Contacts of the strand formed by residues 59 - 65 (chain A) in PDB entry 1WSQ
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 ILE 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.6 10.5 - - + -
34A TYR* 3.7 36.8 - - + +
51A VAL* 3.7 14.4 - - + -
53A ALA 3.5 12.1 - - - +
54A GLU* 4.1 11.7 - - + -
58A ALA* 1.3 79.1 - - - +
60A VAL* 1.3 66.5 + - - +
61A PHE* 3.5 32.3 - - + -
73A LEU 3.5 1.0 - - - +
74A LYS* 3.4 3.2 - - - +
75A ARG* 2.9 35.5 + - + +
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Residues in contact with VAL 60 (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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51A VAL* 3.7 2.3 - - - -
52A LEU* 2.7 49.0 + - + -
53A ALA 2.8 19.6 + - - +
55A GLY 5.7 0.9 - - - +
58A ALA* 5.6 0.9 - - + -
59A ILE* 1.3 80.7 - - - +
61A PHE* 1.3 60.3 + - - +
72A ALA* 4.2 9.4 - - + -
73A LEU 3.3 9.4 - - - +
74A LYS* 4.1 18.2 - - + +
126A MET* 5.1 0.4 - - + -
405A KSA 3.8 59.5 - - + +
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Residues in contact with PHE 61 (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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34A TYR* 3.4 51.1 - + + -
39A PHE* 3.9 21.8 - + - -
48A VAL* 3.6 21.1 - - + -
50A GLU 3.5 8.5 - - - +
51A VAL* 3.8 11.2 - - + -
52A LEU* 3.8 5.6 - - - +
59A ILE* 3.5 35.0 - - + -
60A VAL* 1.3 73.8 - - - +
62A LEU* 1.3 59.6 - - - +
63A VAL* 3.8 17.7 - - + -
72A ALA* 3.2 6.8 - - - -
73A LEU* 2.7 51.6 + - + +
75A ARG* 4.2 16.6 - - + -
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Residues in contact with LEU 62 (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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48A VAL* 3.7 0.5 - - - -
49A ASP* 2.8 42.4 + - + +
50A GLU* 2.9 47.7 + - + +
52A LEU* 3.7 20.0 - - + +
61A PHE* 1.3 70.8 - - - +
63A VAL* 1.3 58.0 + - - +
70A LYS* 4.1 25.6 - - + +
71A CYS 3.5 15.5 - - - +
128A PHE* 3.6 44.9 - - + -
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Residues in contact with VAL 63 (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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46A VAL* 3.9 18.2 - - + -
47A THR 3.0 18.2 - - - +
48A VAL* 4.0 11.9 - - + -
49A ASP* 4.3 1.8 - - - +
61A PHE* 3.8 20.0 - - + -
62A LEU* 1.3 80.6 - - - +
64A ARG* 1.3 64.3 + - - +
69A MET 3.7 0.2 - - - +
70A LYS* 3.4 6.1 - - - +
71A CYS* 2.9 40.4 + - + +
73A LEU* 3.8 18.8 - - + -
125A LEU* 3.8 28.3 - - + -
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Residues in contact with ARG 64 (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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46A VAL* 3.4 4.9 - - - -
47A THR* 3.0 45.1 + - - +
49A ASP* 2.5 40.9 + - - +
62A LEU* 6.3 0.2 - - + -
63A VAL* 1.3 76.2 - - - +
65A THR* 1.3 71.1 + - - +
68A GLY* 4.1 15.7 - - - +
69A MET 3.3 3.8 - - - +
70A LYS* 3.8 31.7 - - + +
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Residues in contact with THR 65 (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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45A GLN 4.0 7.9 - - - -
46A VAL* 4.2 14.8 - - + -
63A VAL* 5.9 0.2 - - + -
64A ARG* 1.3 81.2 - - - +
66A SER* 1.3 60.3 + - - +
67A ASN* 3.4 10.7 + - - +
68A GLY* 3.0 16.5 + - - -
69A MET* 3.0 44.3 + - + +
71A CYS* 4.1 17.5 - - - -
125A LEU* 4.5 7.4 - - + -
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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