Contacts of the strand formed by residues 182 - 187 (chain A) in PDB entry 2G5W
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.4 15.5 - - - -
105A CYS 3.1 19.4 + - - -
176A ILE* 4.1 8.1 - - - -
180A PHE* 3.2 9.9 - - - +
181A ASP* 1.3 81.2 - - - +
183A ILE* 1.3 69.0 + - - +
234A LYS* 3.1 17.9 - - - -
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Residues in contact with ILE 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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104A PHE* 3.3 9.3 - - - -
105A CYS* 3.2 13.5 - - + +
107A LEU* 4.0 12.1 - - + -
172A ALA* 4.0 16.2 - - + +
175A ALA* 3.5 28.0 - - + -
176A ILE* 5.7 0.2 - - + -
182A GLY* 1.3 79.0 - - - +
184A GLU* 1.3 60.8 + - - +
185A ILE* 3.6 24.7 - - + -
226A VAL* 3.4 28.0 - - + -
230A ILE* 3.8 19.5 - - + -
234A LYS 2.9 7.6 + - - +
235A VAL* 3.4 9.7 - - + -
236A GLY 2.8 23.7 + - - -
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.5 14.7 - - - +
61A ILE* 3.4 10.1 - - + +
104A PHE* 4.2 2.2 - - + -
105A CYS 3.0 7.1 + - - -
106A GLN* 2.5 37.6 + - + +
107A LEU* 2.8 32.2 + - - +
183A ILE* 1.3 76.0 - - - +
185A ILE* 1.3 69.9 + - - +
186A HIS 3.5 0.7 + - - -
236A GLY 3.3 8.1 - - - +
238A ARG* 3.7 14.6 - - + +
277A TYR* 2.6 35.3 + - + +
279A HIS* 2.9 23.8 + - - -
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Residues in contact with ILE 185 (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 LEU* 4.3 5.8 - - + -
168A TYR* 4.0 19.7 - - + -
183A ILE* 3.6 22.0 - - + -
184A GLU* 1.3 70.9 - - - +
186A HIS* 1.3 58.5 + - - +
187A GLY 3.1 4.4 + - - +
193A ILE* 3.3 31.6 - - + -
219A LEU* 4.0 15.5 - - + -
222A VAL* 4.1 9.4 - - + -
223A VAL* 4.7 7.0 - - + -
226A VAL* 4.0 20.6 - - + -
235A VAL* 4.5 7.2 - - + -
236A GLY 2.8 19.0 + - - +
237A VAL* 4.4 11.4 - - + -
238A ARG* 2.8 31.4 + - - +
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Residues in contact with HIS 186 (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 GLN* 3.0 36.8 + - + +
107A LEU 3.3 23.2 + - - +
108A TRP* 3.3 31.5 + + + -
109A HIS 5.2 2.3 + - - +
168A TYR* 4.8 2.1 + - - -
184A GLU 3.5 2.2 + - - -
185A ILE* 1.3 68.8 - - - +
187A GLY* 1.3 56.8 + - - +
188A ALA* 3.4 27.3 + - + +
189A HIS* 3.4 18.4 - - - -
191A TYR* 3.7 14.9 - + - +
193A ILE* 3.5 16.3 + - - +
238A ARG* 4.4 1.9 - - - -
401A FMN 3.0 27.9 + - - -
402A 8PG 3.4 7.5 + - - -
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Residues in contact with GLY 187 (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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185A ILE* 3.1 5.5 + - - -
186A HIS* 1.3 71.7 - - - +
188A ALA* 1.3 57.5 + - - +
191A TYR* 6.3 0.2 - - - -
193A ILE* 3.7 26.0 - - - -
194A ASP* 4.0 11.1 - - - +
197A LEU* 3.8 21.5 - - - +
219A LEU* 5.1 1.8 - - - -
238A ARG 2.8 21.9 + - - +
239A VAL* 3.8 9.6 - - - +
240A SER 4.3 0.3 + - - -
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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