Contacts of the strand formed by residues 1082 - 1090 (chain A) in PDB entry 4YOC
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 ARG1082 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040A ASN* 3.2 23.4 + - - +
1061A THR* 3.6 8.6 + - - +
1070A GLU* 4.5 8.7 + - - -
1075A TYR* 2.9 70.6 + - + +
1076A SER* 4.8 5.7 - - - +
1078A GLY* 3.4 23.0 + - - -
1079A GLY* 3.4 31.6 + - - +
1080A PRO* 3.8 3.6 + - - +
1081A ASN* 1.3 80.1 - - - +
1083A PHE* 1.3 64.8 + - - +
1362A PHE* 5.0 5.8 - - - -
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Residues in contact with PHE1083 (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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940A TYR* 3.4 29.8 - + - -
993A ILE* 3.6 32.8 - - + -
1023A ARG* 4.2 3.8 - - - -
1039A ILE 4.1 3.8 - - - -
1040A ASN* 3.3 31.0 - - + +
1042A LEU* 3.6 20.0 - - + -
1060A CYS* 4.4 7.0 - - + -
1061A THR 2.8 15.2 + - - +
1062A VAL* 4.0 6.7 - - + -
1063A GLU 3.0 14.7 + - - -
1075A TYR* 2.8 17.8 + - - -
1081A ASN 4.3 5.6 - - - -
1082A ARG* 1.3 77.2 - - - +
1084A TYR* 1.3 62.0 + - - +
1361A PRO* 3.9 15.0 - - + -
1362A PHE* 3.5 34.8 - + - -
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Residues in contact with TYR1084 (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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1038A ASP* 2.8 25.2 + - - +
1040A ASN* 3.2 40.2 + - - +
1041A LEU* 3.6 32.5 - - + +
1042A LEU* 2.9 26.2 + - - +
1062A VAL* 4.9 0.4 - - - -
1063A GLU 3.1 13.2 - - - +
1065A GLY* 4.4 9.0 - - - +
1068A LEU* 4.8 0.9 - - + -
1072A VAL* 3.5 37.7 - - + +
1075A TYR* 4.1 13.2 - + + -
1076A SER* 4.4 1.1 - - - -
1083A PHE* 1.3 78.2 - - - +
1085A PHE* 1.3 67.8 + - - +
1086A LEU* 4.0 22.8 - - + +
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Residues in contact with PHE1085 (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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995A ARG* 3.7 15.3 - - - -
1021A PHE* 3.7 21.3 - + - -
1041A LEU* 4.7 0.4 - - - -
1042A LEU* 3.2 27.1 - - + +
1043A TYR* 4.2 2.0 - - - -
1044A TRP* 4.0 20.0 - + + +
1062A VAL* 3.8 8.7 - - + -
1063A GLU 2.9 24.2 + - - -
1064A TYR* 3.1 35.7 - + + -
1065A GLY 2.9 22.3 + - - -
1084A TYR* 1.3 74.7 - - - +
1086A LEU* 1.3 62.5 + - - +
1087A GLU 3.8 19.3 - - - +
1099A PRO* 4.1 14.8 - - + -
1103A ALA* 3.6 25.4 - - + -
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Residues in contact with LEU1086 (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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1041A LEU* 4.8 8.3 - - + +
1042A LEU 4.3 2.4 + - - -
1043A TYR* 6.1 0.2 - - - -
1064A TYR* 3.3 23.3 + - - -
1065A GLY* 3.7 31.2 - - - +
1066A GLU* 3.6 25.4 - - + +
1072A VAL* 5.1 4.5 - - + -
1084A TYR* 4.0 22.2 - - + +
1085A PHE* 1.3 74.1 - - - +
1087A GLU* 1.3 72.9 + - + +
1098A ASP* 4.9 2.6 - - - +
1099A PRO* 3.4 8.0 - - - +
862C ARG* 4.1 16.6 - - - +
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Residues in contact with GLU1087 (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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1043A TYR* 3.7 36.5 + - + -
1044A TRP* 3.0 22.7 + - - +
1085A PHE* 3.8 4.9 - - - +
1086A LEU* 1.3 92.0 - - + +
1088A ALA* 1.3 64.9 + - - +
1096A PHE* 3.6 24.4 - - + +
1097A GLU* 3.5 13.7 - - - +
1098A ASP* 5.3 4.5 - - - +
1099A PRO* 3.9 7.6 - - - -
816C ARG* 6.0 3.5 - - - +
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Residues in contact with ALA1088 (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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1043A TYR* 4.7 0.7 - - - -
1044A TRP* 3.2 33.4 - - + +
1045A SER* 5.3 0.2 - - - -
1087A GLU* 1.3 76.2 - - - +
1089A TYR* 1.3 63.0 + - - +
1090A ASN 4.1 0.2 + - - -
1096A PHE* 3.3 8.1 - - - +
1097A GLU* 2.8 44.7 + - + +
1098A ASP 4.3 2.7 - - - +
1099A PRO* 4.0 13.2 - - + -
1100A PRO* 4.3 2.9 - - + -
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Residues in contact with TYR1089 (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 ILE* 3.4 23.4 - - + +
1022A TYR* 3.7 36.0 - + + -
1027A THR* 3.7 11.9 - - + -
1028A HIS* 2.4 49.9 + + - -
1043A TYR* 4.1 18.5 - - + +
1044A TRP 2.8 15.8 + - - +
1045A SER* 4.2 12.8 - - - -
1046A ASP 5.1 0.7 + - - -
1047A GLU* 5.5 0.5 - - - +
1088A ALA* 1.3 75.8 - - - +
1090A ASN* 1.3 66.5 + - - +
1091A ALA* 3.8 16.7 + - - -
1094A LYS* 3.8 3.6 - - - -
1095A SER 3.2 22.9 - - - -
1096A PHE* 3.4 24.5 - + + -
1097A GLU* 5.6 0.9 - - - -
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Residues in contact with ASN1090 (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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1088A ALA 4.1 0.4 + - - -
1089A TYR* 1.3 75.0 + - - +
1091A ALA* 1.3 56.0 + - - +
1092A LYS* 3.3 14.3 + - - +
1093A SER* 3.1 38.3 + - - +
1094A LYS* 2.7 31.4 + - - -
1095A SER* 2.9 22.6 + - - +
1097A GLU* 4.0 21.8 + - - +
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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