Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 1QY4
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 GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A LYS* 1.3 77.2 - - - +
107A GLY* 1.3 58.5 + - - -
119A TRP* 4.2 4.4 - - - -
121A SER* 3.7 6.2 - - - -
122A MET* 2.8 34.1 + - - +
139A VAL 3.3 12.6 - - - -
141A ILE* 3.9 15.3 - - - +
146A PHE* 3.7 12.4 - - - -
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Residues in contact with GLY 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 GLY* 1.3 75.0 - - - -
108A MET* 1.3 62.4 + - - -
119A TRP* 3.3 19.2 - - - -
120A ILE 3.2 12.6 - - - -
122A MET* 3.8 10.5 - - - -
138A THR* 3.2 4.7 - - - -
139A VAL 2.8 32.4 + - - -
146A PHE* 4.0 3.6 - - - -
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Residues in contact with MET 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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99A TYR* 3.4 52.3 - - + -
107A GLY* 1.3 75.4 - - - -
109A LEU* 1.3 64.2 + - - +
110A LEU* 3.9 17.4 - - + +
118A LYS 3.8 0.3 - - - +
119A TRP* 3.3 9.5 - - - -
120A ILE* 2.8 36.8 + - + +
122A MET* 3.9 13.2 - - - -
128A VAL* 3.9 17.3 - - + -
130A VAL* 3.6 19.3 - - - -
136A HIS* 3.8 15.3 - - + -
137A ARG 3.3 16.8 - - - +
138A THR* 3.9 6.1 - - + -
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Residues in contact with LEU 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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84A PHE* 6.2 0.2 - - + -
107A GLY 4.3 0.2 + - - -
108A MET* 1.3 72.4 - - - +
110A LEU* 1.3 69.6 + - - +
117A ALA* 4.5 5.8 - - + -
118A LYS 3.5 7.6 - - - +
119A TRP* 4.1 7.3 - - + -
136A HIS* 3.3 3.5 - - - -
137A ARG* 2.8 60.0 + - + +
139A VAL* 4.5 4.3 - - + -
168A PHE* 3.4 31.1 - - + -
170A LYS* 3.9 31.9 - - + +
171A ILE* 4.8 1.6 - - - -
172A VAL* 3.8 29.2 - - + +
181A VAL* 5.6 2.7 - - + -
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Residues in contact with LEU 110 (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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108A MET* 3.9 29.4 - - - +
109A LEU* 1.3 78.6 - - - +
111A GLN* 1.3 63.4 + - - +
117A ALA* 3.1 6.4 - - - +
118A LYS* 2.7 35.9 + - + +
120A ILE* 3.7 31.0 - - + -
128A VAL* 5.3 0.2 - - + -
129A TYR 4.9 0.2 - - - +
130A VAL* 3.8 31.6 - - + -
134A TRP* 3.6 21.3 - - + -
135A ALA 3.2 7.2 - - - +
136A HIS* 4.3 2.5 - - + -
168A PHE* 4.4 1.8 - - - -
5B PRO* 3.7 27.8 - - + -
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Residues in contact with GLN 111 (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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89A PHE* 4.5 3.9 - - + -
110A LEU* 1.3 78.5 - - - +
112A THR* 1.3 66.4 - - - +
113A PRO 5.6 0.3 - - - +
115A GLY* 3.9 13.3 + - - -
116A ASP 3.0 16.6 - - - +
117A ALA* 4.1 2.1 - - - +
134A TRP* 3.5 7.2 - - - -
135A ALA* 2.9 38.7 + - + +
163A ILE* 4.2 7.8 - - - +
166A LYS* 5.6 3.1 - - - -
167A GLY 3.8 12.0 - - - +
168A PHE* 3.3 26.3 - - + +
169A SER* 2.7 41.4 + - - +
170A LYS 4.7 0.2 - - - +
187A TRP* 4.1 7.8 - - - -
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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