Contacts of the strand formed by residues 122 - 129 (chain A) in PDB entry 1GQC
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A MET* 4.3 0.4 - - - -
120A LEU* 3.2 11.3 - - - +
121A PRO* 1.3 88.6 - - + +
123A ALA* 1.3 71.6 + - - +
176A TYR* 4.3 10.3 - - + -
177A ALA 3.2 9.9 - - - +
178A TYR* 3.8 14.4 - - + -
182A VAL* 3.8 21.5 - - + -
205A LEU* 3.7 25.8 - - + -
210A ILE* 4.5 2.9 - - + -
211A ASN 3.5 8.5 + - - +
212A ILE* 3.3 23.7 - - + -
213A ARG 3.0 22.1 + - - -
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Residues in contact with ALA 123 (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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110A LEU* 3.8 13.1 - - + +
114A MET* 3.6 26.5 - - + -
120A LEU* 4.0 3.6 - - + -
122A VAL* 1.3 79.5 - - - +
124A THR* 1.3 64.4 + - - +
176A TYR* 3.5 2.8 - - - -
177A ALA* 2.9 32.1 + - + +
212A ILE* 4.7 0.2 - - - -
213A ARG 3.3 6.1 - - - +
215A PHE* 3.9 21.5 - - + -
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Residues in contact with THR 124 (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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110A LEU* 3.4 10.5 - - - +
123A ALA* 1.3 75.6 - - - +
125A LEU* 1.3 61.8 + - - +
153A PHE* 4.2 5.6 - - + -
172A HIS* 2.7 36.4 + - + +
173A VAL 3.2 1.4 + - - -
175A ILE 2.6 23.6 + - - -
176A TYR* 3.9 9.8 - - - -
212A ILE* 3.8 20.9 - - + -
213A ARG 3.0 10.8 + - - +
214A THR* 4.1 14.6 - - - +
215A PHE* 3.2 27.4 + - - +
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Residues in contact with LEU 125 (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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102A ILE* 5.2 0.4 - - + -
106A ASP* 3.9 35.7 - - + +
109A THR* 5.1 0.9 - - + -
110A LEU* 3.7 27.1 - - + +
124A THR* 1.3 82.9 + - - +
126A CYS* 1.3 61.8 + - - +
172A HIS* 3.2 11.8 - - - -
173A VAL* 2.9 40.3 + - + +
175A ILE* 3.7 32.6 + - + -
214A THR* 5.2 0.2 - - - -
215A PHE* 3.5 22.2 - - + +
217A VAL* 3.8 20.6 - - + -
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Residues in contact with CYS 126 (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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125A LEU* 1.3 78.2 - - - +
127A HIS* 1.3 61.9 + - - +
142A VAL* 3.9 18.6 - - + -
170A LEU* 4.2 16.6 - - + -
171A LYS 3.1 14.4 - - - +
172A HIS* 5.4 0.2 - - + -
173A VAL* 4.2 5.4 - - - +
214A THR* 3.1 35.7 - - + +
215A PHE 3.1 10.0 + - - -
216A GLU* 3.1 20.0 - - - -
217A VAL* 2.9 24.7 + - - +
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Residues in contact with HIS 127 (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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126A CYS* 1.3 73.1 - - - +
128A ALA* 1.3 68.2 + - - +
129A ILE* 3.4 26.9 - - + -
133A GLU* 4.9 4.7 - - - -
170A LEU* 4.0 4.3 - - - -
171A LYS* 2.9 49.4 + - + +
173A VAL* 3.9 14.1 - - + -
216A GLU* 4.1 4.3 - - - -
217A VAL* 2.9 28.0 - - + +
218A ALA 3.7 5.8 - - - +
219A ALA* 3.7 20.0 - - + +
220A THR* 3.4 35.8 + - + -
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Residues in contact with ALA 128 (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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127A HIS* 1.3 94.1 + - - +
129A ILE* 1.3 59.2 + - - +
168A ARG* 4.4 14.4 - - - +
169A TYR 3.5 10.3 - - - +
170A LEU* 3.9 5.7 - - - +
216A GLU* 4.0 16.7 + - - +
217A VAL 4.6 0.4 + - - -
219A ALA* 5.0 4.2 - - - +
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Residues in contact with ILE 129 (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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127A HIS* 3.4 21.3 - - + -
128A ALA* 1.3 81.4 - - - +
130A SER* 1.3 64.4 + - - +
131A ALA 4.0 0.3 + - - -
133A GLU* 3.8 25.6 - - + +
134A ALA* 3.7 32.3 - - + +
139A THR* 4.3 8.5 - - + -
141A LYS* 4.5 4.5 - - + -
169A TYR* 2.9 42.1 + - + +
170A LEU 4.3 1.1 - - - -
171A LYS* 3.5 31.4 - - + +
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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