Contacts of the helix formed by residues 258 - 272 (chain A) in PDB entry 2GH0
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LEU 4.7 2.2 - - - +
255A CYS 3.1 8.8 + - - +
256A PHE 4.3 2.5 - - - -
257A SER* 1.3 82.4 + - - +
259A PRO* 1.3 75.3 - - - +
260A LEU* 3.3 15.6 + - - +
261A CYS* 2.9 29.6 + - + +
262A ARG* 3.1 20.3 + - - +
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Residues in contact with PRO 259 (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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256A PHE 4.9 0.4 - - - +
257A SER 3.9 7.9 - - - +
258A ASP* 1.3 88.6 - - - +
260A LEU* 1.3 61.4 + - - +
262A ARG* 3.5 8.1 + - + +
263A SER* 3.1 24.8 + - - -
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Residues in contact with LEU 260 (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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198A ARG* 4.3 14.1 - - - +
201A LEU* 4.1 29.2 - - + -
258A ASP* 3.3 14.9 + - - +
259A PRO* 1.3 73.6 - - - +
261A CYS* 1.3 68.9 + - - +
263A SER* 3.3 7.4 + - - -
264A ARG* 3.0 63.4 + - + +
298A THR* 5.2 3.6 - - + -
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Residues in contact with CYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A CYS* 2.1 57.9 - - - +
258A ASP* 2.9 20.7 + - + +
260A LEU* 1.3 70.9 - - - +
262A ARG* 1.3 67.5 + - - +
264A ARG* 3.2 1.6 + - - +
265A LEU 3.0 19.6 + - - -
295A LEU* 5.0 1.3 - - - -
298A THR* 3.7 35.0 - - + -
299A ALA* 4.1 7.6 - - + +
300A MET* 3.8 9.2 - - - -
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Residues in contact with ARG 262 (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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255A CYS* 3.7 10.1 + - - +
256A PHE* 3.5 68.0 + - + +
258A ASP 3.1 13.2 + - - +
259A PRO* 3.8 11.4 - - + +
261A CYS* 1.3 75.5 - - - +
263A SER* 1.3 58.2 + - - +
265A LEU* 3.2 4.2 + - - +
266A VAL* 2.8 40.0 + - + +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO 3.1 17.8 + - - -
260A LEU* 3.6 9.4 - - - +
262A ARG* 1.3 77.8 - - - +
264A ARG* 1.3 58.8 + - - +
266A VAL* 3.4 8.4 + - - +
267A ASP* 2.9 35.5 + - - +
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Residues in contact with ARG 264 (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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201A LEU* 3.8 22.0 + - - +
205A GLU* 4.5 24.0 + - - +
260A LEU* 3.0 44.9 + - + +
261A CYS 3.8 2.5 - - - +
263A SER* 1.3 77.8 + - - +
265A LEU* 1.3 58.8 + - - +
267A ASP* 2.7 30.4 + - - +
268A PHE* 3.1 16.5 + - - +
291A ALA 4.4 0.3 - - - +
294A GLY* 3.0 44.9 + - - +
295A LEU* 3.7 16.3 - - + +
298A THR* 4.3 9.2 - - + -
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Residues in contact with LEU 265 (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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252A ARG* 3.8 34.5 - - + -
255A CYS* 4.3 10.3 - - - -
256A PHE* 4.0 13.9 - - + -
261A CYS 3.0 15.6 + - - +
262A ARG* 3.7 4.0 - - - +
264A ARG* 1.3 74.2 - - - +
266A VAL* 1.3 65.1 + - + +
268A PHE* 3.3 9.0 + - + +
269A GLN* 3.1 47.8 + - + +
295A LEU* 3.7 13.8 - - + +
300A MET* 3.9 22.0 - - + -
331A LEU* 5.0 2.2 - - + -
334A PHE* 6.3 0.2 - - + -
335A PHE* 4.1 22.4 - - + -
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 6.4 1.3 - - + -
262A ARG* 2.8 32.6 + - + +
263A SER* 3.6 8.5 - - - +
264A ARG 3.4 0.2 - - - -
265A LEU* 1.3 76.9 - - - +
267A ASP* 1.3 66.0 + - - +
269A GLN* 3.3 15.4 + - - +
270A THR* 3.0 34.8 + - - +
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Residues in contact with ASP 267 (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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263A SER* 2.9 24.1 + - - +
264A ARG* 2.7 34.5 - - - +
265A LEU 3.3 0.2 - - - -
266A VAL* 1.3 78.6 - - + +
268A PHE* 1.3 57.3 + - - +
270A THR* 4.2 5.4 - - - -
271A HIS* 2.9 50.4 + - + +
291A ALA* 3.6 20.6 - - + +
294A GLY* 5.7 0.2 - - - -
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Residues in contact with PHE 268 (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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264A ARG 3.1 11.4 + - - +
265A LEU* 3.7 9.2 - - + +
266A VAL 3.2 0.2 - - - -
267A ASP* 1.3 76.2 + - - +
269A GLN* 1.3 59.5 + - - +
272A CYS* 2.8 68.4 + - + +
291A ALA* 3.7 11.2 - - - +
292A TYR* 3.8 31.4 - + - -
295A LEU* 3.6 19.1 - - + -
334A PHE* 3.1 46.8 - + - -
335A PHE* 3.4 42.4 - + - -
341A LEU* 4.2 8.7 - - + -
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Residues in contact with GLN 269 (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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252A ARG* 5.3 6.5 - - - +
256A PHE* 6.1 0.6 - - - -
265A LEU* 3.1 40.1 + - + +
266A VAL* 3.3 17.7 + - - +
268A PHE* 1.3 78.7 - - + +
270A THR* 1.3 56.6 + - - +
273A HIS* 3.2 28.1 + - - +
331A LEU* 5.0 10.3 - - - +
334A PHE* 3.7 24.2 - - + -
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Residues in contact with THR 270 (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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266A VAL* 3.0 26.6 + - - +
267A ASP* 3.3 7.4 + - - -
269A GLN* 1.3 76.2 - - - +
271A HIS* 1.3 81.8 + - + +
273A HIS* 4.5 0.3 - - - +
282A ALA* 3.4 22.3 - - - +
283A THR* 4.5 7.1 - - + +
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Residues in contact with HIS 271 (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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267A ASP* 2.9 39.8 + - + +
270A THR* 1.3 92.2 - - + +
272A CYS* 1.3 62.7 + - - +
273A HIS 3.4 1.4 + - - -
281A CYS* 3.7 15.9 - - - +
282A ALA 3.8 4.2 + - - -
283A THR* 2.9 40.8 + - + +
287A ARG* 3.5 44.2 + - + +
288A CYS* 3.6 15.3 - - - +
291A ALA* 4.3 5.1 - - + +
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Residues in contact with CYS 272 (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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268A PHE* 2.8 51.7 + - + +
271A HIS* 1.3 76.2 - - - +
273A HIS* 1.3 62.7 + - - +
274A PRO 3.5 1.2 - - - -
288A CYS* 2.2 62.4 - - - -
291A ALA* 4.7 0.4 - - - -
292A TYR 4.5 0.2 - - - -
334A PHE* 3.8 4.3 - - + -
338A ASN* 3.0 26.9 + - - +
340A CYS* 3.5 6.5 - - - -
341A LEU* 4.5 1.6 - - + -
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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