Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 3WSZ
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A HIS* 4.3 1.6 - - - +
103A ASN* 1.3 78.1 + - - +
105A MET* 1.3 72.7 + - - +
106A VAL* 4.3 5.0 - - + +
120A LEU 3.7 0.4 - - - +
121A ALA* 3.3 5.4 - - - +
122A ARG* 2.8 80.3 + - + +
123A ASP 4.0 11.0 - - - +
124A SER* 4.2 14.5 + - - +
125A LEU 5.8 0.2 - - - +
610A TRP* 4.5 1.4 + - - -
10C ALA* 5.3 2.6 - - - +
11C ALA* 3.1 35.9 + - - +
12C ALA* 4.3 1.2 + - - -
13C ALA* 4.4 7.7 + - - +
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Residues in contact with MET 105 (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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98A LEU* 4.0 17.7 - - + -
104A GLN* 1.3 81.3 + - - +
106A VAL* 1.3 61.9 + - - +
107A VAL* 3.9 16.5 + - + +
119A ALA* 4.2 24.0 - - - -
120A LEU 3.4 9.6 - - - +
121A ALA* 4.5 9.9 - - + -
600A PHE* 4.1 13.2 - - + -
610A TRP* 3.4 62.8 - - + -
612A ILE* 4.5 10.3 - - + -
11C ALA 3.2 4.9 + - - +
12C ALA* 3.2 6.2 - - + -
13C ALA 2.9 24.9 + - - +
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Residues in contact with VAL 106 (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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104A GLN* 4.4 7.9 - - + +
105A MET* 1.3 77.2 - - - +
107A VAL* 1.3 61.3 + - - +
118A VAL 3.8 0.7 - - - +
119A ALA* 3.3 2.9 - - - -
120A LEU* 2.7 51.2 + - + +
122A ARG* 3.5 39.3 - - - +
166A GLN* 6.6 0.2 - - + -
167A PHE* 3.9 12.4 - - + -
13C ALA* 3.6 9.9 - - + -
14C ALA 3.8 11.7 - - - +
15C ALA* 3.3 26.2 - - + +
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Residues in contact with VAL 107 (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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105A MET* 3.9 12.3 - - + +
106A VAL* 1.3 79.0 - - - +
108A HIS* 1.3 64.0 + - - +
109A TRP* 3.5 36.1 - - + -
117A ILE* 4.1 16.2 - - + -
118A VAL 3.4 6.1 - - - +
119A ALA* 4.4 10.1 - - + -
167A PHE* 4.8 0.2 - - - -
587A LEU* 5.4 2.2 - - + -
600A PHE* 3.5 35.2 - - + -
612A ILE* 5.5 0.9 - - + -
12C ALA* 5.8 1.1 - - + -
13C ALA 2.9 13.4 + - - +
14C ALA* 3.6 25.3 - - - +
15C ALA 3.9 2.9 + - - -
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Residues in contact with HIS 108 (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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107A VAL* 1.3 75.3 - - - +
109A TRP* 1.3 86.6 + - - +
110A ALA* 4.0 3.1 + - - -
117A ILE* 3.3 7.3 - - - +
118A VAL* 2.7 40.2 + - + +
167A PHE* 3.6 25.8 - + + -
169A HIS* 3.6 34.9 + + + -
174A ASN* 6.0 2.5 - - + -
177A TYR* 3.2 41.4 + + - -
15C ALA* 4.2 19.1 - - - +
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Residues in contact with TRP 109 (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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107A VAL* 3.5 35.4 - - + -
108A HIS* 1.3 91.0 + - - +
110A ALA* 1.3 66.0 + - - +
111A GLY* 3.2 4.9 + - - +
116A VAL 4.0 2.9 - - - -
117A ILE* 3.5 32.9 - - + +
141A TYR* 3.9 17.4 + + - -
587A LEU* 4.3 24.2 - - + -
588A THR 3.8 19.5 - - - -
589A GLU* 3.3 41.8 - - + +
590A PRO* 3.9 20.7 - - + +
598A THR* 3.7 24.5 + - + -
600A PHE* 4.8 2.9 - + - -
614A GLN* 5.0 1.4 - - - +
14C ALA* 5.5 7.2 - - + -
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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