Contacts of the helix formed by residues 252 - 262 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2100A GOL 4.5 4.2 + - - +
99G MSE 3.8 37.7 - - + -
100G ARG* 3.8 22.9 - - + +
103G ASN* 4.1 6.1 - - - +
251G PHE* 1.3 77.4 - - - +
253G LEU* 1.3 65.4 + - - +
254G TYR* 3.3 9.1 + - - +
255G ASP* 2.9 42.8 + - - +
256G VAL* 3.1 17.7 + - - +
275G ILE* 3.4 6.7 - - - -
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Residues in contact with LEU 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ALA 4.0 13.9 - - - +
289E GLU* 4.0 27.8 - - + +
290E ALA* 3.9 14.8 - - + +
99G MSE 5.2 1.5 - - - -
252G THR* 1.3 74.0 - - - +
254G TYR* 1.3 67.5 + - + +
256G VAL* 3.3 6.9 + - - +
257G TYR* 3.1 26.2 + - - +
275G ILE* 3.2 13.7 - - + +
280G PRO 5.0 1.1 - - - +
283G LYS* 3.6 47.1 - - + +
284G ALA* 3.7 9.4 - - + +
287G VAL* 3.9 11.2 - - + +
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Residues in contact with TYR 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A VAL* 4.7 8.6 - - + +
228A TRP* 3.5 55.0 - + + +
229A SER* 4.3 9.6 - - - -
2100A GOL 3.4 23.3 - - - +
289E GLU* 3.4 42.9 + - + +
290E ALA* 3.3 23.3 - - - -
292E GLY 4.9 0.2 - - - -
99G MSE 4.0 24.7 - - + -
252G THR* 3.1 2.0 - - - +
253G LEU* 1.3 87.0 - - + +
255G ASP* 1.3 64.1 + - - +
257G TYR* 3.4 6.6 + - - +
258G GLU* 3.0 27.8 + - + +
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Residues in contact with ASP 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2100A GOL 2.9 28.6 + - - -
100G ARG* 3.0 35.5 + - - -
230G ILE* 4.9 3.2 - - + +
249G ALA 3.7 15.3 - - - +
250G ALA* 3.9 1.1 - - - -
251G PHE 3.1 9.4 + - - +
252G THR* 2.9 37.9 + - - +
254G TYR* 1.3 72.7 - - - +
256G VAL* 1.3 67.7 + - - +
258G GLU* 3.2 4.3 + - - +
259G ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ALA* 4.4 9.2 - - + -
252G THR 3.1 15.0 + - - +
253G LEU* 3.5 8.3 - - - +
254G TYR 3.3 0.2 - - - -
255G ASP* 1.3 77.1 - - - +
257G TYR* 1.3 62.5 + - - +
259G ILE* 3.2 10.0 + - - +
260G CYS* 3.0 25.0 + - - -
268G ILE* 3.8 23.5 - - + +
270G ILE* 3.9 23.8 - - + -
284G ALA* 3.9 34.1 - - + +
287G VAL* 4.1 13.0 - - + -
288G ALA* 4.5 2.5 - - + +
295G ILE* 5.5 0.7 - - + -
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Residues in contact with TYR 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 6.0 0.2 - - - -
231A PRO* 5.3 2.9 - - + -
257E TYR* 3.8 33.0 - + - -
260E CYS* 3.3 36.5 + - + +
261E ARG* 3.4 6.7 + - - -
263E ARG* 4.4 7.1 + - - -
287E VAL* 4.7 4.7 - - + -
290E ALA* 3.7 31.6 - - + +
291E ALA* 3.7 23.5 - - + +
253G LEU 3.1 16.7 + - - +
254G TYR 3.7 4.7 - - - +
255G ASP 3.3 0.2 - - - -
256G VAL* 1.3 77.4 - - - +
258G GLU* 1.3 63.5 + - - +
260G CYS* 3.2 2.2 + - - +
261G ARG* 2.7 60.0 + - + +
287G VAL* 3.9 16.8 - - + +
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Residues in contact with GLU 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 6.2 0.4 - - - -
231A PRO* 3.4 20.9 - - - +
258A GLU* 4.9 1.4 - - - +
262A GLN* 4.4 3.8 - - - +
2100A GOL 3.8 18.8 - - - +
230G ILE* 4.6 9.2 - - + -
254G TYR* 3.0 18.1 + - + +
255G ASP* 3.2 8.0 + - - +
257G TYR* 1.3 86.0 - - - +
259G ILE* 1.3 62.2 + - - +
261G ARG* 2.7 45.1 + - - +
262G GLN* 2.8 53.7 + - - +
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Residues in contact with ILE 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ILE* 3.7 20.2 - - + -
233G MSE 4.1 3.6 - - + -
246G ALA* 3.9 13.9 - - + -
249G ALA 4.0 7.4 - - - +
250G ALA* 3.4 37.5 - - + -
255G ASP 2.9 18.3 + - - +
256G VAL* 3.6 7.2 - - - +
258G GLU* 1.3 75.8 - - - +
260G CYS* 1.3 59.5 + - - +
263G ARG* 2.9 8.5 + - - -
264G ALA* 2.9 35.5 + - + -
265G ALA* 3.9 33.7 - - + +
268G ILE* 4.1 15.5 - - + -
293G LEU* 5.5 1.7 - - + +
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Residues in contact with CYS 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E TYR* 3.2 23.0 + - + +
256G VAL* 3.0 19.0 + - - +
257G TYR* 3.6 8.5 - - - +
259G ILE* 1.3 76.8 - - - +
261G ARG* 1.3 63.0 - - - +
263G ARG* 3.0 26.2 + - - +
268G ILE* 3.9 15.3 - - - -
287G VAL* 4.1 7.6 - - - -
288G ALA* 3.9 20.4 - - - -
291G ALA* 3.5 24.2 - - + -
293G LEU* 4.1 11.7 - - - -
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Residues in contact with ARG 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PRO* 3.9 13.5 - - - +
261A ARG* 4.7 2.8 - - - +
262A GLN* 3.8 26.6 + - - +
257E TYR* 3.4 10.5 + - - +
261E ARG* 4.8 26.4 + - + +
257G TYR* 2.7 48.3 + - + +
258G GLU* 2.7 42.0 + - - +
260G CYS* 1.3 75.1 - - - +
262G GLN* 1.3 73.3 + - - +
263G ARG* 3.5 6.8 + - - +
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Residues in contact with GLN 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLU* 4.5 3.0 + - - -
261A ARG* 3.5 24.3 + - - +
230G ILE* 3.4 22.5 - - - +
231G PRO* 3.7 13.5 - - - +
234G ALA* 4.4 9.2 - - + +
238G GLU* 5.1 3.5 - - - +
258G GLU* 2.8 50.3 + - - +
259G ILE 4.2 1.6 - - - +
261G ARG* 1.3 92.7 - - - +
263G ARG* 1.3 73.6 + - - +
264G ALA* 3.0 9.6 + - + +
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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