Contacts of the helix formed by residues 262 - 277 (chain A) in PDB entry 4PS1
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 GLY 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A HIS* 5.2 0.4 - - - -
261A ASN* 1.3 73.3 - - - +
263A THR* 1.3 63.9 + - - +
264A HIS* 3.1 18.4 + - - -
265A LEU* 3.0 20.5 + - - +
266A ASP 3.7 0.9 + - - -
413A ARG* 4.6 3.4 - - - -
414A ASN 4.1 4.5 - - - -
415A PRO* 3.5 25.7 + - - -
418A GLY* 3.6 13.3 - - - -
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASN* 2.6 31.2 + - - +
242A HIS* 3.7 30.1 - - + -
260A ARG* 3.0 49.7 + - - +
262A GLY* 1.3 76.5 - - - +
264A HIS* 1.3 65.3 + - + +
266A ASP* 3.1 10.5 + - - +
267A ALA* 3.0 21.7 + - - +
315A LEU* 3.7 9.5 - - - +
413A ARG* 4.3 3.9 - - - +
419A THR* 5.9 0.2 - - - -
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASN* 4.6 4.0 - - - +
242A HIS* 5.9 0.2 - - - -
262A GLY* 3.1 19.3 + - - -
263A THR* 1.3 84.2 - - + +
265A LEU* 1.3 92.9 + - + +
267A ALA* 3.4 8.4 + - - +
268A GLY* 3.0 25.5 + - - -
415A PRO 4.5 4.7 - - - -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLY 3.0 9.5 + - - +
264A HIS* 1.3 109.1 - - + +
266A ASP* 1.3 58.0 + - - +
268A GLY* 4.0 1.6 - - - -
269A ALA* 3.1 22.9 + - - +
415A PRO 4.2 3.1 - - - +
416A ALA 3.4 29.8 - - - +
417A GLU* 3.4 27.8 - - - +
418A GLY 3.8 1.3 - - - +
423A GLN* 3.2 10.7 + - - +
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 5.0 1.0 + - - -
262A GLY 3.7 3.0 + - - -
263A THR* 3.1 12.1 + - - +
265A LEU* 1.3 75.1 - - - +
267A ALA* 1.3 66.1 + - - +
269A ALA* 3.3 1.6 + - - +
270A LEU* 2.9 29.8 + - - +
315A LEU* 3.9 14.1 - - + +
358A GLN* 4.2 2.6 - - - +
418A GLY* 3.3 2.3 - - - -
419A THR* 2.6 54.2 + - - +
422A ILE* 3.5 22.7 - - + +
423A GLN* 2.8 22.1 + - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 3.9 17.3 - - + +
240A ASN* 3.5 31.9 - - + +
263A THR 3.0 6.4 + - - +
264A HIS* 3.8 8.3 - - - +
266A ASP* 1.3 76.7 - - - +
268A GLY* 1.3 54.0 + - - +
270A LEU* 3.8 1.7 - - - +
271A THR* 2.8 39.6 + - - +
283A PRO* 6.3 2.7 - - + -
315A LEU* 4.1 6.2 - - - +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A HIS 3.0 15.9 + - - -
265A LEU* 4.0 2.0 - - - -
267A ALA* 1.3 77.2 - - - +
269A ALA* 1.3 56.2 + - - +
271A THR* 3.3 6.2 + - - -
272A THR* 3.0 33.4 + - - -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU 3.1 18.6 + - - +
266A ASP 3.8 3.1 - - - +
268A GLY* 1.3 73.4 - - - +
270A LEU* 1.3 60.4 + - - +
272A THR* 3.5 4.5 + - - -
273A THR* 2.7 34.9 + - - +
422A ILE* 5.1 0.2 - - + -
423A GLN* 3.9 20.0 - - - +
426A CYS* 3.6 23.1 - - + -
430A ARG* 6.2 2.5 - - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A CYS* 5.3 0.2 - - - -
238A ILE* 3.9 15.7 - - + -
266A ASP 2.9 20.3 + - - +
267A ALA 3.8 2.7 - - - +
269A ALA* 1.3 77.7 - - - +
271A THR* 1.3 58.4 + - - +
273A THR* 4.4 0.9 - - - -
274A PHE* 2.9 58.4 + - + +
281A ILE* 4.6 0.2 - - - +
313A CYS* 3.8 33.2 - - + -
315A LEU* 4.1 21.1 - - + -
422A ILE* 3.7 21.8 - - + -
425A LEU* 4.5 12.6 - - + -
426A CYS* 3.6 17.9 - - - -
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 3.5 13.2 - - - +
267A ALA* 2.8 26.7 + - - +
268A GLY* 3.7 5.8 - - - -
269A ALA 3.2 0.2 - - - -
270A LEU* 1.3 78.3 - - - +
272A THR* 1.3 54.6 + - - +
275A GLU* 2.8 62.8 + - - +
281A ILE* 3.7 22.4 - - + +
283A PRO* 5.6 2.4 - - - +
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLY 3.0 16.9 + - - -
269A ALA* 3.8 5.4 - - - -
271A THR* 1.3 77.3 - - - +
273A THR* 1.3 64.8 + - - +
275A GLU* 4.0 6.5 - - - +
276A GLU* 3.1 51.0 + - + +
430A ARG* 4.8 16.8 - - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA 2.7 21.4 + - - -
270A LEU* 3.9 2.9 - - - -
272A THR* 1.3 80.7 - - - +
274A PHE* 1.3 66.2 + - + +
276A GLU* 3.4 9.5 + - - +
277A LEU* 3.3 32.6 + - + +
426A CYS* 3.4 21.5 - - - +
429A LEU* 3.7 41.1 - - + -
430A ARG* 3.4 22.2 - - + +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A CYS* 3.9 20.2 - - - -
270A LEU* 2.9 52.3 + - + +
273A THR* 1.3 73.8 - - + +
275A GLU* 1.3 66.2 + - - +
277A LEU* 3.2 26.8 + - + +
278A HIS 3.2 0.2 + - - -
279A PHE* 2.9 36.2 + + + +
281A ILE* 3.7 17.3 - - + -
311A ILE* 3.5 25.4 - - + -
313A CYS* 4.8 0.7 - - - -
356A PHE* 3.9 25.4 - + - -
425A LEU* 5.4 0.2 - - + -
429A LEU* 3.7 26.0 - - + -
476A PHE* 4.2 12.3 - + - -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A THR* 2.8 42.9 + - - +
272A THR* 4.0 6.1 - - - +
274A PHE* 1.3 73.4 - - - +
276A GLU* 1.3 57.9 + - + +
278A HIS* 2.9 23.9 + - - -
279A PHE 3.9 10.9 - - - +
280A GLU* 6.0 0.2 - - - -
281A ILE* 3.6 21.0 + - + +
290B GLU* 5.5 2.9 - - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 3.1 39.0 + - + +
273A THR* 3.6 5.4 - - - +
275A GLU* 1.3 77.9 - - + +
277A LEU* 1.3 64.1 + - + +
278A HIS* 3.2 19.2 + - - -
430A ARG* 4.3 25.8 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ARG* 3.2 23.4 + - - +
273A THR* 3.3 25.1 + - + +
274A PHE* 3.2 29.9 + - + +
275A GLU 3.1 1.0 - - - -
276A GLU* 1.3 80.8 - - + +
278A HIS* 1.3 68.6 + - - +
279A PHE* 3.4 12.1 + - + -
429A LEU* 4.8 2.2 - - + +
433A CYS* 3.9 25.4 - - + -
434A PRO* 6.0 0.4 - - + -
476A PHE* 3.6 42.3 - - + +
477A PRO 4.4 7.4 - - - +
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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