Contacts of the helix formed by residues 252 - 262 (chain F) in PDB entry 2PGW
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 THR 252 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F MSE 3.6 40.1 - - + -
100F ARG* 3.8 23.1 - - + +
103F ASN* 3.9 9.2 - - - +
251F PHE* 1.3 80.2 - - - +
253F LEU* 1.3 65.1 + - - +
254F TYR* 3.3 9.8 + - - +
255F ASP* 3.0 27.1 + - - +
256F VAL* 3.0 25.6 + - - +
275F ILE* 4.3 4.7 - - - -
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Residues in contact with LEU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C ALA 4.2 4.0 - - - +
289C GLU* 4.0 36.1 - - + +
290C ALA* 3.8 17.7 - - + +
99F MSE 5.2 1.5 - - - -
252F THR* 1.3 75.0 - - - +
254F TYR* 1.3 68.2 + - + +
256F VAL* 3.4 6.8 + - - +
257F TYR* 3.0 25.5 + - - +
275F ILE* 4.0 16.4 - - + +
283F LYS* 3.9 36.1 - - + +
284F ALA* 4.0 4.9 - - + +
287F VAL* 3.9 28.1 - - + +
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Residues in contact with TYR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B VAL* 5.3 5.6 - - + +
228B TRP* 3.4 66.0 - + + +
229B SER* 4.5 8.1 - - - -
289C GLU* 3.4 42.9 + - + +
290C ALA* 3.2 24.7 - - - -
292C GLY* 4.8 0.9 - - - -
99F MSE 4.0 24.5 - - + -
252F THR* 3.1 5.3 - - - +
253F LEU* 1.3 84.0 - - + +
255F ASP* 1.3 66.8 + - - +
257F TYR* 3.2 7.5 + - - +
258F GLU* 2.9 29.2 + - + +
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Residues in contact with ASP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ARG* 3.0 35.8 + - - -
230F ILE* 5.0 3.6 - - + +
249F ALA 3.6 15.7 - - - +
250F ALA* 3.9 1.3 - - - -
251F PHE 3.1 9.2 + - - +
252F THR* 3.0 34.2 + - - +
254F TYR* 1.3 77.0 - - - +
256F VAL* 1.3 64.1 + - - +
258F GLU* 3.1 8.6 + - - +
259F ILE* 2.9 29.8 + - - +
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ALA* 4.4 9.2 - - + -
252F THR 3.0 14.7 + - - +
253F LEU* 3.4 9.2 - - - +
255F ASP* 1.3 76.4 - - - +
257F TYR* 1.3 63.2 + - - +
259F ILE* 3.3 5.2 + - - +
260F CYS* 3.0 26.0 + - - -
268F ILE* 3.9 25.5 - - + +
270F ILE* 3.8 25.1 - - + -
284F ALA* 3.9 34.1 - - + +
287F VAL* 3.9 14.4 - - + -
288F ALA* 4.5 1.8 - - + +
295F ILE* 5.6 0.7 - - + -
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Residues in contact with TYR 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 5.9 0.7 - - - -
231B PRO* 5.3 4.7 - - + -
257C TYR* 3.8 28.0 - + - -
260C CYS* 3.2 15.4 + - + +
261C ARG* 3.2 29.6 + - - -
263C ARG* 4.6 5.5 + - - -
287C VAL* 4.8 4.5 - - + -
290C ALA* 3.6 33.7 - - + +
291C ALA* 3.7 23.6 - - + +
253F LEU 3.0 13.8 + - - +
254F TYR* 3.2 7.8 + - - +
256F VAL* 1.3 75.4 - - - +
258F GLU* 1.3 68.1 + - - +
260F CYS* 3.3 1.8 + - - +
261F ARG* 2.8 54.7 + - + +
287F VAL* 3.9 21.3 - - + +
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Residues in contact with GLU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PRO* 3.4 18.2 - - - +
258B GLU* 4.8 1.2 - - - +
262B GLN* 4.3 6.1 + - - -
230F ILE* 4.5 10.5 - - + -
254F TYR* 2.9 19.2 + - + +
255F ASP* 3.1 10.5 + - - +
257F TYR* 1.3 80.2 - - + +
259F ILE* 1.3 65.8 + - - +
261F ARG* 2.7 45.1 + - - -
262F GLN* 2.8 54.9 + - - +
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Residues in contact with ILE 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ILE* 3.5 28.9 - - + -
233F MSE 4.0 3.4 - - + -
246F ALA* 3.9 14.6 - - + -
249F ALA 4.1 0.7 - - - +
250F ALA* 3.4 35.9 - - + +
255F ASP 2.9 19.6 + - - +
256F VAL* 3.7 5.2 - - - +
258F GLU* 1.3 75.2 - - - +
260F CYS* 1.3 58.2 + - - +
263F ARG* 2.9 8.1 + - - -
264F ALA* 2.9 36.5 + - + -
265F ALA* 3.7 35.0 - - + +
268F ILE* 4.0 15.7 - - + -
293F LEU* 5.3 1.6 - - + +
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Residues in contact with CYS 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C TYR* 3.3 20.0 + - + +
256F VAL* 3.0 25.0 + - - +
257F TYR* 3.5 7.0 - - - +
259F ILE* 1.3 76.1 - - - +
261F ARG* 1.3 58.4 + - - +
263F ARG* 2.9 33.8 + - - -
268F ILE* 4.1 7.9 - - - -
287F VAL* 4.0 9.4 - - + -
288F ALA* 3.9 20.0 - - - -
291F ALA* 3.6 22.7 - - + -
293F LEU* 4.0 17.9 - - - -
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Residues in contact with ARG 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PRO* 3.5 23.4 - - - +
261B ARG* 4.9 2.4 - - - +
262B GLN* 3.6 19.8 + - - +
257C TYR* 3.3 11.2 + - - +
261C ARG* 4.9 27.0 + - + +
263C ARG* 6.5 0.9 - - - +
257F TYR* 2.8 48.0 + - + +
258F GLU* 2.7 43.0 + - - +
260F CYS* 1.3 74.6 - - - +
262F GLN* 1.3 69.6 + - + +
263F ARG* 3.6 6.1 + - - +
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Residues in contact with GLN 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B GLU* 4.7 3.2 + - - -
261B ARG* 3.9 17.7 + - - +
230F ILE* 3.5 23.9 - - - +
231F PRO* 3.7 22.5 - - - +
234F ALA* 4.3 10.3 - - + +
238F GLU* 5.1 3.1 - - - +
258F GLU* 2.8 49.3 + - - +
259F ILE 4.2 1.3 - - - +
261F ARG* 1.3 86.3 - - + +
263F ARG* 1.3 72.5 + - - +
264F ALA* 3.1 9.8 + - + +
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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