Contacts of the strand formed by residues 1059 - 1066 (chain A) in PDB entry 2W18
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 VAL1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A LEU* 6.2 0.2 - - + -
1015A THR* 3.8 21.8 - - + -
1057A ALA 4.2 0.6 - - - -
1058A SER* 1.3 77.1 - - - +
1060A CYS* 1.3 62.7 + - - +
1061A HIS* 3.6 26.0 + - + +
1074A LEU* 3.4 7.9 - - - +
1075A SER* 3.1 56.6 + - - +
1118A PHE* 5.4 2.7 - - + -
2188A GOL 5.7 3.6 - - - +
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Residues in contact with CYS1060 (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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1015A THR* 3.1 15.1 + - - +
1016A PHE 4.1 5.4 - - - +
1017A ALA* 3.6 17.1 - - + +
1027A LEU* 4.0 12.6 - - + -
1029A THR* 3.8 18.6 - - + -
1058A SER 3.9 0.6 + - - -
1059A VAL* 1.3 73.1 - - - +
1061A HIS* 1.3 60.9 + - - +
1062A LYS 3.2 31.9 - - - -
1063A ALA* 4.1 4.0 - - - -
1072A ILE* 4.2 9.9 - - + -
1073A VAL 3.3 6.5 - - - -
1074A LEU* 3.7 9.6 - - + -
2188A GOL 3.8 18.0 - - - -
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Residues in contact with HIS1061 (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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1017A ALA* 5.3 1.1 - - - -
1059A VAL* 3.6 18.6 - - + +
1060A CYS* 1.3 72.1 - - - +
1062A LYS* 1.3 66.5 + - - +
1073A VAL* 2.7 12.8 + - + +
1075A SER* 2.5 49.4 + - - -
1090A PHE* 3.7 14.6 - + - -
1118A PHE* 3.7 16.7 - + - -
1121A GLY 3.7 24.5 + - - -
1122A ASP* 4.5 1.2 + - - -
1123A VAL* 3.2 32.6 + - + +
2188A GOL 4.7 14.9 + - - -
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Residues in contact with LYS1062 (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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1017A ALA* 4.6 4.5 - - - +
1018A GLU 4.6 6.8 + - - +
1020A GLN* 3.1 30.8 + - - +
1060A CYS* 3.2 11.8 + - - -
1061A HIS* 1.3 85.5 - - - +
1063A ALA* 1.3 65.0 + - - +
1064A TYR* 3.0 47.8 - - + +
1072A ILE* 3.4 0.5 - - - -
1073A VAL* 2.7 45.6 + - + +
1123A VAL* 3.7 17.7 - - + +
1124A LYS* 5.7 0.2 - - - +
1125A ASP 4.2 14.1 - - - +
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Residues in contact with ALA1063 (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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1017A ALA* 3.9 21.4 - - + +
1018A GLU 3.6 5.2 + - - +
1019A VAL* 4.2 16.6 - - + -
1020A GLN* 3.1 24.3 + - - +
1027A LEU* 4.2 19.5 - - + -
1060A CYS* 4.2 5.8 - - - -
1062A LYS* 1.3 80.1 + - - +
1064A TYR* 1.3 64.8 + - - +
1070A LEU* 5.7 1.3 - - + -
1071A PHE 3.2 7.0 - - - +
1072A ILE* 4.2 2.7 - - + -
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Residues in contact with TYR1064 (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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1019A VAL* 4.2 3.4 - - - -
1020A GLN* 3.5 31.2 - - - +
1062A LYS* 3.0 40.0 - - + +
1063A ALA* 1.3 72.3 - - - +
1065A SER* 1.3 61.9 + - - +
1066A GLU* 5.5 6.5 - - - +
1070A LEU* 3.5 6.2 - - - +
1071A PHE* 2.6 67.6 + - + -
1073A VAL* 3.6 21.1 - - + -
1092A LEU* 4.4 6.3 - - + -
1123A VAL* 3.7 0.2 - - - +
1125A ASP 2.7 21.3 + - - -
1126A HIS* 3.4 29.3 + + + -
1142A LEU* 3.2 20.9 - - + +
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Residues in contact with SER1065 (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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1019A VAL* 3.7 19.1 - - - -
1020A GLN 2.8 16.8 + - - +
1021A GLY* 3.9 16.8 + - - +
1022A MET* 4.0 19.7 - - - +
1064A TYR* 1.3 76.9 - - - +
1066A GLU* 1.3 72.1 + - - +
1068A GLY* 4.9 4.5 + - - -
1069A LEU 3.2 16.3 + - - -
1070A LEU* 4.3 7.5 - - - +
1071A PHE* 4.7 0.2 - - - -
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Residues in contact with GLU1066 (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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1020A GLN* 5.5 4.5 + - - -
1064A TYR* 5.5 6.3 - - - +
1065A SER* 1.3 83.0 + - - +
1067A MET* 1.3 78.8 + - + +
1068A GLY 3.3 2.0 - - - -
1069A LEU* 3.0 24.9 + - - +
1071A PHE* 3.9 21.4 - - + -
1126A HIS* 5.6 6.1 + - - -
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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