Contacts of the strand formed by residues 1059 - 1065 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1022B ARG* 3.6 32.8 - - + +
1025B ILE* 3.5 41.1 - - + -
1026B ARG 4.6 1.6 - - - +
1029B LEU* 5.0 0.4 - - + -
1044B LEU* 3.6 30.1 - - + -
1048B SER* 3.6 18.4 - - - +
1058B ASP* 1.3 70.9 - - - +
1060B ASP* 1.3 64.0 + - - +
1061B VAL* 4.1 9.6 - - + -
1116B LEU* 5.1 6.0 - - + +
1117B GLU 2.7 14.8 + - - +
1118B VAL* 3.4 16.6 - - + +
1119B ASP 2.9 25.6 + - - -
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Residues in contact with ASP1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044B LEU* 3.5 6.8 - - - +
1045B PHE* 3.0 61.9 + - + +
1046B GLY* 3.9 16.0 - - - -
1047B SER* 4.1 5.4 + - - -
1048B SER* 4.7 1.5 + - - -
1058B ASP* 3.1 37.6 + - - +
1059B LEU* 1.3 71.7 - - - +
1061B VAL* 1.3 59.2 + - - +
1119B ASP* 3.7 12.2 - - - +
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Residues in contact with VAL1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B ARG* 5.0 4.0 - - + -
1029B LEU* 5.0 4.3 - - + -
1042B LEU* 3.8 43.1 - - + -
1043B SER 3.5 6.7 - - - +
1044B LEU* 3.7 18.8 - - + -
1045B PHE* 3.4 4.6 - - - -
1059B LEU* 3.8 17.3 - - + +
1060B ASP* 1.3 76.3 - - - +
1062B CYS* 1.3 62.1 + - - +
1118B VAL* 3.9 15.9 - - + -
1119B ASP 2.8 10.9 + - - +
1120B ILE* 3.3 14.7 - - + -
1121B SER* 3.0 28.2 + - - -
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Residues in contact with CYS1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B LYS 3.4 1.9 - - - +
1042B LEU* 3.3 3.8 - - - -
1043B SER* 2.8 41.5 + - - +
1045B PHE* 3.5 16.6 - - + -
1061B VAL* 1.3 74.7 - - - +
1063B MET* 1.3 63.2 + - - +
1064B THR* 4.2 11.6 - - - +
1121B SER* 3.6 3.8 - - - -
1123B TYR* 4.0 6.3 - - - -
1124B ASN* 3.5 31.2 - - + -
1125B THR 5.0 0.2 - - - -
1128B LEU* 4.0 28.7 - - + -
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Residues in contact with MET1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B ILE* 4.1 4.9 - - + -
1037B PHE* 4.0 24.5 - - + -
1040B THR* 3.2 30.5 - - + +
1041B LYS 3.3 4.5 - - - -
1042B LEU* 3.6 17.3 - - + -
1061B VAL 4.1 0.6 + - - -
1062B CYS* 1.3 73.2 - - - +
1064B THR* 1.3 69.3 + - - +
1065B ILE* 4.2 15.9 - - + -
1079B THR* 5.0 4.5 - - + -
1083B LEU* 4.0 30.3 - - + -
1120B ILE* 3.9 8.5 - - + -
1121B SER 2.8 16.6 + - - +
1122B LEU* 3.6 21.9 - - + +
1123B TYR* 3.1 24.6 + - - -
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Residues in contact with THR1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B THR* 3.3 5.0 - - - -
1041B LYS* 2.7 58.6 + - - +
1043B SER* 5.6 0.5 + - - -
1062B CYS* 4.2 15.5 - - - +
1063B MET* 1.3 81.6 - - - +
1065B ILE* 1.3 65.5 + - - +
1066B ASN* 5.2 0.7 + - - -
1068B LEU 5.2 0.4 - - - -
1123B TYR* 3.7 36.6 - - + -
1125B THR* 6.1 0.2 - - - +
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Residues in contact with ILE1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B PHE* 4.5 16.6 - - + -
1038B PRO 4.2 17.0 - - - +
1039B GLY 3.6 3.1 - - - +
1040B THR* 4.5 4.3 - - - +
1063B MET* 4.2 22.4 - - + -
1064B THR* 1.3 80.3 - - - +
1066B ASN* 1.3 78.3 + - - +
1068B LEU* 3.0 41.9 + - + +
1074B LEU* 5.4 9.4 - - + -
1079B THR* 5.1 10.1 - - + -
1122B LEU* 5.7 1.6 - - + -
1123B TYR* 3.0 18.9 + - + +
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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