Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 1GQF
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 PHE 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A LYS* 3.5 20.4 - - + -
166A ILE* 3.7 27.8 - - + -
198A PHE* 4.4 2.2 - - - -
215A LEU* 4.4 1.8 - - + -
218A ALA* 4.0 16.6 - - + -
224A HIS* 4.2 17.3 - + - +
229A CYS* 1.3 77.6 - - - +
231A ALA* 1.3 69.8 + - - +
232A CYS* 3.9 20.9 - - + -
265A PHE* 3.6 36.1 - + - -
273A LEU* 3.8 22.7 - - + -
277A PRO 3.1 6.8 + - - +
278A LYS* 3.4 11.6 - - + -
279A LEU* 2.7 33.9 + - - +
280A PHE* 4.5 6.1 - + - -
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Residues in contact with ALA 231 (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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164A LYS 3.0 7.4 + - - +
165A CYS* 3.0 15.4 - - - -
166A ILE 2.9 22.7 + - - -
193A PHE* 4.4 11.0 - - + -
198A PHE* 3.6 28.0 - - + -
230A PHE* 1.3 83.9 - - - +
232A CYS* 1.3 60.3 + - - +
279A LEU* 3.2 18.4 - - + +
281A PHE* 4.4 2.2 - - + -
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Residues in contact with CYS 232 (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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166A ILE* 3.3 13.9 - - + +
215A LEU* 4.1 21.1 - - + -
230A PHE* 3.9 14.3 - - + -
231A ALA* 1.3 74.7 - - - +
233A ILE* 1.3 67.7 + - - +
234A LEU* 3.3 28.2 - - - +
261A LEU* 5.9 0.2 - - - -
279A LEU 2.8 6.5 + - - +
280A PHE* 3.4 31.6 - - + +
281A PHE* 2.8 25.5 + - - +
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Residues in contact with ILE 233 (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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165A CYS* 4.0 9.2 - - - -
166A ILE 2.7 14.1 + - - +
167A ILE* 3.9 23.6 - - + -
168A ILE 2.9 28.1 + - - +
189A LEU* 3.6 34.8 - - + -
193A PHE* 3.8 35.7 - - + -
232A CYS* 1.3 79.4 - - - +
234A LEU* 1.3 68.8 + - - +
235A LEU* 3.7 13.9 - - + -
281A PHE* 3.1 26.0 - - + +
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Residues in contact with LEU 234 (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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168A ILE* 3.8 24.0 - - + -
211A MET* 4.7 7.0 - - + -
232A CYS* 3.3 32.1 - - - +
233A ILE* 1.3 75.3 - - - +
235A LEU* 1.3 66.4 + - - +
236A SER 4.0 1.1 - - - -
243A ILE* 4.6 13.5 - - + -
258A ILE* 5.1 4.0 - - + -
261A LEU* 4.0 26.7 - - + -
280A PHE* 4.7 8.1 - - + -
281A PHE 2.8 10.5 + - - +
282A ILE* 3.5 42.1 - - + -
283A GLN 2.9 28.6 + - - +
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Residues in contact with LEU 235 (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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167A ILE* 4.6 4.0 - - + -
168A ILE* 3.0 15.1 + - - +
169A ASN* 3.5 24.2 - - + +
170A ASN* 3.1 28.8 + - - +
179A ARG* 3.7 15.7 + - - +
182A THR 4.2 2.0 - - - +
185A ASP* 4.3 4.5 - - + +
186A ALA* 3.8 20.2 - - + +
189A LEU* 3.7 24.7 - - + -
211A MET* 6.1 0.4 - - - +
233A ILE* 3.7 19.3 - - + -
234A LEU* 1.3 86.6 - - - +
236A SER* 1.3 58.9 + - - +
282A ILE 5.6 0.2 - - - -
283A GLN* 3.6 22.4 - - + -
350A VAL* 4.6 6.3 - - + -
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Residues in contact with SER 236 (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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170A ASN* 4.0 9.4 - - - -
173A PHE* 3.0 14.2 - - - -
179A ARG* 3.1 25.0 + - - +
211A MET* 5.4 0.7 - - - -
235A LEU* 1.3 78.2 - - - +
237A HIS* 1.3 69.5 + - - +
243A ILE* 3.3 17.5 - - - +
244A TYR* 2.6 30.9 + - - +
283A GLN 3.1 8.0 + - - +
284A ALA* 3.1 20.3 - - - -
285A ALA 3.7 1.0 + - - -
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Residues in contact with HIS 237 (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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173A PHE* 3.5 22.4 - + - -
176A MET* 3.3 44.4 - - + +
177A GLY 2.8 29.3 + - - -
178A VAL 5.1 0.7 - - - -
179A ARG* 3.3 24.1 - - + +
236A SER* 1.3 80.7 + - - +
238A GLY* 1.3 60.5 + - - +
243A ILE* 3.3 5.2 - - - +
244A TYR* 2.9 45.8 + - + +
284A ALA* 3.9 0.4 - - - -
285A ALA 3.3 7.6 + - - +
286A ARG 4.9 0.4 + - - -
287A GLY* 4.3 9.6 - - - +
288A THR* 5.5 3.6 - - + -
1403A SO4 4.1 12.6 + - - -
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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