Contacts of the strand formed by residues 950 - 957 (chain A) in PDB entry 1D0H
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 PHE 950 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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944A ASN 5.2 2.5 - - - +
945A ASP* 3.9 26.2 - - + -
948A ASN 3.7 14.6 - - - +
949A ASN* 1.3 74.5 - - - +
951A THR* 1.3 57.9 + - - +
952A VAL* 4.0 17.5 - - + -
991A TRP* 3.6 37.2 - + - -
1002A TRP* 3.9 8.5 - + - -
1004A LEU* 3.8 20.0 - - + -
1038A ASN* 2.7 70.4 + - + +
1040A ARG* 5.3 5.4 - - - -
1064A ILE* 5.3 3.8 - - + -
1091A ILE* 4.6 10.5 - - + -
1092A PHE 3.3 13.5 - - - +
1093A CYS* 4.8 1.8 - - - -
1094A LYS 3.3 7.7 - - - +
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Residues in contact with THR 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A PHE* 1.3 74.2 - - - +
952A VAL* 1.3 69.7 - - - +
1035A THR* 3.6 27.4 - - + -
1036A ILE 3.2 12.6 - - - +
1037A THR* 3.5 7.1 - - + +
1091A ILE* 3.3 6.6 - - - +
1092A PHE* 2.8 40.5 + - + -
1094A LYS 2.7 20.0 + - - -
1095A ALA* 3.5 2.4 - - - -
1096A LEU* 3.0 36.7 + - + -
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Residues in contact with VAL 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A PHE* 4.0 24.5 - - + -
951A THR* 1.3 80.3 - - - +
953A SER* 1.3 62.5 + - - +
954A PHE* 4.0 15.8 - - + -
991A TRP* 4.2 14.1 - - + -
993A VAL* 5.3 0.4 - - + -
1002A TRP* 4.2 21.1 - - + -
1034A ILE 4.1 0.3 - - - +
1035A THR* 3.6 1.7 - - - -
1036A ILE* 2.9 35.1 + - + +
1089A PHE* 3.5 29.4 - - + -
1090A ARG 3.4 3.4 - - - -
1091A ILE* 3.9 17.5 - - + -
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Residues in contact with SER 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A THR 4.4 0.2 + - - -
952A VAL* 1.3 74.9 - - - +
954A PHE* 1.3 67.6 + - - +
1033A PHE* 3.8 17.3 - - - -
1034A ILE 3.2 12.8 - - - -
1035A THR* 4.1 6.7 - - - -
1088A LYS 3.5 2.3 + - - +
1089A PHE* 3.5 0.9 - - - -
1090A ARG* 2.8 45.0 + - - +
1092A PHE* 3.4 21.7 - - - -
1104A LEU* 3.7 14.4 - - - +
1108A TYR* 4.9 0.9 + - - -
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Residues in contact with PHE 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952A VAL* 4.0 17.7 - - + -
953A SER* 1.3 81.5 - - - +
955A TRP* 1.3 71.0 + - - +
956A LEU* 3.8 21.1 - - + -
976A ILE* 5.1 0.4 - - + -
977A ILE* 4.0 26.5 - - + -
993A VAL* 4.0 34.5 - - + -
1000A LEU* 5.6 0.4 - - + -
1033A PHE* 3.8 9.9 - - - -
1034A ILE* 2.8 69.6 + - + -
1036A ILE* 4.6 2.7 - - + -
1086A ILE* 4.2 7.9 - - + -
1087A ASP 3.5 12.1 - - - +
1088A LYS 4.2 3.4 - - - -
1089A PHE* 4.0 13.7 - + + -
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Residues in contact with TRP 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ILE* 3.8 31.6 - - + +
954A PHE* 1.3 78.5 - - - +
956A LEU* 1.3 58.9 + - - +
1031A TRP* 3.9 21.8 - - + -
1032A VAL* 3.3 26.7 - - - -
1033A PHE* 3.4 30.8 - + + -
1049A ASN* 4.7 0.7 - - - -
1086A ILE* 3.5 4.3 - - - -
1087A ASP* 2.7 36.7 + - + +
1088A LYS* 3.6 25.1 - - + -
1105A TYR* 3.8 29.8 - + - -
1108A TYR* 3.2 42.0 - - + +
1109A LEU* 3.8 12.3 - - + -
1251A TYR* 3.5 21.3 - - - -
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Residues in contact with LEU 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954A PHE* 3.8 17.3 - - + -
955A TRP* 1.3 75.4 - - - +
957A ARG* 1.3 66.5 + - - +
958A VAL* 3.8 27.4 - - + -
976A ILE* 3.9 23.1 - - + -
1000A LEU* 4.2 22.2 - - + -
1027A LEU* 4.2 12.3 - - + -
1031A TRP* 3.5 5.2 - - - -
1032A VAL* 2.7 39.4 + - + +
1034A ILE* 3.9 23.8 - - + -
1084A VAL* 4.6 2.7 - - + -
1085A SER 3.6 10.1 - - - +
1086A ILE* 4.5 5.6 - - + -
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Residues in contact with ARG 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A VAL* 6.4 0.2 - - - +
956A LEU* 1.3 75.4 - - - +
958A VAL* 1.3 63.2 + - - +
959A PRO* 4.3 1.4 - - - +
1029A ASN* 2.9 49.1 + - - +
1030A LYS 3.9 12.6 - - - -
1031A TRP* 3.7 37.5 - - + +
1032A VAL* 5.6 0.2 - - - -
1083A TYR* 5.8 2.9 - - - -
1084A VAL* 3.6 5.0 - - - -
1085A SER* 3.0 40.9 + - - -
1118A TRP* 3.3 28.7 + - - +
1120A ASN* 3.3 22.2 - - - +
1309A ASP* 3.4 19.7 + - - -
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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