Contacts of the strand formed by residues 1361 - 1368 (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 THR1361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A ILE* 3.5 26.5 - - + +
1010A HIS 3.4 4.7 - - - +
1011A ALA* 4.1 1.3 - - - +
1357A LEU* 2.8 36.4 + - - +
1358A LYS* 3.4 16.4 + - - +
1359A LYS 5.2 0.5 - - - -
1360A TYR* 1.3 78.6 - - - +
1362A LYS* 1.3 63.9 + - - +
1363A SER 3.5 16.6 - - - +
1364A THR* 3.9 9.2 - - - +
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Residues in contact with LYS1362 (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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1010A HIS* 2.6 47.8 + - + +
1011A ALA 4.4 0.7 - - - -
1012A GLU* 2.6 37.0 + - + +
1030A ASP* 2.9 26.5 + - - -
1360A TYR 4.1 8.5 - - - +
1361A THR* 1.3 76.7 - - - +
1363A SER* 1.3 61.9 + - - +
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Residues in contact with SER1363 (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 1.7 + - - +
1009A ILE* 3.8 0.7 - - - -
1010A HIS* 3.1 45.8 + - - +
1032A TYR* 5.1 2.8 + - - -
1361A THR* 3.5 6.5 - - - +
1362A LYS* 1.3 82.8 - - - +
1364A THR* 1.3 67.6 + - - +
1365A GLU* 6.0 0.5 - - - +
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Residues in contact with THR1364 (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* 4.6 19.1 - - + -
1008A LEU 3.7 4.0 - - - -
1009A ILE* 4.3 9.3 - - + +
1361A THR* 3.9 12.5 - - - +
1363A SER* 1.3 78.8 + - - +
1365A GLU* 1.3 69.7 + - - +
1366A GLU* 4.8 7.4 - - + +
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Residues in contact with GLU1365 (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 3.8 0.3 - - - +
1007A ARG* 3.4 1.6 - - - -
1008A LEU* 2.8 49.0 + - + +
1069A LYS* 3.5 35.0 + - - +
1363A SER* 6.0 0.4 - - - +
1364A THR* 1.3 79.0 - - - +
1366A GLU* 1.3 67.3 - - - +
1367A ILE* 4.0 20.4 - - + +
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Residues in contact with GLU1366 (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* 3.1 36.9 + - + +
1006A ALA 3.4 4.5 - - - +
1007A ARG* 3.7 31.3 + - + +
1364A THR* 4.8 8.2 - - + +
1365A GLU* 1.3 78.1 - - - +
1367A ILE* 1.3 66.8 + - - +
1368A LEU* 4.2 5.0 + - + +
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Residues in contact with ILE1367 (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* 3.3 3.6 - - - +
1006A ALA* 2.6 44.8 + - + +
1008A LEU* 3.6 33.9 - - + -
1069A LYS* 4.2 12.6 - - + -
1073A LEU* 3.7 21.1 - - + -
1365A GLU* 4.0 15.7 - - + +
1366A GLU* 1.3 80.9 - - - +
1368A LEU* 1.3 75.1 + - - +
1369A LEU* 3.5 10.8 + - + +
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Residues in contact with LEU1368 (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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1004A GLN* 4.2 3.4 - - + +
1005A LYS* 4.5 23.8 - - + +
1077A ALA* 5.7 0.7 - - - +
1366A GLU* 4.2 4.2 + - + -
1367A ILE* 1.3 83.5 - - - +
1369A LEU* 1.3 63.4 + - - +
1370A ASN* 3.4 18.3 + - + +
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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