Contacts of the strand formed by residues 1059 - 1065 (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 LEU1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1022A ARG* 3.6 41.3 - - + +
1025A ILE* 3.4 40.2 - - + -
1026A ARG 4.5 2.5 - - - +
1029A LEU* 5.1 0.4 - - + -
1044A LEU* 3.7 24.5 - - + -
1048A SER* 3.6 14.4 - - - +
1058A ASP* 1.3 71.2 - - - +
1060A ASP* 1.3 63.3 + - - +
1061A VAL* 4.2 4.5 - - + -
1116A LEU* 5.1 7.2 - - + +
1117A GLU 2.7 14.5 + - - +
1118A VAL* 3.4 22.3 - - + +
1119A ASP 2.9 26.2 + - - -
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Residues in contact with ASP1060 (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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1044A LEU* 3.4 8.7 - - - +
1045A PHE* 3.0 64.9 + - + +
1046A GLY* 3.9 15.1 - - - -
1047A SER* 4.2 5.9 + - - -
1048A SER* 4.8 1.4 + - - -
1058A ASP* 3.0 36.1 + - - +
1059A LEU* 1.3 71.8 - - - +
1061A VAL* 1.3 58.8 + - - +
1119A ASP* 3.7 12.5 - - - +
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Residues in contact with VAL1061 (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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1026A ARG* 5.1 3.8 - - + -
1029A LEU* 5.1 4.3 - - + -
1042A LEU* 3.8 44.4 - - + -
1043A SER 3.5 6.7 - - - +
1044A LEU* 3.9 16.4 - - + -
1045A PHE* 3.5 5.7 - - - -
1059A LEU* 3.8 17.7 - - + +
1060A ASP* 1.3 77.9 - - - +
1062A CYS* 1.3 61.5 + - - +
1118A VAL* 3.9 16.2 - - + -
1119A ASP 2.9 11.2 + - - +
1120A ILE* 3.3 15.0 - - + -
1121A SER* 2.9 28.4 + - - +
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Residues in contact with CYS1062 (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 LYS 3.4 1.7 - - - +
1042A LEU* 3.4 3.1 - - - -
1043A SER* 2.7 45.4 + - - +
1045A PHE* 3.7 15.9 - - + -
1061A VAL* 1.3 75.0 - - - +
1063A MET* 1.3 61.9 + - - +
1064A THR* 4.0 18.7 + - - +
1121A SER* 3.5 3.8 - - - -
1123A TYR* 4.2 0.4 - - - -
1124A ASN* 3.6 31.6 - - + -
1125A THR* 5.5 0.2 - - - -
1128A LEU* 3.9 29.4 - - + -
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Residues in contact with MET1063 (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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1033A ILE* 4.4 7.0 - - + -
1037A PHE* 4.6 13.9 - - + -
1040A THR* 3.3 36.8 - - + +
1041A LYS 3.3 3.8 - - - -
1042A LEU* 3.8 13.9 - - + -
1061A VAL 4.1 0.4 + - - -
1062A CYS* 1.3 73.1 - - - +
1064A THR* 1.3 67.5 + - - +
1065A ILE* 4.7 17.9 - - + -
1079A THR* 5.0 8.3 - - + -
1083A LEU* 3.9 31.4 - - + -
1120A ILE* 3.9 7.4 - - + -
1121A SER 2.8 16.3 + - - +
1122A LEU* 3.6 21.1 - - + +
1123A TYR* 3.0 27.4 + - - -
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Residues in contact with THR1064 (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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1040A THR* 3.5 5.0 - - - -
1041A LYS* 2.8 56.0 + - - +
1043A SER* 5.2 2.6 + - - +
1062A CYS* 4.1 18.1 + - - +
1063A MET* 1.3 82.1 - - - +
1065A ILE* 1.3 67.6 + - - +
1066A ASN* 4.2 0.7 + - - -
1068A LEU 5.4 0.4 - - - -
1123A TYR* 3.8 33.7 - - + -
1125A THR* 6.0 0.2 - - - +
1128A LEU* 5.9 2.2 - - + -
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Residues in contact with ILE1065 (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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1037A PHE* 6.3 2.5 - - + -
1038A PRO 5.0 5.8 - - - +
1039A GLY* 3.6 11.0 - - - +
1040A THR* 5.1 3.4 - - - +
1063A MET* 4.7 16.8 - - + -
1064A THR* 1.3 83.5 - - - +
1066A ASN* 1.3 76.6 + - - +
1068A LEU* 3.0 29.9 + - + +
1074A LEU* 4.0 31.2 - - + -
1079A THR* 5.7 3.1 - - + -
1122A LEU* 6.5 0.4 - - + -
1123A TYR* 3.1 19.0 + - + +
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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