Contacts of the helix formed by residues 252 - 263 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E MSE 3.6 41.1 - - + -
100E ARG* 3.8 20.9 - - + +
103E ASN* 3.8 11.4 - - - +
251E PHE* 1.3 77.9 - - - +
253E LEU* 1.3 65.9 + - - +
254E TYR* 3.3 9.6 + - - +
255E ASP* 3.1 37.4 + - - +
256E VAL* 3.1 16.5 + - - +
275E ILE* 3.4 6.5 - - - -
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E MSE 5.2 1.9 - - - -
252E THR* 1.3 74.4 - - - +
254E TYR* 1.3 72.7 + - + +
256E VAL* 3.4 6.7 + - + +
257E TYR* 3.1 21.8 + - - +
275E ILE* 3.2 15.2 - - + +
280E PRO 5.3 0.2 - - - +
283E LYS* 3.8 35.7 - - + +
284E ALA* 4.0 7.4 - - + +
287E VAL* 3.7 26.2 - - + -
286G ALA 4.1 14.4 - - - +
289G GLU* 4.2 25.6 - - + +
290G ALA* 3.8 13.7 - - + +
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Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D VAL* 4.8 6.0 - - + +
228D TRP* 3.4 66.8 - + + +
229D SER* 4.4 8.1 - - - -
99E MSE 3.9 26.0 - - + -
252E THR* 3.1 5.5 - - - +
253E LEU* 1.3 86.5 - - + +
255E ASP* 1.3 61.1 + - - +
257E TYR* 3.4 6.3 + - - +
258E GLU* 3.0 34.4 + - + +
289G GLU* 3.5 44.8 + - + +
290G ALA* 3.4 19.7 - - - -
292G GLY* 4.9 1.1 - - - -
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Residues in contact with ASP 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ARG* 2.8 35.8 + - - -
230E ILE* 4.7 6.5 - - + +
249E ALA 3.7 11.2 - - - +
250E ALA* 3.9 1.1 - - - -
251E PHE 3.0 23.2 + - - +
252E THR* 3.1 29.3 + - - +
254E TYR* 1.3 74.2 - - - +
256E VAL* 1.3 62.1 + - - +
258E GLU* 3.2 6.8 + - - +
259E ILE* 2.9 35.3 + - - +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E ALA* 4.4 8.7 - - + -
252E THR 3.1 14.8 + - - +
253E LEU* 3.6 7.4 - - - +
254E TYR 3.3 0.2 - - - -
255E ASP* 1.3 76.4 - - - +
257E TYR* 1.3 57.1 + - - +
259E ILE* 3.3 5.9 + - - +
260E CYS* 2.9 36.8 + - - -
268E ILE* 3.7 26.7 - - + -
270E ILE* 3.9 24.7 - - + -
284E ALA* 3.9 34.3 - - + +
287E VAL* 4.3 7.6 - - + -
288E ALA* 4.5 2.2 - - + +
295E ILE* 5.5 0.9 - - + -
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Residues in contact with TYR 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 5.9 0.2 - - - -
231D PRO* 5.3 4.0 - - + -
253E LEU 3.1 11.3 + - - +
254E TYR 3.7 7.4 - - - +
256E VAL* 1.3 79.1 - - - +
258E GLU* 1.3 70.2 + - - +
260E CYS* 3.3 2.5 + - - +
261E ARG* 2.8 55.2 + - + +
287E VAL* 4.0 22.6 - - + +
257G TYR* 3.8 27.4 - + - -
260G CYS* 3.2 36.5 + - + +
261G ARG* 3.4 6.5 + - - -
263G ARG* 4.5 6.6 + - - -
287G VAL* 4.8 4.9 - - + -
290G ALA* 3.6 31.2 - - + +
291G ALA* 3.8 22.4 - - + +
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Residues in contact with GLU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ILE* 6.2 0.4 - - - -
231D PRO* 3.5 19.0 - - - +
258D GLU* 4.7 1.6 - - - +
262D GLN* 4.4 4.7 - - - +
230E ILE* 3.7 17.3 - - + -
254E TYR* 3.0 22.5 + - + +
255E ASP* 3.6 6.3 - - - +
257E TYR* 1.3 86.2 - - - +
259E ILE* 1.3 63.6 + - - +
261E ARG* 2.7 43.9 + - - +
262E GLN* 2.9 49.0 + - - +
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Residues in contact with ILE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ILE* 3.8 14.4 - - + -
233E MSE 4.0 10.1 - - + -
246E ALA* 3.9 14.8 - - + -
249E ALA 3.9 8.5 - - - +
250E ALA* 3.4 38.1 - - + +
255E ASP 2.9 19.2 + - - +
256E VAL* 3.7 5.2 - - - +
258E GLU* 1.3 75.4 - - - +
260E CYS* 1.3 59.2 + - - +
263E ARG* 3.0 7.1 + - - -
264E ALA* 2.9 35.7 + - + -
265E ALA* 3.9 33.2 + - + +
268E ILE* 4.0 15.9 - - + -
293E LEU* 5.3 2.3 - - + +
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Residues in contact with CYS 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E VAL* 2.9 28.4 + - - +
257E TYR* 3.7 5.6 - - - +
259E ILE* 1.3 75.9 - - - +
261E ARG* 1.3 64.0 + - - +
263E ARG* 3.2 25.9 + - - +
268E ILE* 3.9 8.7 - - - -
287E VAL* 4.1 5.8 - - - -
288E ALA* 3.9 17.9 - - - -
291E ALA* 3.5 23.1 - - + -
293E LEU* 3.8 22.0 - - - -
257G TYR* 3.3 21.6 + - + +
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Residues in contact with ARG 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D PRO* 3.9 16.9 - - - +
261D ARG* 4.9 2.2 - - - +
262D GLN* 3.9 20.0 + - - +
257E TYR* 2.8 49.4 + - + +
258E GLU* 2.7 41.6 + - - +
260E CYS* 1.3 73.5 - - - +
262E GLN* 1.3 73.7 + - - +
263E ARG* 3.6 4.2 + - - +
257G TYR* 3.4 10.0 + - - +
261G ARG* 4.8 27.2 + - + +
263G ARG* 6.4 1.8 - - - +
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Residues in contact with GLN 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLU* 4.4 4.0 + - - -
261D ARG* 3.8 15.8 + - - +
230E ILE* 3.7 20.8 - - - +
231E PRO* 3.6 26.9 - - - +
234E ALA* 4.3 10.2 - - + +
238E GLU* 4.9 4.0 - - - +
258E GLU* 2.9 45.1 + - - +
259E ILE 4.4 0.2 - - - +
261E ARG* 1.3 91.6 - - - +
263E ARG* 1.3 71.2 + - - +
264E ALA* 3.1 10.2 + - + +
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Residues in contact with ARG 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.9 0.4 - - - +
229A SER* 4.2 0.8 + - - -
231A PRO* 3.8 26.1 - - + +
232A ALA* 3.7 21.0 - - - +
235A HIS* 3.0 38.6 + - + +
234E ALA* 4.6 1.7 - - - +
237E ARG* 2.7 44.3 + - - +
259E ILE 3.0 6.9 + - - -
260E CYS* 3.2 17.8 + - - +
261E ARG 4.7 3.8 - - - +
262E GLN* 1.3 81.7 - - - +
264E ALA* 1.3 54.2 + - - +
265E ALA 3.3 5.4 - - - +
291E ALA* 2.5 45.9 + - - +
293E LEU* 4.0 16.7 - - - +
257G TYR* 4.4 4.9 + - - -
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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