Contacts of the helix formed by residues 258 - 272 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B LEU 3.6 6.0 + - - +
255B CYS 3.0 7.3 + - - +
256B PHE 4.4 0.4 - - - -
257B SER* 1.3 78.7 - - - +
259B PRO* 1.3 65.3 - - - +
260B LEU* 3.6 11.8 + - - +
261B CYS* 3.0 31.1 + - + +
262B ARG* 2.8 35.5 + - - +
299B ALA* 6.5 0.4 - - + -
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Residues in contact with PRO 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B SER 4.1 4.5 - - - +
258B ASP* 1.3 89.6 - - - +
260B LEU* 1.3 63.3 + - - +
262B ARG* 3.7 28.7 - - + +
263B SER* 3.0 24.3 + - - -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ARG* 5.1 10.1 - - - +
201B LEU* 4.1 28.7 - - + -
205B GLU* 5.8 1.6 - - - +
258B ASP* 3.3 10.5 + - - +
259B PRO* 1.3 78.9 - - - +
261B CYS* 1.3 64.8 + - - +
263B SER* 3.1 11.5 + - - -
264B ARG* 2.9 58.7 + - + +
298B THR* 5.6 2.0 - - + -
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Residues in contact with CYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B CYS* 2.1 64.3 - - - +
258B ASP* 3.0 22.1 + - + +
260B LEU* 1.3 73.3 - - - +
262B ARG* 1.3 64.0 + - - +
264B ARG* 3.1 3.1 + - - +
265B LEU 2.9 21.0 + - - -
295B LEU* 5.6 0.9 - - - -
298B THR* 3.6 40.6 - - - +
299B ALA* 4.1 9.0 - - + +
300B MET* 4.4 3.1 - - - -
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B CYS* 3.3 11.8 + - - +
256B PHE* 2.9 54.2 + - + +
257B SER* 4.7 6.9 + - - +
258B ASP 2.8 19.7 + - - +
259B PRO* 3.7 28.1 - - - +
261B CYS* 1.3 71.9 - - - +
263B SER* 1.3 64.4 + - - +
265B LEU* 3.3 3.4 + - - +
266B VAL* 3.0 35.2 + - + +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PRO 3.0 14.5 + - - -
260B LEU* 3.1 16.8 + - - -
262B ARG* 1.3 77.3 - - - +
264B ARG* 1.3 63.9 + - - +
266B VAL* 3.3 6.3 + - - +
267B ASP* 3.0 35.9 + - - +
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 3.8 19.0 + - - +
204B PHE* 6.4 0.4 - - - +
205B GLU* 4.1 27.7 + - - +
260B LEU* 2.9 49.1 + - + +
261B CYS 3.1 6.0 + - - +
263B SER* 1.3 77.6 - - - +
265B LEU* 1.3 61.5 + - - +
267B ASP* 3.4 16.1 + - - +
268B PHE* 3.1 22.5 + - - +
291B ALA 4.6 2.3 - - - +
294B GLY* 2.8 54.3 + - - +
295B LEU* 3.7 12.6 - - + +
298B THR* 4.3 9.6 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 3.7 32.3 - - + -
255B CYS* 3.7 12.8 - - - -
256B PHE* 3.8 18.4 - - + -
261B CYS 2.9 15.8 + - - +
262B ARG* 3.8 4.3 - - - +
264B ARG* 1.3 74.1 - - - +
266B VAL* 1.3 66.3 + - + +
268B PHE* 3.1 16.4 + - + -
269B GLN* 2.9 52.8 + - + +
295B LEU* 3.9 10.9 - - + +
300B MET* 3.8 27.8 - - + -
331B LEU* 5.5 2.9 - - + -
335B PHE* 5.9 0.2 - - + -
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 6.1 3.8 - - + -
262B ARG* 3.0 24.8 + - + +
263B SER* 3.7 9.0 - - - +
265B LEU* 1.3 75.2 - - + +
267B ASP* 1.3 67.3 + - - +
269B GLN* 3.2 15.8 + - - +
270B THR* 2.9 34.8 + - - +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B SER* 3.0 28.1 + - - +
264B ARG* 3.5 19.7 - - - +
265B LEU 3.2 0.2 - - - -
266B VAL* 1.3 81.5 - - - +
268B PHE* 1.3 57.3 + - - +
270B THR* 3.2 4.3 + - - -
271B HIS* 2.9 49.8 + - + +
291B ALA* 3.7 14.0 - - + +
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Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ARG 3.1 10.5 + - - +
265B LEU* 3.1 19.5 + - + +
267B ASP* 1.3 79.2 - - - +
269B GLN* 1.3 60.7 + - + +
272B CYS* 3.0 66.5 + - + +
291B ALA* 3.5 12.5 - - - +
292B TYR* 3.9 27.8 - + - -
295B LEU* 3.6 22.4 - - + -
334B PHE* 3.2 32.4 - + - -
335B PHE* 3.4 35.9 - + - -
341B LEU* 4.1 12.6 - - + -
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ARG* 5.2 8.9 - - - +
256B PHE* 5.8 4.1 - - - -
265B LEU* 2.9 50.6 + - + +
266B VAL* 3.6 16.9 - - - +
268B PHE* 1.3 80.4 - - + +
270B THR* 1.3 61.8 + - - +
273B HIS* 3.6 21.7 + - - +
331B LEU* 5.5 5.3 - - - +
334B PHE* 3.9 19.3 - - + -
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Residues in contact with THR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B VAL* 2.9 26.7 + - - +
267B ASP* 3.6 6.0 - - - -
269B GLN* 1.3 81.2 - - - +
271B HIS* 1.3 79.5 + - + +
272B CYS 3.7 0.2 + - - -
273B HIS* 4.0 1.0 + - - +
282B ALA* 3.2 26.2 - - - +
283B THR* 4.5 7.0 - - + +
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 2.9 39.1 + - + +
270B THR* 1.3 89.7 - - + +
272B CYS* 1.3 60.7 + - - +
273B HIS 3.4 0.6 + - - -
281B CYS* 3.6 21.7 - - - +
282B ALA 4.0 2.4 + - - -
283B THR* 2.8 44.0 + - + +
284B GLU 4.3 0.2 - - - +
287B ARG* 3.7 47.2 + - + +
288B CYS* 3.6 6.2 - - - +
291B ALA* 4.3 4.1 - - + +
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Residues in contact with CYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.0 47.2 + - + +
271B HIS* 1.3 75.6 - - - +
273B HIS* 1.3 63.1 + - - +
274B PRO 3.3 1.0 - - - -
288B CYS* 2.1 62.8 - - - -
291B ALA* 4.7 2.0 - - - -
292B TYR 4.6 0.2 - - - -
334B PHE* 4.0 7.4 - - + -
338B ASN* 2.9 23.2 - - - +
340B CYS* 3.4 9.7 - - - -
341B LEU* 4.3 2.0 - - + -
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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