Contacts of the strand formed by residues 1116 - 1122 (chain A) in PDB entry 5W0N
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 LEU1116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A ALA* 6.5 0.9 - - + -
1022A ARG* 3.9 35.7 - - + +
1025A ILE* 4.4 9.0 - - + -
1055A LYS 3.8 18.2 - - - +
1056A GLN* 4.1 20.9 - - - +
1057A SER 3.6 18.8 - - - +
1059A LEU* 5.1 5.8 - - + -
1110A PHE* 3.8 3.6 - - - -
1111A HIS* 2.9 30.5 + - + +
1114A SER* 3.2 29.3 + - - +
1115A GLY* 1.3 79.4 - - - +
1117A GLU* 1.3 66.5 + - - +
1118A VAL* 3.9 3.5 + - + -
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Residues in contact with GLU1117 (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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1056A GLN 5.9 0.6 + - - -
1057A SER 5.7 0.2 - - - -
1058A ASP* 3.2 16.1 - - + +
1059A LEU* 2.7 33.8 + - - +
1095A ASN 5.4 0.3 - - - +
1108A LYS* 3.5 27.0 - - - +
1109A PHE* 3.1 37.1 + - - +
1110A PHE* 3.9 15.9 - - + +
1115A GLY 4.1 0.8 + - - -
1116A LEU* 1.3 74.4 - - - +
1118A VAL* 1.3 53.7 + - - +
1119A ASP* 3.7 14.4 - - - +
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Residues in contact with VAL1118 (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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1025A ILE* 4.8 4.5 - - + -
1029A LEU* 4.1 7.6 - - + -
1059A LEU* 3.4 28.0 - - + +
1061A VAL* 3.9 19.3 - - + -
1107A VAL 4.0 0.4 - - - +
1108A LYS* 3.0 6.6 - - - +
1109A PHE* 2.9 71.3 + - + -
1111A HIS* 4.2 11.9 - - + -
1116A LEU* 4.1 11.4 - - + +
1117A GLU* 1.3 76.7 - - - +
1119A ASP* 1.3 66.9 + - - +
1120A ILE* 4.2 3.6 - - + -
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Residues in contact with ASP1119 (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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1045A PHE* 5.0 1.4 - - - -
1058A ASP* 3.8 20.2 - - - +
1059A LEU 2.9 9.4 + - - +
1060A ASP* 3.7 11.1 - - - +
1061A VAL 2.9 27.9 + - - +
1106A ILE* 3.4 30.5 - - + +
1107A VAL 3.8 4.3 - - - -
1108A LYS* 3.6 17.6 + - - +
1117A GLU* 3.7 15.4 - - - +
1118A VAL* 1.3 81.1 - - - +
1120A ILE* 1.3 62.4 + - - +
1121A SER* 4.0 0.7 + - - -
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Residues in contact with ILE1120 (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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1029A LEU* 4.8 6.7 - - + -
1033A ILE* 4.4 18.4 - - + -
1042A LEU* 4.8 2.9 - - + -
1061A VAL* 3.3 26.2 - - + +
1063A MET* 3.9 22.7 - - + +
1080A ILE* 4.4 2.5 - - + +
1083A LEU* 3.8 18.6 - - + -
1087A LEU* 4.2 13.2 - - + -
1106A ILE* 3.2 7.9 - - - -
1107A VAL* 3.0 38.3 + - + +
1109A PHE* 3.7 32.5 - - + -
1118A VAL* 4.3 3.1 - - + -
1119A ASP* 1.3 75.4 - - - +
1121A SER* 1.3 64.4 + - - +
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Residues in contact with SER1121 (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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1045A PHE* 3.8 8.7 - - - -
1061A VAL 2.9 10.5 + - - -
1062A CYS* 3.5 1.9 - - - -
1063A MET* 2.8 32.4 + - - +
1080A ILE* 5.1 0.9 - - - -
1104A VAL* 3.9 15.7 - - - -
1105A PRO 3.9 9.2 - - - -
1106A ILE* 3.9 16.8 - - - -
1119A ASP 4.0 0.6 + - - -
1120A ILE* 1.3 75.0 - - - +
1122A LEU* 1.3 60.9 + - - +
1124A ASN* 3.2 26.3 + - - +
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Residues in contact with LEU1122 (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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1063A MET* 3.6 36.6 - - + +
1065A ILE* 6.5 0.7 - - + -
1074A LEU* 4.6 8.7 - - + -
1076A CYS* 3.3 51.1 - - + +
1079A THR* 3.6 31.4 - - + -
1080A ILE* 3.8 21.5 - - + -
1083A LEU* 5.2 3.8 - - + -
1105A PRO* 4.5 5.4 + - + +
1121A SER* 1.3 74.8 - - - +
1123A TYR* 1.3 74.8 + - + +
1124A ASN* 3.1 4.8 + - - +
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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