Contacts of the helix formed by residues 262 - 271 (chain D) in PDB entry 4GQS
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 ASP 262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D THR* 5.7 0.9 - - - -
144D ARG* 5.2 4.9 - - - +
181D ILE 4.3 3.1 - - - +
182D ILE 3.1 18.2 - - - +
183D PHE* 3.3 1.9 - - - -
184D GLN* 2.5 33.3 + - - +
251D HIS* 2.7 34.4 + - - -
260D PRO* 3.4 5.2 - - - +
261D ARG* 1.3 77.7 - - - +
263D PHE* 1.3 64.8 + - - +
264D ILE 3.2 2.9 + - - -
265D ASP* 2.9 32.0 + - - +
266D CYS* 3.3 12.3 + - - +
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Residues in contact with PHE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 3.6 25.0 - + - -
127D SER* 3.9 18.2 - - - -
130D THR* 3.6 33.8 - - + +
131D LEU* 3.5 27.4 - - + -
181D ILE* 3.6 23.1 + - + +
182D ILE* 3.6 19.1 - - + +
262D ASP* 1.3 77.2 - - - +
264D ILE* 1.3 64.8 + - + +
266D CYS* 3.0 14.9 + - - +
267D PHE* 3.2 14.3 + + + +
287D LEU* 5.2 11.2 - - + -
290D THR* 4.4 18.8 - - + -
291D ALA* 6.0 4.7 - - + -
294D LEU* 4.3 15.0 - - + -
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Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ILE* 3.7 14.1 + - + +
183D PHE* 3.6 37.2 - - + -
244D ILE* 5.2 1.8 - - + +
247D LYS* 4.0 7.6 - - + -
248D VAL* 3.8 41.5 - - + +
251D HIS* 3.9 27.6 - - + +
262D ASP* 3.2 6.0 + - - +
263D PHE* 1.3 76.9 - - + +
265D ASP* 1.3 52.9 + - - +
267D PHE* 3.3 8.2 + - - +
268D LEU* 2.6 40.0 + - + +
287D LEU* 4.2 14.1 - - + -
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Residues in contact with ASP 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D HIS* 3.3 15.3 - - - +
255D MET* 3.0 23.2 - - + +
260D PRO* 3.9 8.1 - - + -
261D ARG* 3.0 62.9 + - - +
262D ASP* 2.9 25.2 + - - +
264D ILE* 1.3 79.4 - - - +
266D CYS* 1.3 57.8 + - - +
268D LEU* 3.1 1.5 + - - -
269D ILE* 2.8 36.0 + - - +
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Residues in contact with CYS 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.1 19.5 - - + -
130D THR* 4.1 22.0 - - + -
260D PRO* 4.1 22.9 - - - +
262D ASP 3.3 6.8 + - - +
263D PHE 3.0 10.1 + - - +
265D ASP* 1.3 77.7 - - - +
267D PHE* 1.3 55.9 + - - +
269D ILE* 2.8 29.2 + - - +
270D LYS* 2.8 14.8 + - - +
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Residues in contact with PHE 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 4.1 14.4 - - + -
126D PHE* 3.9 23.9 - + + -
263D PHE* 3.2 10.9 + + + +
264D ILE 3.6 3.8 - - - +
266D CYS* 1.3 79.1 - - - +
268D LEU* 1.3 56.9 + - - +
270D LYS* 3.4 4.7 + - - +
271D MET* 2.9 37.8 + - + +
282D PHE* 3.5 45.3 - + - -
283D THR 3.0 28.5 - - - -
286D ASN* 4.2 4.5 - - + -
287D LEU* 3.3 53.8 - - + -
290D THR* 5.0 4.7 - - + -
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Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D VAL* 3.7 34.1 - - + +
251D HIS* 3.5 18.4 - - + +
252D GLN* 3.4 50.3 - - + +
255D MET* 3.5 17.6 - - + +
264D ILE* 2.6 22.1 + - + +
265D ASP 3.2 8.1 - - - +
267D PHE* 1.3 75.9 - - - +
269D ILE* 1.3 58.6 + - - +
271D MET* 3.6 22.5 - - + +
272D GLU* 3.7 7.8 + - - +
287D LEU* 4.3 5.2 - - + -
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D MET* 3.5 18.6 - - + -
257D ILE* 3.5 44.4 - - + +
260D PRO* 4.2 21.5 - - + -
265D ASP 2.8 22.1 + - - +
266D CYS* 2.8 11.8 + - - +
268D LEU* 1.3 74.9 - - - +
270D LYS* 1.3 66.7 + - - +
271D MET 3.1 1.6 - - - -
272D GLU* 2.9 21.7 + - + +
273D LYS* 3.3 35.7 + - - +
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Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.8 10.8 - - + -
266D CYS 2.8 13.8 + - - +
267D PHE* 3.8 8.3 - - - +
269D ILE* 1.3 78.3 - - - +
271D MET* 1.3 63.3 + - - +
272D GLU 3.1 1.0 + - - -
273D LYS* 3.1 16.3 + - + +
274D GLU* 3.1 46.2 + - - +
282D PHE* 3.8 49.1 - - + -
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Residues in contact with MET 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D VAL* 5.8 0.2 - - + -
252D GLN* 4.9 14.6 - - - -
267D PHE* 2.9 36.2 + - + +
268D LEU* 3.6 17.0 - - + +
269D ILE 3.1 0.2 - - - -
270D LYS* 1.3 77.8 - - - +
272D GLU* 1.3 58.7 + - - +
274D GLU* 3.7 3.4 + - - +
275D LYS* 3.4 19.6 + - - +
282D PHE* 3.4 22.7 - - - +
283D THR* 3.5 6.7 - - - -
284D ILE* 3.3 43.5 - - + +
287D LEU* 4.3 7.9 - - + -
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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