Contacts of the strand formed by residues 1005 - 1021 (chain A) in PDB entry 1WUF
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 LYS1005 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A PHE 3.5 0.2 - - - -
1004A GLN* 1.3 103.1 + - + +
1006A ALA* 1.3 68.9 + - - +
1007A ARG* 4.1 13.2 - - - +
1036A LEU* 3.8 1.6 - - - -
1037A ILE* 2.9 52.3 + - + +
1366A GLU* 3.1 31.6 + - + +
1367A ILE 3.3 15.7 - - - +
1368A LEU* 4.4 18.3 - - + +
1369A LEU* 3.7 9.7 - - - +
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Residues in contact with ALA1006 (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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1005A LYS* 1.3 78.1 - - - +
1007A ARG* 1.3 60.7 + - - +
1008A LEU* 4.1 2.7 - - + -
1035A GLU 3.3 4.7 - - - -
1036A LEU* 3.7 22.2 - - + -
1037A ILE* 6.0 0.2 - - - -
1073A LEU* 3.8 26.0 - - + -
1365A GLU 3.8 0.9 - - - +
1366A GLU* 3.4 2.8 - - - +
1367A ILE* 2.6 45.3 + - + +
1369A LEU* 4.1 8.0 - - + +
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Residues in contact with ARG1007 (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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1005A LYS* 4.1 6.4 - - + +
1006A ALA* 1.3 75.5 - - - +
1008A LEU* 1.3 62.4 + - - +
1009A ILE* 3.6 15.8 + - + +
1033A ILE 3.3 4.0 - - - +
1035A GLU* 2.8 76.3 + - + +
1037A ILE* 4.0 20.9 - - + +
1043A HIS* 4.5 4.0 + - - -
1364A THR* 4.6 12.3 - - + +
1365A GLU 3.4 4.3 - - - +
1366A GLU* 3.7 37.2 + - + +
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Residues in contact with LEU1008 (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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1006A ALA* 5.2 0.7 - - + -
1007A ARG* 1.3 76.3 - - - +
1009A ILE* 1.3 64.3 + - - +
1010A HIS 3.9 1.4 + - - -
1032A TYR* 4.5 14.4 - - + -
1033A ILE 3.6 2.0 - - - -
1034A ILE* 3.7 35.4 - - + -
1065A ILE* 4.3 14.4 - - + -
1068A ILE* 4.6 2.9 - - + -
1069A LYS* 3.5 35.9 - - + -
1073A LEU* 4.4 15.7 - - + -
1363A SER* 3.9 1.7 + - - +
1364A THR* 3.7 3.3 - - - -
1365A GLU* 2.8 42.1 + - + +
1367A ILE* 3.6 21.3 - - + -
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Residues in contact with ILE1009 (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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1007A ARG* 4.1 20.2 - - + +
1008A LEU* 1.3 74.7 - - - +
1010A HIS* 1.3 63.9 + - - +
1011A ALA* 3.7 1.5 + - + +
1032A TYR* 3.2 5.8 - - - -
1033A ILE* 2.7 63.6 + - + +
1035A GLU* 3.7 22.7 - - - +
1352A LEU* 5.1 2.9 - - + -
1354A LEU* 6.5 0.7 - - + -
1357A LEU* 4.5 27.4 - - + -
1361A THR* 3.5 31.9 - - + +
1363A SER 3.8 2.7 - - - +
1364A THR* 4.3 8.1 - - - +
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Residues in contact with HIS1010 (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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1008A LEU 3.9 1.4 + - - -
1009A ILE* 1.3 70.5 - - - +
1011A ALA* 1.3 54.5 + - - +
1030A ASP* 2.7 31.2 + - - -
1031A PHE 3.2 19.7 - - - -
1032A TYR* 3.2 37.1 + + + -
1061A LEU* 3.9 5.7 - - + +
1361A THR* 3.4 3.6 - - - +
1362A LYS* 2.6 58.3 + - + +
1363A SER* 3.1 31.4 + - - +
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Residues in contact with ALA1011 (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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1009A ILE* 3.7 4.2 + - + +
1010A HIS* 1.3 75.8 - - - +
1012A GLU* 1.3 61.9 + - - +
1013A LEU* 4.9 0.4 - - + -
1029A LYS 3.8 0.5 - - - +
1030A ASP* 3.3 5.3 - - - +
1031A PHE* 3.0 58.8 + - + +
1033A ILE* 5.8 0.2 - - + -
1357A LEU* 4.1 20.4 - - + -
1360A TYR* 3.1 22.4 - - + +
1361A THR* 4.1 1.6 - - - +
1362A LYS* 4.4 0.9 - - - +
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Residues in contact with GLU1012 (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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1011A ALA* 1.3 75.6 - - - +
1013A LEU* 1.3 62.8 + - - +
1014A PRO* 3.9 1.0 - - - +
1027A LYS* 4.8 8.0 + - - +
1028A SER* 2.8 32.2 + - - +
1029A LYS 3.3 8.3 - - - +
1030A ASP* 3.9 10.7 - - - +
1360A TYR* 3.0 31.8 + - - +
1362A LYS* 2.6 43.7 + - + +
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Residues in contact with LEU1013 (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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1011A ALA* 4.9 0.2 - - + -
1012A GLU* 1.3 77.3 - - - +
1014A PRO* 1.3 68.2 - - + +
1015A LEU 3.4 0.2 + - - -
1028A SER* 2.9 21.9 - - - -
1029A LYS 3.0 18.4 + - - +
1031A PHE* 3.9 12.6 - - + -
1295A ALA* 4.3 12.1 - - + -
1324A PHE* 3.7 28.5 - - + -
1326A GLU 3.5 25.1 - - - +
1327A ASP* 3.6 24.0 - - - +
1328A ILE* 3.8 23.1 - - + -
1360A TYR* 4.0 21.5 - - + -
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Residues in contact with PRO1014 (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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1012A GLU 3.9 1.3 - - - +
1013A LEU* 1.3 85.0 - - + +
1015A LEU* 1.3 65.6 + - - +
1016A LEU 3.7 1.2 + - - -
1027A LYS 4.3 1.6 - - - +
1028A SER* 4.2 6.3 - - - -
1324A PHE* 3.7 10.4 - - - +
1325A ALA* 3.9 21.1 + - + +
1326A GLU* 5.3 3.0 + - + +
1360A TYR* 3.3 40.8 - - + +
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Residues in contact with LEU1015 (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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1013A LEU 3.4 0.8 + - - -
1014A PRO* 1.3 76.6 - - - +
1016A LEU* 1.3 67.2 + - - +
1017A ALA* 3.4 17.8 - - - +
1019A PHE* 3.8 29.2 - - + +
1026A LEU* 4.1 2.0 - - + -
1027A LYS 3.2 19.7 + - - +
1028A SER* 3.5 35.2 - - - +
1293A LEU* 4.1 14.8 - - + -
1323A PHE* 3.6 20.6 - - + +
1324A PHE* 3.2 33.7 - - + -
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Residues in contact with LEU1016 (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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1014A PRO 3.7 1.2 + - - -
1015A LEU* 1.3 73.4 - - - +
1017A ALA* 1.3 61.9 + - + +
1018A PRO* 4.8 0.5 - - - +
1321A ASN 3.4 25.4 - - - +
1322A ARG 4.1 7.4 - - - +
1323A PHE* 2.6 31.3 + - - +
1324A PHE 3.8 11.0 - - - +
1325A ALA* 3.8 26.2 - - + +
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Residues in contact with ALA1017 (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 LEU* 3.4 21.1 - - - +
1016A LEU* 1.3 81.8 - - + +
1018A PRO* 1.3 78.4 - - + +
1019A PHE* 3.5 1.4 + - - +
1027A LYS 5.8 0.2 - - - -
1323A PHE* 4.4 5.6 + - - +
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Residues in contact with PRO1018 (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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1016A LEU 4.8 1.1 - - - +
1017A ALA* 1.3 91.0 - - + +
1019A PHE* 1.3 60.6 + - - +
1020A LYS* 3.7 24.6 + - - +
1025A GLU* 4.1 22.7 - - + +
1026A LEU 3.1 14.4 - - - +
1027A LYS* 4.7 6.7 - - + -
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Residues in contact with PHE1019 (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 LEU* 3.8 12.5 - - + +
1017A ALA 3.5 1.5 + - - +
1018A PRO* 1.3 73.1 - - - +
1020A LYS* 1.3 80.2 + - + +
1021A THR* 3.7 17.8 + - + -
1025A GLU* 3.2 2.8 - - - -
1026A LEU* 2.5 52.6 + - + -
1051A PHE* 4.6 14.1 - + - -
1292A MET* 6.2 0.4 - - - -
1293A LEU* 3.4 39.9 - - + -
1323A PHE* 4.7 17.3 - + - -
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Residues in contact with LYS1020 (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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1018A PRO* 3.7 25.5 + - - +
1019A PHE* 1.3 89.6 - - + +
1021A THR* 1.3 64.1 + - - +
1024A GLY 3.8 7.6 - - - +
1025A GLU* 4.1 20.7 + - + +
1164A LYS* 5.6 12.1 - - + -
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Residues in contact with THR1021 (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 PHE* 3.7 21.9 + - + +
1020A LYS* 1.3 80.5 - - - +
1022A SER* 1.3 68.0 + - - +
1024A GLY* 2.9 35.3 + - - +
1025A GLU 3.9 0.2 + - - -
1026A LEU* 4.2 18.3 - - + +
1051A PHE* 4.3 23.1 - - + -
1053A LEU* 5.6 0.3 - - - +
1055A ASP* 2.8 23.2 + - - +
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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