Contacts of the strand formed by residues 1116 - 1122 (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 LEU1116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021B ALA* 6.5 0.9 - - + -
1022B ARG* 3.7 42.4 - - + +
1025B ILE* 4.2 9.6 - - + -
1055B LYS 3.7 12.3 - - - +
1056B GLN* 4.0 20.6 - - - +
1057B SER 3.7 18.8 - - - +
1059B LEU* 5.1 5.2 - - + -
1110B PHE* 3.8 3.4 - - - -
1111B HIS* 2.9 31.6 + - + +
1114B SER* 3.1 30.4 + - - +
1115B GLY* 1.3 79.2 - - - +
1117B GLU* 1.3 66.4 + - - +
1118B VAL* 3.8 3.3 + - + -
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Residues in contact with GLU1117 (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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1113A ARG* 2.6 43.4 + - - +
1056B GLN 5.9 0.4 + - - -
1058B ASP* 3.3 15.0 - - + +
1059B LEU* 2.7 32.9 + - - +
1095B ASN 5.4 0.3 - - - +
1108B LYS* 3.6 24.7 - - + +
1109B PHE* 3.2 34.7 + - - +
1110B PHE* 3.9 0.5 - - - -
1115B GLY 4.1 1.4 + - - -
1116B LEU* 1.3 73.7 - - - +
1118B VAL* 1.3 54.1 + - - +
1119B ASP* 3.8 14.1 - - - +
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Residues in contact with VAL1118 (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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1025B ILE* 4.8 4.7 - - + -
1029B LEU* 4.1 7.6 - - + -
1059B LEU* 3.4 26.9 - - + +
1061B VAL* 3.9 19.3 - - + -
1107B VAL 3.9 1.1 - - - +
1108B LYS* 3.0 6.1 - - - +
1109B PHE* 2.9 69.0 + - + +
1111B HIS* 4.2 12.3 - - + -
1116B LEU* 4.0 11.7 - - + +
1117B GLU* 1.3 78.9 - - - +
1119B ASP* 1.3 68.1 + - - +
1120B ILE* 4.2 4.7 - - + -
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Residues in contact with ASP1119 (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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1045B PHE* 5.1 1.6 - - - -
1058B ASP* 3.9 18.8 - - - +
1059B LEU 2.9 6.9 + - - -
1060B ASP* 3.7 12.8 - - - +
1061B VAL 2.8 28.9 + - - +
1106B ILE* 3.3 33.8 - - + +
1107B VAL 3.8 3.6 - - - -
1108B LYS* 3.5 16.5 + - - -
1117B GLU* 3.8 16.5 - - - +
1118B VAL* 1.3 82.0 - - - +
1120B ILE* 1.3 62.7 + - - +
1121B SER* 5.1 0.3 + - - -
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Residues in contact with ILE1120 (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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1029B LEU* 4.8 8.1 - - + -
1033B ILE* 4.1 24.9 - - + -
1042B LEU* 4.9 2.0 - - + -
1061B VAL* 3.3 24.2 - - + +
1063B MET* 3.9 16.2 - - + +
1080B ILE* 4.4 1.8 - - - +
1083B LEU* 3.8 18.6 - - + -
1087B LEU* 4.3 8.3 - - + -
1106B ILE* 3.1 6.8 - - - -
1107B VAL* 3.0 40.5 + - + +
1109B PHE* 3.7 32.1 - - + -
1118B VAL* 4.3 3.4 - - + -
1119B ASP* 1.3 75.9 - - - +
1121B SER* 1.3 71.3 + - - +
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Residues in contact with SER1121 (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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1045B PHE* 3.9 8.0 - - - -
1061B VAL 3.0 11.5 + - - -
1062B CYS* 3.6 1.3 - - - -
1063B MET* 2.8 34.1 + - - +
1080B ILE* 4.9 1.6 - - - -
1104B VAL* 4.0 19.5 - - - -
1105B PRO 3.8 17.0 - - - -
1106B ILE* 4.0 6.7 - - - -
1119B ASP 4.1 0.4 + - - -
1120B ILE* 1.3 73.4 - - - +
1122B LEU* 1.3 59.9 + - - +
1124B ASN* 3.5 24.8 + - - +
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Residues in contact with LEU1122 (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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1063B MET* 3.6 36.6 - - + +
1064B THR* 5.5 0.2 - - - -
1065B ILE* 5.7 2.0 - - + -
1074B LEU* 4.6 4.9 - - + -
1076B CYS* 3.6 41.5 - - + +
1079B THR* 3.6 35.0 - - + -
1080B ILE* 3.8 20.8 - - + +
1083B LEU* 5.5 2.0 - - + -
1104B VAL* 6.0 1.2 - - - +
1105B PRO* 4.5 5.0 + - + -
1121B SER* 1.3 74.2 - - - +
1123B TYR* 1.3 83.5 + - + +
1124B ASN* 3.1 5.1 + - - +
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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