Contacts of the strand formed by residues 44 - 53 (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 GLN 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLY* 3.4 1.4 - - - -
41A ILE* 2.7 49.6 + - + +
43A ARG* 1.3 107.6 - - - +
45A GLN* 1.3 62.0 + - - +
46A VAL* 5.2 3.4 - - + -
66A SER* 5.2 1.2 + - - -
108A ASP* 4.9 7.6 - - - +
140B GLN* 3.0 26.1 + - - +
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Residues in contact with GLN 45 (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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38A VAL* 3.6 26.2 - - + +
39A PHE 3.3 4.3 - - - +
40A GLY* 4.7 5.8 - - - -
43A ARG 4.4 4.5 - - - +
44A GLN* 1.3 76.3 - - - +
46A VAL* 1.3 65.6 + - - +
47A THR* 5.5 0.2 - - - -
65A THR* 4.0 1.0 - - - -
66A SER* 3.9 17.6 + - - -
131B GLY 4.6 7.9 + - - -
132B GLY* 5.9 0.2 - - - -
133B GLN 4.8 0.6 + - - -
136B ASN* 3.3 46.2 + - + +
137B LEU* 3.1 31.5 - - - +
140B GLN* 2.8 25.2 + - - +
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Residues in contact with VAL 46 (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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37A ARG 3.7 0.7 - - - +
38A VAL* 3.1 5.5 - - - -
39A PHE* 2.8 54.1 + - + +
41A ILE* 4.4 19.3 - - + -
44A GLN* 4.9 4.0 - - + +
45A GLN* 1.3 80.0 - - - +
47A THR* 1.3 63.5 + - - +
63A VAL* 3.9 21.8 - - + -
64A ARG 3.4 7.2 - - - +
65A THR* 4.2 23.8 - - + -
73A LEU* 4.1 13.7 - - + -
125A LEU* 4.3 15.3 - - + -
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Residues in contact with THR 47 (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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36A GLY* 4.2 15.5 - - - +
37A ARG 3.4 7.9 - - - +
38A VAL* 3.6 16.1 - - + +
45A GLN* 5.5 0.3 - - - +
46A VAL* 1.3 74.9 - - - +
48A VAL* 1.3 72.9 + - - +
49A ASP* 3.4 9.9 + - - +
63A VAL* 3.0 7.0 - - - -
64A ARG* 3.0 45.9 + - - +
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Residues in contact with VAL 48 (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* 3.3 29.8 - - + +
35A ILE* 3.8 4.5 - - + +
36A GLY* 2.8 27.2 + - - -
37A ARG 2.8 19.2 + - - +
39A PHE* 3.6 31.4 - - + -
47A THR* 1.3 72.6 - - - +
49A ASP* 1.3 65.4 + - - +
50A GLU 3.7 15.9 - - - +
51A VAL 4.8 0.2 - - - +
61A PHE* 3.6 33.2 - - + -
62A LEU 3.7 4.0 - - - +
63A VAL* 4.0 6.7 - - + -
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Residues in contact with ASP 49 (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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35A ILE* 3.9 22.9 - - - +
47A THR* 3.4 6.6 + - - +
48A VAL* 1.3 79.1 - - - +
50A GLU* 1.3 68.4 + - + +
62A LEU* 2.8 29.8 + - + +
63A VAL 4.7 0.5 - - - -
64A ARG* 2.5 63.1 + - - +
70A LYS* 4.5 5.4 + - - -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.8 6.5 - - + -
48A VAL* 3.7 8.1 - - - +
49A ASP* 1.3 88.3 - - + +
51A VAL* 1.3 66.7 + - - +
52A LEU* 4.8 9.7 - - + +
61A PHE* 3.5 3.8 - - - -
62A LEU* 2.9 55.7 + - + +
128A PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.7 53.4 - - + +
31A GLY* 4.6 5.8 - - - +
34A TYR* 4.2 4.5 - - + -
35A ILE* 5.2 3.4 - - + +
48A VAL* 5.1 1.1 - - + -
50A GLU* 1.3 75.9 - - - +
52A LEU* 1.3 64.5 + - - +
53A ALA* 4.2 7.6 - - - +
59A ILE* 3.7 26.9 - - + -
60A VAL 4.0 2.7 - - - +
61A PHE* 3.8 20.4 - - + -
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Residues in contact with LEU 52 (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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50A GLU* 4.8 11.4 - - + +
51A VAL* 1.3 76.4 - - - +
53A ALA* 1.3 61.0 + - - +
60A VAL* 2.7 25.6 + - + +
61A PHE 3.8 8.1 - - - +
62A LEU* 3.7 31.6 - - + +
72A ALA* 4.3 4.3 - - + -
128A PHE* 3.9 32.3 - - + -
133A GLN* 5.1 1.6 + - - -
405A KSA 3.9 51.1 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.7 0.2 - - - -
51A VAL* 3.7 5.1 - - - -
52A LEU* 1.3 82.4 - - - +
54A GLU* 1.3 61.2 + - - +
55A GLY 3.8 1.7 + - - +
59A ILE* 3.5 4.6 - - - +
60A VAL* 2.8 28.5 + - - +
133A GLN* 4.5 4.5 - - - +
405A KSA 3.3 48.0 - - + +
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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