Contacts of the helix formed by residues 262 - 277 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D HIS* 5.3 0.4 - - - -
261D ASN* 1.3 73.6 - - - +
263D THR* 1.3 62.7 + - - +
264D HIS* 3.2 18.6 + - - -
265D LEU* 3.2 20.0 + - - +
266D ASP 3.6 0.9 + - - -
413D ARG* 4.5 3.8 - - - -
414D ASN 4.1 4.3 - - - -
415D PRO* 3.4 25.9 + - - -
418D GLY* 3.5 14.0 - - - -
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Residues in contact with THR 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ASN* 2.6 30.6 + - - +
241D ASN 4.1 0.7 - - - +
242D HIS* 3.8 28.5 - - + -
260D ARG* 2.9 50.3 + - - +
261D ASN 3.4 0.4 + - - -
262D GLY* 1.3 78.3 - - - +
264D HIS* 1.3 58.9 + - + +
266D ASP* 3.0 11.7 + - - +
267D ALA* 2.9 27.4 + - - +
315D LEU* 3.8 8.8 - - - +
413D ARG* 4.2 3.9 - - - +
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Residues in contact with HIS 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ASN* 4.8 3.6 - - - +
262D GLY* 3.2 19.3 + - - -
263D THR* 1.3 83.2 - - + +
265D LEU* 1.3 96.2 + - + +
267D ALA* 3.4 7.8 + - - +
268D GLY* 2.9 25.6 + - - -
415D PRO 4.4 4.9 - - - -
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D GLY 3.2 7.7 + - - +
264D HIS* 1.3 107.5 - - + +
266D ASP* 1.3 59.3 + - - +
268D GLY* 4.0 0.8 - - - -
269D ALA* 3.0 23.2 + - - +
415D PRO 4.1 2.7 - - - +
416D ALA* 3.3 31.0 - - - +
417D GLU* 3.5 28.0 - - - +
418D GLY 3.7 1.1 - - - +
423D GLN* 3.2 10.4 + - - +
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Residues in contact with ASP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ARG* 4.9 2.3 + - - -
262D GLY 3.6 2.2 + - - -
263D THR* 3.0 12.1 + - - +
265D LEU* 1.3 74.8 - - - +
267D ALA* 1.3 67.7 + - - +
269D ALA* 3.3 1.7 + - - +
270D LEU* 2.9 30.1 + - - +
315D LEU* 4.1 12.9 - - + +
358D GLN* 4.2 2.4 - - - +
418D GLY* 3.3 2.3 - - - -
419D THR* 2.6 56.3 + - - +
422D ILE* 3.4 19.1 - - + +
423D GLN* 2.9 20.6 + - - +
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Residues in contact with ALA 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 4.1 10.6 - - + +
240D ASN* 3.7 31.2 - - + +
263D THR 2.9 10.6 + - - +
264D HIS* 3.9 5.4 - - - +
266D ASP* 1.3 77.8 - - - +
268D GLY* 1.3 53.5 + - - +
270D LEU* 3.3 4.8 + - - +
271D THR* 2.8 40.7 + - - +
285D ASP* 5.4 0.9 - - - +
315D LEU* 4.1 8.4 - - + +
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Residues in contact with GLY 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D HIS 2.9 16.0 + - - -
265D LEU* 4.0 2.0 - - - -
267D ALA* 1.3 76.2 - - - +
269D ALA* 1.3 63.1 + - - +
271D THR* 3.4 5.8 + - - -
272D THR* 3.0 29.3 + - - -
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU 3.0 18.3 + - - +
266D ASP* 3.7 3.8 - - - +
268D GLY* 1.3 76.8 - - - +
270D LEU* 1.3 57.5 + - - +
272D THR* 4.0 3.2 - - - -
273D THR* 2.7 35.5 + - - -
422D ILE* 5.1 0.2 - - + -
423D GLN* 3.8 19.7 - - - +
426D CYS* 3.7 22.4 - - + -
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Residues in contact with LEU 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.9 15.7 - - + -
266D ASP 2.9 21.6 + - - +
267D ALA 3.8 3.1 - - - +
269D ALA* 1.3 73.0 - - - +
271D THR* 1.3 61.4 + - - +
273D THR* 4.5 0.7 - - - -
274D PHE* 2.9 59.2 + - + +
313D CYS* 3.9 32.5 - - + -
315D LEU* 4.0 21.3 - - + -
422D ILE* 3.7 22.2 - - + -
425D LEU* 4.6 11.9 - - + -
426D CYS* 3.7 17.3 - - - -
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Residues in contact with THR 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.6 13.7 - - - +
267D ALA* 2.8 25.4 + - - +
268D GLY* 3.6 6.7 - - - -
270D LEU* 1.3 77.7 - - - +
272D THR* 1.3 59.0 + - - +
275D GLU* 2.9 59.6 + - - +
281D ILE* 3.9 19.5 - - + +
283D PRO* 5.9 1.7 - - - +
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Residues in contact with THR 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLY 3.0 17.0 + - - -
269D ALA* 4.0 4.0 - - - -
271D THR* 1.3 76.9 - - - +
273D THR* 1.3 65.4 + - - +
275D GLU* 3.8 8.8 + - - +
276D GLU* 3.0 45.3 + - + +
430D ARG* 5.4 9.9 - - - +
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Residues in contact with THR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D ALA* 2.7 23.1 + - - -
270D LEU* 4.0 2.9 - - - -
272D THR* 1.3 79.7 - - - +
274D PHE* 1.3 64.6 + - + +
276D GLU* 3.3 11.6 + - - +
277D LEU* 3.2 31.6 + - + +
426D CYS* 3.5 19.6 - - - +
429D LEU* 3.8 40.2 - - + -
430D ARG* 3.6 24.5 - - + +
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D CYS* 4.1 18.6 - - - -
270D LEU* 2.9 48.3 + - + +
273D THR* 1.3 77.4 - - + +
275D GLU* 1.3 63.7 + - - +
277D LEU* 3.2 24.9 + - + +
278D HIS 3.1 5.4 + - - -
279D PHE* 2.9 35.4 + + + +
281D ILE* 3.9 16.4 - - + -
311D ILE* 3.4 27.6 - - + -
313D CYS* 4.9 0.7 - - - -
356D PHE* 3.8 25.6 - + - -
425D LEU* 5.4 0.2 - - + -
429D LEU* 3.5 28.5 - - + -
476D PHE* 4.3 11.7 - + - -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D THR* 2.9 41.2 + - - +
272D THR* 3.8 7.5 + - - +
274D PHE* 1.3 75.2 - - - +
276D GLU* 1.3 60.6 + - + +
278D HIS* 2.9 23.2 + - - -
279D PHE 3.9 10.0 - - - +
281D ILE* 3.5 21.5 + - + +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D THR* 3.0 39.5 + - + +
273D THR* 3.6 11.0 - - - +
274D PHE 3.3 0.2 - - - -
275D GLU* 1.3 77.0 - - + +
277D LEU* 1.3 63.4 - - + +
278D HIS* 3.2 19.2 + - - -
430D ARG* 4.4 20.3 + - - +
477D PRO 5.2 0.7 - - - +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ARG* 3.3 23.2 + - - +
273D THR* 3.2 24.1 + - + +
274D PHE* 3.7 31.6 - - + +
275D GLU 3.1 0.6 - - - -
276D GLU* 1.3 80.4 - - + +
278D HIS* 1.3 68.8 + - - +
279D PHE* 3.4 11.9 + - + -
429D LEU* 4.8 2.9 - - + +
433D CYS* 3.9 26.5 - - + -
476D PHE* 3.7 40.6 - - + +
477D PRO 4.2 8.3 - - - +
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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