Contacts of the helix formed by residues 262 - 277 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242C HIS* 5.2 0.2 - - - -
261C ASN* 1.3 72.6 - - - +
263C THR* 1.3 62.7 + - - +
264C HIS* 3.2 19.5 + - - -
265C LEU* 3.1 21.6 + - - +
266C ASP 3.6 0.9 + - - -
413C ARG* 4.6 3.1 - - - -
414C ASN 4.1 4.7 - - - -
415C PRO* 3.5 24.6 + - - -
418C GLY* 3.5 14.6 - - - -
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Residues in contact with THR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASN* 2.5 33.5 + - - +
241C ASN 4.1 0.4 - - - +
242C HIS* 3.8 27.4 - - + -
260C ARG* 3.0 48.4 + - - +
261C ASN 3.5 0.2 - - - -
262C GLY* 1.3 78.1 - - - +
264C HIS* 1.3 66.7 + - + +
266C ASP* 3.0 11.2 + - - +
267C ALA 3.0 17.7 + - - -
315C LEU* 3.7 9.5 - - - +
413C ARG* 4.3 3.9 - - - +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASN* 4.3 11.0 - - - +
262C GLY* 3.8 20.2 + - - -
263C THR* 1.3 84.7 - - + +
265C LEU* 1.3 89.5 + - + +
267C ALA* 3.4 3.5 + - - +
268C GLY* 2.9 25.1 + - - -
415C PRO 4.6 4.3 - - - -
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C GLY 3.1 9.1 + - - +
264C HIS* 1.3 107.7 - - + +
266C ASP* 1.3 59.6 + - - +
268C GLY* 3.8 1.5 - - - +
269C ALA* 2.9 23.2 + - - +
415C PRO 4.3 3.1 - - - +
416C ALA* 3.3 31.0 - - - +
417C GLU* 3.4 27.4 - - - +
418C GLY 3.8 1.1 - - - +
423C GLN* 3.2 11.0 + - - +
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Residues in contact with ASP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 5.0 1.4 + - - -
262C GLY 3.6 1.9 + - - -
263C THR* 3.0 12.7 + - - +
265C LEU* 1.3 75.8 - - - +
267C ALA* 1.3 65.3 + - - +
269C ALA* 3.2 1.4 + - - +
270C LEU* 2.9 30.2 + - - +
315C LEU* 4.1 13.7 - - + +
358C GLN* 4.2 2.3 - - - +
418C GLY* 3.3 2.8 - - - -
419C THR* 2.5 58.6 + - - +
422C ILE* 3.4 22.8 - - + +
423C GLN* 2.9 18.9 + - - +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ILE* 3.9 16.7 - - + +
240C ASN* 3.4 32.1 - - + +
263C THR 3.0 6.3 + - - -
264C HIS* 3.8 6.3 - - - +
265C LEU 3.4 0.2 - - - -
266C ASP* 1.3 77.1 - - - +
268C GLY* 1.3 54.4 + - - +
270C LEU* 4.6 0.2 - - - -
271C THR* 2.8 39.2 + - - +
283C PRO* 6.3 2.7 - - + -
315C LEU* 4.2 8.4 - - + +
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Residues in contact with GLY 268 (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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264C HIS 2.9 16.9 + - - -
265C LEU* 3.5 2.4 + - - -
267C ALA* 1.3 78.4 - - - +
269C ALA* 1.3 60.5 + - - +
271C THR* 3.5 4.7 + - - -
272C THR* 3.0 28.6 + - - -
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Residues in contact with ALA 269 (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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255B HIS* 6.4 0.4 - - + -
265C LEU 2.9 18.2 + - - +
266C ASP* 3.2 3.8 + - - +
268C GLY* 1.3 75.2 - - - +
270C LEU* 1.3 56.0 + - - +
272C THR* 3.4 5.1 + - - -
273C THR* 2.7 37.9 + - - -
422C ILE* 5.1 0.4 - - + -
423C GLN* 3.8 20.2 - - - +
426C CYS* 3.6 22.0 - - + -
430C ARG* 5.3 2.6 - - - +
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Residues in contact with LEU 270 (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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236C CYS* 5.7 0.2 - - - -
238C ILE* 3.9 18.4 - - + -
266C ASP 2.9 24.0 + - - +
269C ALA* 1.3 72.9 - - - +
271C THR* 1.3 59.2 + - - +
273C THR* 4.4 0.4 - - - -
274C PHE* 2.8 58.8 + - + +
281C ILE* 4.7 0.8 - - - +
313C CYS* 3.9 31.6 - - + -
315C LEU* 4.1 21.1 - - + -
422C ILE* 3.7 22.9 - - + -
425C LEU* 4.6 11.2 - - + -
426C CYS* 3.7 17.0 - - - -
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ILE* 3.7 12.8 - - - +
267C ALA* 2.8 23.8 + - - +
268C GLY* 3.7 6.3 - - - -
269C ALA 3.3 0.2 - - - -
270C LEU* 1.3 73.0 - - - +
272C THR* 1.3 66.9 + - - +
275C GLU* 2.9 49.3 + - - +
281C ILE* 3.7 25.3 - - + +
283C PRO* 5.7 2.1 - - - +
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Residues in contact with THR 272 (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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249B GLU* 5.1 4.7 - - + +
268C GLY 3.0 18.3 + - - -
269C ALA* 3.8 5.4 - - - -
271C THR* 1.3 77.2 - - - +
273C THR* 1.3 64.1 + - - +
275C GLU* 3.9 4.7 - - - +
276C GLU* 3.1 49.3 + - + +
430C ARG* 4.3 23.6 - - - +
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Residues in contact with THR 273 (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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269C ALA 2.7 22.3 + - - -
270C LEU* 3.8 2.9 - - - -
272C THR* 1.3 79.1 - - - +
274C PHE* 1.3 65.7 + - + +
276C GLU* 3.5 6.1 + - - +
277C LEU* 3.3 28.7 + - + +
426C CYS* 3.3 21.6 - - - +
429C LEU* 3.7 41.3 - - + -
430C ARG* 3.4 26.9 - - + +
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Residues in contact with PHE 274 (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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236C CYS* 3.8 21.3 - - - -
270C LEU* 2.8 49.9 + - + +
273C THR* 1.3 74.4 - - + +
275C GLU* 1.3 63.4 + - - +
277C LEU* 3.2 25.5 + - + +
278C HIS 3.1 4.7 + - - -
279C PHE* 2.9 35.5 + + + +
281C ILE* 3.7 17.5 - - + -
311C ILE* 3.5 24.9 - - + -
313C CYS* 4.7 0.9 - - - -
356C PHE* 3.8 27.1 - + - -
425C LEU* 5.5 0.2 - - + -
429C LEU* 3.7 25.1 - - + -
476C PHE* 4.2 13.2 - + - -
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Residues in contact with GLU 275 (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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271C THR* 2.9 36.3 + - - +
272C THR* 3.9 4.5 - - - +
274C PHE* 1.3 76.4 - - - +
276C GLU* 1.3 60.2 + - + +
278C HIS* 2.9 24.3 + - - -
279C PHE 3.9 12.5 - - - +
281C ILE* 3.8 20.2 + - + +
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Residues in contact with GLU 276 (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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272C THR* 3.1 33.5 + - + +
273C THR 3.6 4.9 - - - +
274C PHE 3.3 0.2 - - - -
275C GLU* 1.3 77.8 - - + +
277C LEU* 1.3 60.0 + - + +
278C HIS* 3.1 21.7 + - - -
430C ARG* 4.1 28.0 + - - +
478C SER* 4.2 12.3 + - - +
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Residues in contact with LEU 277 (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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233C ARG* 3.3 19.8 + - - +
273C THR* 3.3 25.3 + - + +
274C PHE* 3.2 28.6 + - + +
275C GLU 3.1 1.0 - - - -
276C GLU* 1.3 77.5 - - + +
278C HIS* 1.3 73.0 + - - +
279C PHE* 3.4 12.3 + - + -
429C LEU* 4.9 2.0 - - + +
430C ARG* 6.6 0.2 - - - -
433C CYS* 3.9 22.2 - - + -
434C PRO* 5.7 0.2 - - + -
476C PHE* 3.6 35.6 - - + +
477C PRO 4.5 2.6 - - - +
478C SER* 3.6 32.1 - - - +
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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
------------------------------------------------------------
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