5.4 0.2 - - - -
1187M SER* 2.9 36.1 + - - -
1188M VAL* 3.8 24.9 - - + -
1191M ALA* 3.5 21.2 - - + +
1194M ARG* 4.9 1.4 + - - -
36N M3L 3.7 29.4 - - - -
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Residues in contact with PRO1100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089M VAL 3.4 7.4 - - - +
1090M TRP* 3.6 22.7 - - + -
1099M TYR* 1.3 103.9 - - + +
1101M ALA* 1.3 60.6 + - - +
1147M PHE* 3.6 0.7 - - - -
1148M PHE* 3.0 28.2 + - + -
1165M LEU* 3.7 16.2 - - + -
1188M VAL* 3.9 7.9 - - + +
1191M ALA* 3.7 23.1 - - + +
1192M TYR* 3.6 26.7 - - - +
1195M ALA* 4.2 1.1 - - + -
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Residues in contact with ALA1101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 3.4 6.1 - - - +
1089M VAL* 2.9 33.1 + - + +
1091M ALA* 4.1 8.3 - - + -
1099M TYR 4.1 3.6 - - - +
1100M PRO* 1.3 76.8 - - - +
1102M LEU* 1.3 61.8 + - - +
1145M VAL* 3.9 17.7 - - + -
1146M LEU 3.3 16.2 - - - +
1147M PHE* 3.8 17.5 - - + -
1148M PHE* 3.6 12.3 - - - -
1165M LEU* 4.8 0.6 - - - +
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Residues in contact with LEU1102 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086M LEU* 3.3 40.4 - - + +
1087M ASP 3.5 3.8 - - - +
1088M LEU* 4.0 12.1 - - + -
1101M ALA* 1.3 74.3 - - - +
1103M ILE* 1.3 69.9 + - - +
1104M ILE* 3.6 23.2 + - + +
1120M ILE* 4.7 6.1 - - + -
1121M PRO* 5.4 2.5 - - + -
1145M VAL* 3.4 3.9 - - - -
1146M LEU* 2.8 39.1 + - + +
1148M PHE* 4.1 11.9 - - + -
1152M ARG* 4.9 9.4 - - - +
1198M HIS* 3.9 33.4 - - + +
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Residues in contact with ILE1103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083M LEU* 3.5 34.8 - - + -
1084M ASP 3.7 22.7 - - - +
1085M ALA* 3.9 8.3 - - + +
1086M LEU* 2.6 32.8 + - - +
1087M ASP* 2.9 19.6 + - + +
1089M VAL* 3.9 26.9 - - + -
1102M LEU* 1.3 74.3 - - - +
1104M ILE* 1.3 66.0 + - - +
1143M TYR* 4.0 24.9 - - + -
1144M LEU 3.4 10.8 - - - +
1145M VAL* 4.5 7.4 - - + +
1162M LEU* 4.4 3.1 - - + -
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Residues in contact with ILE1104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085M ALA* 4.4 2.7 - - - -
1086M LEU* 4.3 2.0 - - + -
1102M LEU* 3.6 34.1 - - + +
1103M ILE* 1.3 81.5 - - - +
1105M ASP* 1.3 65.8 + - - +
1106M PRO* 3.2 13.9 - - - +
1108M MET* 3.7 25.6 - - - -
1120M ILE* 3.6 26.7 - - + -
1121M PRO 4.2 2.5 - - - +
1123M PRO* 4.1 6.7 - - + -
1144M LEU* 2.8 24.4 + - + +
1146M LEU* 3.8 15.5 - - + +
1154M TRP* 3.6 35.2 - - + -
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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