Contacts of the strand formed by residues 49 - 56 (chain A) in PDB entry 4WLQ
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 VAL 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.2 22.2 - - + -
46A LEU 3.7 15.7 - - - +
47A LYS* 4.0 7.4 - - + +
48A PRO* 1.3 76.5 - - - +
50A HIS* 1.3 64.9 + - - +
51A GLY 3.6 23.1 - - - +
52A LEU* 4.0 16.6 - - + -
196A TRP* 3.3 31.3 + - + -
197A ILE* 4.4 14.9 - - + +
222A ALA* 4.1 3.4 - - + -
223A ILE 3.7 7.0 - - - +
224A VAL* 4.1 11.0 - - + -
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Residues in contact with HIS 50 (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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30A ALA* 5.1 1.1 - - + -
48A PRO* 4.2 6.0 + - + -
49A VAL* 1.3 75.0 + - - +
51A GLY* 1.3 55.7 + - - +
96A VAL* 3.7 12.7 - - + +
97A LEU* 6.3 0.7 - - + -
100A CYS* 3.4 29.2 - - + +
102A HIS* 3.1 42.9 - + + +
105A VAL* 3.5 20.3 - - + +
169A VAL* 3.4 21.3 - - - +
170A PRO* 3.8 7.3 - - - +
196A TRP* 4.1 3.6 - - - +
223A ILE* 2.7 28.9 + - + +
224A VAL 3.6 15.3 - - - -
225A SER* 2.8 25.6 + - - -
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Residues in contact with GLY 51 (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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49A VAL* 3.6 6.6 - - - +
50A HIS* 1.3 80.4 - - - +
52A LEU* 1.3 65.2 + - - -
96A VAL* 3.9 12.7 - - - +
168A TYR 3.3 12.8 - - - -
196A TRP* 4.1 6.7 - - - -
222A ALA* 3.5 3.1 - - - -
223A ILE* 2.9 31.0 + - - -
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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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35A ILE* 4.9 2.5 - - + -
38A LEU* 6.2 1.6 - - + -
43A PHE* 4.6 19.3 - - + -
49A VAL* 4.0 9.4 - - + -
51A GLY* 1.3 82.1 - - - +
53A ILE* 1.3 63.1 + - - +
54A PHE 4.1 0.4 - - - -
167A SER* 3.2 4.9 - - - -
168A TYR* 2.6 44.9 + - + +
196A TRP* 3.9 10.3 - - + -
197A ILE* 5.4 1.3 - - + -
200A VAL* 4.0 37.5 - - + -
204A ILE* 4.1 14.1 - - + -
220A LEU* 3.9 15.5 - - + -
221A MET 3.2 12.1 - - - +
222A ALA* 3.8 15.3 - - + -
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Residues in contact with ILE 53 (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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18A PHE* 6.2 3.4 - - + -
32A VAL* 6.0 3.1 - - + -
52A LEU* 1.3 78.7 - - - +
54A PHE* 1.3 61.2 + - - +
55A LEU* 4.0 4.1 + - + +
92A ALA* 4.3 4.3 - - + -
93A ILE* 3.5 39.5 - - + +
96A VAL* 4.2 10.8 - - + -
165A PHE* 3.6 34.8 - - + -
166A VAL 3.3 7.6 - - - +
167A SER* 4.3 6.7 - - - -
219A ASN 4.1 0.5 - - - +
220A LEU* 3.4 5.0 - - - +
221A MET* 2.8 42.5 + - + +
223A ILE* 3.7 23.6 - - + -
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Residues in contact with PHE 54 (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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52A LEU 4.1 0.6 - - - -
53A ILE* 1.3 74.9 - - - +
55A LEU* 1.3 60.5 + - - +
56A PHE* 3.4 28.4 - + - -
164A HIS 3.8 0.5 - - - +
165A PHE* 3.6 1.6 - - - -
166A VAL* 2.6 44.6 + - + +
168A TYR* 3.6 25.5 - + + -
204A ILE* 4.6 5.8 - - + -
207A ARG* 3.7 21.3 - - + -
208A ILE* 3.5 30.7 - - + -
211A TYR* 3.4 40.8 - + - -
218A PHE* 4.1 21.1 - + + -
219A ASN 3.9 0.9 - - - -
220A LEU* 4.0 21.3 - - + -
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Residues in contact with LEU 55 (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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13A SER* 4.1 14.6 - - - +
18A PHE* 5.0 0.2 - - + -
53A ILE* 5.1 5.6 - - + +
54A PHE* 1.3 75.1 - - - +
56A PHE* 1.3 63.0 + - - +
163A PHE* 3.5 29.8 - - + -
164A HIS 3.1 12.6 - - - +
165A PHE* 3.4 37.2 - - + -
218A PHE* 3.1 3.6 - - - +
219A ASN* 2.6 70.9 + - + +
221A MET* 4.0 28.5 - - + -
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Residues in contact with PHE 56 (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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54A PHE* 3.4 36.8 - + + -
55A LEU* 1.3 78.8 - - - +
57A LYS* 1.3 72.8 + - - +
58A TRP* 3.3 23.0 + + - -
59A GLN* 4.0 20.2 - - + -
62A GLU* 4.9 1.6 - - - -
163A PHE* 3.6 8.2 - - - -
164A HIS* 2.8 51.9 + + - +
166A VAL* 4.1 15.3 - - + -
179A ASP* 5.3 0.4 - - - -
207A ARG* 3.4 24.9 - - - -
211A TYR* 4.1 7.2 - + + -
216A ILE* 4.8 2.5 - - + -
217A ARG 3.5 8.5 - - - +
218A PHE* 3.7 15.7 - - + +
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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