Contacts of the strand formed by residues 103 - 109 (chain A) in PDB entry 4QPL
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 TYR 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASN* 2.9 39.0 + - + +
101A GLY 3.8 0.4 - - - -
102A GLU* 1.3 93.5 - - + +
104A ALA* 1.3 65.6 + - - +
105A TRP* 4.7 5.4 - + - -
121A SER* 6.6 0.2 - - - -
125A GLU* 3.3 49.3 + - + +
167A ARG* 3.8 26.2 - - + +
168A ASP 3.5 11.4 - - - +
169A ILE* 4.3 1.1 - - - +
170A ILE* 3.7 4.8 - - - +
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Residues in contact with ALA 104 (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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100A ASN* 3.7 16.4 - - - +
103A TYR* 1.3 80.6 - - - +
105A TRP* 1.3 68.1 + - - +
106A TYR* 3.8 23.3 - - + +
115A GLN* 4.2 13.9 - - - +
121A SER* 5.9 0.4 - - - +
167A ARG* 3.3 6.3 - - - +
168A ASP 2.8 31.2 + - - +
170A ILE* 3.9 13.9 - - + -
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Residues in contact with TRP 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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103A TYR* 4.7 4.3 - + - -
104A ALA* 1.3 78.7 - - - +
106A TYR* 1.3 62.5 + - - +
115A GLN* 3.5 10.4 - - - +
116A TYR* 2.9 37.4 + - + +
121A SER* 3.8 30.0 + - - +
124A LEU* 3.6 39.7 - - + -
125A GLU* 2.9 28.5 + - + +
128A PHE* 3.6 25.4 - + + -
148A LEU* 4.0 22.0 - - + -
151A MET* 3.8 23.3 - - + -
165A ILE* 4.4 9.6 - - + -
166A LYS 3.5 16.2 - - - -
167A ARG* 3.5 27.2 - - + +
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Residues in contact with TYR 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 ALA* 3.8 27.5 - - + +
105A TRP* 1.3 75.3 - - - +
107A TYR* 1.3 61.6 + - - +
113A TRP* 3.7 29.4 - - + -
114A TRP 3.1 18.2 - - - +
115A GLN* 3.7 17.5 - - + -
116A TYR* 3.5 5.4 - - - -
165A ILE* 3.1 9.5 - - - +
166A LYS* 2.9 38.2 + - + +
168A ASP* 4.1 11.7 - - + -
169A ILE 2.9 26.4 + - - -
170A ILE* 3.4 7.6 + - - -
172A ILE* 3.5 24.4 - - + +
174A LYS* 3.2 37.1 + - + -
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Residues in contact with TYR 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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106A TYR* 1.3 72.6 - - - +
108A GLU* 1.3 64.3 + - - +
113A TRP* 3.5 6.1 - - - -
114A TRP* 2.8 65.1 + + + +
115A GLN 3.5 15.5 - - - -
116A TYR* 3.7 31.6 - + + +
153A GLN* 4.2 6.1 - - - +
163A ARG* 3.9 19.5 - - + -
164A LYS 3.4 7.9 - - - +
165A ILE* 4.1 1.8 - - + -
178A ALA* 3.1 20.3 - - - -
179A GLY 3.3 1.9 + - - -
201A V3L 2.7 72.2 + + - -
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Residues in contact with GLU 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 TYR* 1.3 74.4 - - - +
109A GLY* 1.3 69.4 + - - +
112A GLY 4.3 1.3 - - - +
113A TRP* 3.7 12.8 - - + -
114A TRP* 4.4 0.4 - - - -
162A ARG 4.5 3.2 - - - +
163A ARG* 2.9 37.9 + - + +
164A LYS* 2.8 59.2 + - + +
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Residues in contact with GLY 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 TYR 3.4 2.2 + - - -
108A GLU* 1.3 85.4 - - - +
110A ARG* 1.3 64.7 + - - -
111A ASN 3.3 2.8 + - - -
112A GLY 2.8 23.6 + - - +
114A TRP* 3.7 11.4 - - - -
163A ARG* 4.0 5.4 - - - -
175A LYS* 4.3 0.7 - - - -
201A V3L 3.4 12.8 - - - -
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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