Contacts of the helix formed by residues 262 - 277 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B HIS* 5.1 0.4 - - - -
261B ASN* 1.3 73.7 - - - +
263B THR* 1.3 64.2 + - - +
264B HIS* 3.2 19.5 + - - -
265B LEU* 3.1 12.9 + - - +
266B ASP 3.7 0.5 + - - -
413B ARG* 4.6 2.9 - - - -
414B ASN 4.2 4.3 - - - -
415B PRO* 3.4 25.5 + - - -
418B GLY* 3.4 22.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASN* 2.5 30.3 + - - +
241B ASN 4.1 0.7 - - - +
242B HIS* 3.8 28.5 - - + -
260B ARG* 3.0 48.6 + - - +
261B ASN 3.4 0.4 + - - -
262B GLY* 1.3 78.2 - - - +
264B HIS* 1.3 65.2 + - + +
266B ASP* 3.0 10.6 + - - +
267B ALA* 3.0 22.2 + - - +
315B LEU* 3.7 9.7 - - - +
413B ARG* 4.2 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASN* 4.4 10.8 - - - +
262B GLY* 3.9 18.0 + - - -
263B THR* 1.3 82.4 - - + +
265B LEU* 1.3 91.3 + - + +
267B ALA* 3.4 2.7 + - - +
268B GLY* 3.0 24.8 + - - -
415B PRO 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLY 3.1 7.9 + - - +
264B HIS* 1.3 106.3 - - + +
266B ASP* 1.3 61.9 + - - +
268B GLY* 3.5 1.5 + - - +
269B ALA* 3.0 23.4 + - - +
415B PRO 4.2 2.9 - - - +
416B ALA 3.5 29.6 - - - +
417B GLU* 3.6 26.0 - - - +
418B GLY 3.9 1.3 - - - +
423B GLN* 3.2 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 4.9 1.4 + - - -
262B GLY 3.7 2.6 + - - -
263B THR* 3.0 13.7 + - - +
265B LEU* 1.3 76.3 - - - +
267B ALA* 1.3 64.9 + - - +
269B ALA* 3.2 2.1 + - - +
270B LEU* 2.9 30.3 + - - +
315B LEU* 4.0 13.3 - - + +
358B GLN* 4.2 2.8 - - - +
418B GLY* 3.4 2.5 - - - -
419B THR* 2.5 56.6 + - - +
422B ILE* 3.4 23.2 - - + +
423B GLN* 3.0 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 4.0 12.4 - - + +
240B ASN* 3.3 32.8 - - - +
263B THR 3.0 6.4 + - - +
264B HIS* 3.8 7.0 - - - +
266B ASP* 1.3 75.9 - - - +
268B GLY* 1.3 54.6 + - - +
270B LEU* 3.8 4.8 - - - +
271B THR* 2.8 39.3 + - - +
283B PRO* 6.3 2.7 - - + -
285B ASP* 5.7 0.2 - - - +
315B LEU* 4.1 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS 3.0 16.9 + - - -
265B LEU* 3.9 2.5 - - - -
267B ALA* 1.3 76.3 - - - +
269B ALA* 1.3 56.0 + - - +
271B THR* 3.4 5.9 + - - -
272B THR* 3.0 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU 3.0 19.3 + - - +
266B ASP 3.2 3.1 + - - +
268B GLY* 1.3 73.5 - - - +
270B LEU* 1.3 57.0 + - - +
272B THR* 3.4 5.2 + - - -
273B THR* 2.7 37.6 + - - -
422B ILE* 5.0 0.4 - - + -
423B GLN* 3.7 20.9 - - - +
426B CYS* 3.6 22.4 - - + -
430B ARG* 6.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.9 15.9 - - + -
266B ASP 2.9 19.9 + - - +
267B ALA 3.8 2.7 - - - +
269B ALA* 1.3 77.1 - - - +
271B THR* 1.3 58.4 + - - +
273B THR* 4.4 0.9 - - - -
274B PHE* 2.9 59.1 + - + +
281B ILE* 4.7 0.3 - - - +
313B CYS* 3.9 33.2 - - + -
315B LEU* 4.1 21.3 - - + -
422B ILE* 3.8 22.7 - - + -
425B LEU* 4.6 11.2 - - + -
426B CYS* 3.7 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.7 12.5 - - - +
267B ALA* 2.8 24.3 + - - +
268B GLY* 3.7 7.1 - - - -
270B LEU* 1.3 76.1 - - - +
272B THR* 1.3 57.5 + - - +
275B GLU* 2.9 59.4 + - - +
281B ILE* 3.9 21.6 - - + +
283B PRO* 5.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLY 3.0 19.8 + - - -
269B ALA* 3.7 5.6 - - - -
271B THR* 1.3 78.0 - - - +
273B THR* 1.3 65.6 + - - +
275B GLU* 4.1 4.4 - - - +
276B GLU* 3.2 43.7 + - + +
430B ARG* 4.4 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ALA 2.7 24.3 + - - -
270B LEU* 3.8 3.1 - - - -
272B THR* 1.3 79.0 - - - +
274B PHE* 1.3 65.9 + - + +
276B GLU* 3.4 5.4 + - - +
277B LEU* 3.2 33.5 + - + +
426B CYS* 3.3 23.5 - - - +
429B LEU* 3.7 40.2 - - + -
430B ARG* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B CYS* 4.0 20.2 - - - -
270B LEU* 2.9 50.9 + - + +
273B THR* 1.3 74.4 - - + +
275B GLU* 1.3 63.7 + - - +
277B LEU* 3.3 22.3 + - + -
278B HIS 3.2 4.7 + - - -
279B PHE* 2.9 37.3 + + + +
281B ILE* 3.7 17.7 - - + -
311B ILE* 3.4 26.5 - - + -
313B CYS* 4.7 0.7 - - - -
356B PHE* 3.8 25.8 - + - -
429B LEU* 3.7 24.9 - - + -
476B PHE* 4.3 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 2.9 39.3 + - - +
249A GLU* 5.2 0.9 - - - +
271B THR* 2.9 33.8 + - - +
272B THR* 4.1 4.0 - - - +
274B PHE* 1.3 76.9 - - - +
276B GLU* 1.3 59.7 + - + +
278B HIS* 2.9 23.4 + - - -
279B PHE 3.9 12.0 - - - +
281B ILE* 3.5 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.2 33.6 + - + +
273B THR 3.5 5.3 - - - +
274B PHE 3.3 0.2 - - - -
275B GLU* 1.3 80.1 - - - +
277B LEU* 1.3 61.3 + - + +
278B HIS* 3.1 21.8 + - - -
430B ARG* 4.3 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.2 23.0 + - - +
273B THR* 3.2 26.5 + - + +
274B PHE* 3.3 28.5 + - + +
275B GLU 3.2 0.6 - - - -
276B GLU* 1.3 78.1 - - + +
278B HIS* 1.3 69.5 + - - +
279B PHE* 3.5 12.9 + - + -
429B LEU* 4.9 2.5 - - + +
430B ARG* 6.5 0.2 - - - -
433B CYS* 3.9 24.9 - - + -
434B PRO* 5.8 1.6 - - + -
476B PHE* 3.6 41.2 - - + +
477B PRO 4.6 7.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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