Contacts of the helix formed by residues 252 - 262 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C MSE 3.6 39.9 - - + -
100C ARG* 3.8 24.2 - - + +
103C ASN* 3.9 7.2 - - - +
251C PHE* 1.3 77.8 - - - +
253C LEU* 1.3 64.1 + - - +
254C TYR* 3.3 10.8 + - - +
255C ASP* 3.0 38.3 + - - +
256C VAL* 3.0 16.5 + - - +
275C ILE* 3.5 8.1 - - - -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MSE 5.2 1.0 - - - -
252C THR* 1.3 74.2 - - - +
254C TYR* 1.3 69.7 + - + +
256C VAL* 3.3 6.8 + - + +
257C TYR* 3.0 25.8 + - - +
275C ILE* 3.2 15.6 - - + +
283C LYS* 3.8 46.7 - - + +
284C ALA* 4.0 6.3 - - + +
287C VAL* 3.9 14.3 - - + +
286F ALA 4.0 10.5 - - - +
289F GLU* 4.1 21.8 - - + +
290F ALA* 3.7 24.6 - - + +
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MSE 4.0 23.8 - - + -
252C THR* 3.1 5.1 - - - +
253C LEU* 1.3 86.4 - - + +
255C ASP* 1.3 61.6 + - - +
257C TYR* 3.4 6.8 + - - +
258C GLU* 2.9 35.3 + - + +
289F GLU* 3.5 41.5 + - + +
290F ALA* 3.3 23.1 - - - -
292F GLY* 4.8 1.1 - - - -
226H VAL* 4.5 8.6 - - + +
228H TRP* 3.4 62.9 - + + +
229H SER* 4.2 12.1 - - - -
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 3.0 35.6 + - - -
230C ILE* 4.1 2.4 - - - +
249C ALA 3.7 15.7 - - - +
250C ALA* 4.0 1.3 - - - -
251C PHE 3.1 9.1 + - - +
252C THR* 3.0 35.9 + - - +
254C TYR* 1.3 76.9 - - - +
256C VAL* 1.3 57.6 + - - +
258C GLU* 3.2 6.6 + - - +
259C ILE* 2.9 35.9 + - - +
2300C GOL 3.9 16.1 + - - -
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA* 4.5 9.6 - - + -
252C THR 3.0 14.4 + - - +
253C LEU* 3.5 8.7 - - - +
255C ASP* 1.3 76.5 - - - +
257C TYR* 1.3 62.6 + - - +
259C ILE* 3.3 10.3 + - - +
260C CYS* 3.0 24.8 + - - -
268C ILE* 3.9 22.7 - - + -
270C ILE* 4.0 23.6 - - + -
284C ALA* 4.0 33.9 - - + +
287C VAL* 4.0 13.9 - - + -
288C ALA* 4.6 2.0 - - + +
295C ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU 3.0 15.8 + - - +
254C TYR 3.7 5.2 - - - +
256C VAL* 1.3 75.8 - - - +
258C GLU* 1.3 70.8 + - - +
260C CYS* 3.2 2.3 + - - +
261C ARG* 2.8 54.4 + - + +
287C VAL* 3.9 15.9 - - + +
257F TYR* 3.8 31.6 - + - -
260F CYS* 3.3 35.7 + - + +
261F ARG* 3.3 7.1 + - - -
263F ARG* 4.5 5.8 + - - -
287F VAL* 4.8 4.7 - - + -
290F ALA* 3.6 33.2 - - + +
291F ALA* 3.7 24.6 - - + +
229H SER* 6.0 0.4 - - - -
231H PRO* 5.1 5.6 - - + -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE* 3.7 17.9 - - + -
254C TYR* 2.9 23.0 + - + +
255C ASP* 3.2 5.8 + - - +
257C TYR* 1.3 82.4 - - - +
259C ILE* 1.3 63.6 + - - +
261C ARG* 2.7 41.9 + - - -
262C GLN* 2.9 51.8 + - - +
2300C GOL 6.0 0.2 - - - +
230H ILE* 6.3 0.2 - - - -
231H PRO* 3.3 23.9 - - - +
258H GLU* 4.9 0.9 - - - +
262H GLN* 4.6 7.4 + - - -
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE* 3.9 14.1 - - + -
233C MSE 4.1 10.5 - - + -
246C ALA* 3.8 13.7 - - + -
249C ALA 4.1 5.2 - - - +
250C ALA* 3.4 39.0 - - + +
255C ASP 2.9 20.7 + - - +
256C VAL* 3.6 5.6 - - - +
258C GLU* 1.3 76.0 - - - +
260C CYS* 1.3 57.4 + - - +
263C ARG* 3.0 7.6 + - - -
264C ALA* 3.0 34.8 + - + -
265C ALA* 3.9 32.8 - - + +
268C ILE* 4.1 16.4 - - + -
293C LEU* 5.3 1.8 - - + +
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Residues in contact with CYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL* 3.0 20.6 + - - +
257C TYR* 3.5 6.7 - - - +
259C ILE* 1.3 74.2 - - - +
261C ARG* 1.3 66.1 + - - +
263C ARG* 3.0 27.7 + - - -
268C ILE* 3.8 20.6 - - - -
287C VAL* 4.1 8.3 - - + -
288C ALA* 3.9 13.9 - - - -
291C ALA* 3.6 23.1 - - + -
293C LEU* 3.9 12.6 - - - -
257F TYR* 3.2 20.3 + - + +
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Residues in contact with ARG 261 (chain C).
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* 2.8 47.7 + - + +
258C GLU* 2.7 58.5 + - - +
260C CYS* 1.3 74.1 - - - +
262C GLN* 1.3 70.5 + - + +
263C ARG* 3.6 6.5 + - - +
257F TYR* 3.2 11.4 + - - +
261F ARG* 4.9 26.2 + - + +
231H PRO* 3.8 19.3 - - - +
261H ARG* 5.3 1.8 - - - +
262H GLN* 4.1 14.6 + - - +
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Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE* 3.6 22.4 - - - +
231C PRO* 3.7 14.1 - - - +
234C ALA* 4.4 9.8 - - + +
238C GLU* 5.0 4.3 - - - +
258C GLU* 2.9 50.2 + - - +
259C ILE 4.2 1.6 - - - +
261C ARG* 1.3 88.8 - - + +
263C ARG* 1.3 71.1 + - - +
264C ALA* 3.1 10.4 + - + +
258H GLU* 4.4 3.8 + - - -
261H ARG* 3.6 26.7 + - - +
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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