Contacts of the strand formed by residues 176 - 183 (chain A) in PDB entry 2GDZ
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.6 34.5 - - + -
122A MET* 3.9 34.1 - - + +
123A SER* 3.9 2.5 - - - +
131A GLY 3.2 12.8 - - - +
133A ILE* 3.8 25.4 - - + -
169A ALA* 3.2 24.4 - - - +
174A SER* 3.1 16.6 + - - +
175A GLY* 1.3 78.8 - - - +
177A ARG* 1.3 67.2 + - - +
178A LEU* 3.6 4.8 - - + +
239A ASN* 4.2 2.4 + - - +
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Residues in contact with ARG 177 (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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1A HIS* 3.4 20.4 + - - -
6A LYS* 5.7 1.0 - - - +
131A GLY 3.0 12.4 + - - +
132A ILE* 3.2 27.9 - - + +
133A ILE 2.8 25.5 + - - -
175A GLY 5.1 3.4 - - - +
176A VAL* 1.3 76.3 - - - +
178A LEU* 1.3 61.2 + - - +
179A ASN* 3.9 2.4 - - - +
232A LEU 2.9 20.6 + - - -
233A ILE* 2.9 28.9 + - - +
235A ASP 3.0 13.8 + - - -
236A ASP* 3.3 24.2 + - - +
238A LEU 3.0 34.3 + - - +
239A ASN* 3.2 14.6 - - + +
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Residues in contact with LEU 178 (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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115A THR* 3.4 33.4 - - + +
119A LEU* 4.6 8.5 - - + -
133A ILE* 3.3 23.1 - - + +
135A ASN* 5.2 3.4 - - - +
162A THR* 3.7 15.6 - - + +
165A ALA* 3.7 34.8 - - + +
166A ALA* 3.7 11.0 - - - +
169A ALA* 3.7 8.7 - - + -
176A VAL* 3.6 24.9 - - + +
177A ARG* 1.3 76.7 - - - +
179A ASN* 1.3 57.5 + - - +
239A ASN* 2.9 7.1 + - - +
240A GLY* 2.7 34.0 + - - -
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Residues in contact with ASN 179 (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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132A ILE* 3.7 25.9 - - - +
133A ILE 3.0 8.2 + - - +
134A ILE* 3.3 6.8 - - + -
135A ASN* 3.0 22.2 + - - -
162A THR* 3.5 10.7 - - - +
177A ARG* 3.9 3.6 - - - +
178A LEU* 1.3 73.8 - - - +
180A ALA* 1.3 59.4 + - - +
232A LEU* 4.0 31.9 - - + +
238A LEU 3.0 22.7 + - - +
239A ASN* 3.3 5.0 - - - -
240A GLY 3.1 8.0 + - - -
241A ALA* 2.8 35.7 + - - +
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Residues in contact with ALA 180 (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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135A ASN 3.0 14.8 - - - +
137A SER* 4.4 16.4 - - - -
158A ILE* 4.5 3.4 - - + +
159A VAL* 5.2 1.3 - - + -
162A THR* 3.9 14.9 - - - +
179A ASN* 1.3 74.1 - - - +
181A ILE* 1.3 65.7 + - - +
182A CYS* 5.0 2.0 - - - -
232A LEU* 4.6 1.1 - - - +
241A ALA 3.0 8.7 + - - +
242A ILE* 3.6 21.0 - - + -
243A MET* 2.9 29.1 + - - +
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Residues in contact with ILE 181 (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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21A PHE* 4.3 6.5 - - + -
134A ILE* 3.8 19.7 - - + -
135A ASN 3.1 5.9 + - - -
136A MET* 3.8 18.4 - - + -
137A SER 2.8 32.6 + - - -
180A ALA* 1.3 73.0 - - - +
182A CYS* 1.3 63.3 + - - +
183A PRO* 3.4 21.5 - - + +
225A ILE* 4.2 5.8 - - + +
228A GLY 4.4 1.1 - - - -
229A LEU* 4.0 28.0 - - + +
232A LEU* 3.6 25.4 - - + -
243A MET* 3.3 11.4 - - - +
245A ILE* 3.7 27.1 - - + -
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Residues in contact with CYS 182 (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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137A SER* 3.7 19.7 - - - -
138A SER 3.3 27.8 - - - +
139A LEU* 3.6 8.4 - - - +
142A LEU* 4.1 9.0 - - + -
159A VAL* 4.2 5.2 - - - -
180A ALA* 5.0 0.9 - - - -
181A ILE* 1.3 72.4 - - - +
183A PRO* 1.3 66.3 - - - +
242A ILE* 3.5 30.1 - - - -
243A MET 2.6 13.9 + - - +
244A LYS* 3.3 15.3 - - + -
245A ILE 3.2 18.2 + - - -
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Residues in contact with PRO 183 (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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17A ILE* 4.8 0.9 - - + -
136A MET* 3.7 19.3 - - + -
137A SER 3.9 0.4 - - - +
138A SER* 3.7 5.1 + - - -
139A LEU* 2.9 22.1 + - - +
181A ILE* 3.4 20.2 - - + +
182A CYS* 1.3 87.0 - - - +
184A GLY* 1.3 72.2 + - - +
186A VAL* 3.8 15.3 - - + -
225A ILE* 3.9 20.9 - - + -
245A ILE* 3.4 8.7 - - + +
300A NAD 3.6 26.3 - - + -
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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