Contacts of the helix formed by residues 265 - 280 (chain G) in PDB entry 4D1Q
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 CYS 265 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G VAL* 4.3 2.0 - - - +
247G THR 2.6 21.7 + - - +
248G ASP* 4.1 7.7 - - - +
264G ASN* 1.3 68.8 - - - +
266G SER* 1.3 57.4 + - - +
267G SER* 2.9 29.2 + - - -
268G HIS* 3.1 17.6 + - + +
269G LEU* 3.0 24.7 + - - +
319G TRP* 4.7 2.0 - - - -
566G ALA 4.2 0.2 - - - -
567G SER* 3.1 35.7 - - - +
568G SER* 3.3 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ASN 2.8 7.4 + - - -
265G CYS* 1.3 70.9 - - - +
267G SER* 1.3 56.8 + - - +
269G LEU* 3.9 6.3 - - - -
270G LEU* 3.2 24.6 + - - +
374G LEU* 3.5 30.2 - - - +
385G VAL* 3.7 7.0 - - - +
421G TRP* 3.3 34.1 + - - +
425G LEU* 4.3 1.0 - - - +
429G HIS* 3.4 24.1 + - - -
566G ALA 3.3 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G CYS* 2.9 20.4 - - - -
266G SER* 1.3 77.4 - - - +
268G HIS* 1.3 58.5 + - - +
270G LEU 3.2 1.9 + - - -
271G SER* 3.0 22.0 + - - -
319G TRP* 3.7 28.5 - - - -
371G PHE* 3.3 26.2 - - - -
374G LEU* 4.1 9.2 - - - +
375G GLN* 3.9 11.4 - - - +
567G SER* 3.7 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G ASP* 4.4 0.6 + - - -
248G ASP* 2.8 42.1 - - + +
249G ARG* 4.2 5.2 - - + +
265G CYS* 3.1 12.2 + - + +
267G SER* 1.3 71.2 - - - +
269G LEU* 1.3 62.2 + - + +
271G SER* 2.8 8.8 + - - +
272G ASN* 2.7 46.2 + - - +
319G TRP* 2.9 43.2 + + - +
568G SER* 3.9 8.0 + - - -
572G GLU* 3.2 21.7 + - - -
16J G 4.4 10.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ARG* 3.9 27.8 - - + +
264G ASN* 3.7 25.8 - - + +
265G CYS 3.0 26.5 + - - +
266G SER* 4.0 2.7 - - - -
268G HIS* 1.3 82.4 - - + +
270G LEU* 1.3 57.5 + - - +
272G ASN* 3.8 7.9 - - - +
273G VAL* 2.9 34.1 + - - +
420G ILE* 3.8 9.6 - - + +
421G TRP* 3.7 35.7 - - + +
424G ASN* 3.7 31.2 - - + +
425G LEU* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G SER 3.2 19.9 + - - +
267G SER 3.7 4.9 - - - +
268G HIS 3.1 0.8 - - - -
269G LEU* 1.3 72.8 - - - +
271G SER* 1.3 59.8 + - - +
273G VAL* 3.4 13.1 + - + -
274G LEU* 2.7 25.6 + - - +
367G PHE* 3.2 41.5 - - + +
370G ILE* 4.0 26.0 - - + -
371G PHE* 3.4 36.8 - - + -
374G LEU* 5.6 1.6 - - + -
392G VAL* 5.0 1.3 - - + -
417G VAL* 6.4 0.2 - - + -
421G TRP* 4.1 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G SER 3.0 6.2 + - - -
268G HIS* 2.8 9.6 + - - -
270G LEU* 1.3 73.0 - - - +
272G ASN* 1.3 59.2 + - - -
274G LEU* 2.5 29.5 + - - +
275G GLU* 2.8 19.1 + - - +
318G ARG 4.3 3.5 + - - -
319G TRP* 2.9 46.5 - - - -
320G ASN 4.4 1.9 + - - -
371G PHE* 3.8 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ARG* 2.8 38.6 - - - +
268G HIS* 2.7 33.7 + - - +
269G LEU* 3.8 6.4 - - - +
271G SER* 1.3 70.8 - - - +
273G VAL* 1.3 63.5 + - - +
275G GLU* 3.3 14.5 + - - +
276G ASN* 3.2 30.7 + - - +
420G ILE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G LEU 2.9 20.7 + - - +
270G LEU* 3.6 20.4 - - + +
272G ASN* 1.3 77.2 - - - +
274G LEU* 1.3 63.3 + - + +
276G ASN* 4.1 0.5 - - - -
277G SER* 2.9 38.5 + - - +
367G PHE* 5.2 0.2 - - + -
413G ILE* 4.5 18.8 - - + +
416G ASN* 3.5 17.2 - - + +
417G VAL* 4.2 9.2 - - + +
420G ILE* 3.4 38.1 - - + -
421G TRP* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G LEU 2.7 14.9 + - - +
271G SER* 2.5 16.6 + - - +
273G VAL* 1.3 72.5 - - + +
275G GLU* 1.3 59.7 + - - +
277G SER* 3.6 7.0 + - - -
278G PHE* 3.3 42.2 + - + -
320G ASN* 3.8 29.4 - - - +
364G LEU* 3.9 17.9 - - + -
367G PHE* 3.8 40.4 - - + -
371G PHE* 4.2 15.0 - - + -
409G LEU* 6.3 0.4 - - + -
413G ILE* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G SER* 2.8 17.4 + - - +
272G ASN* 3.5 17.5 - - - +
274G LEU* 1.3 69.5 - - - +
276G ASN* 1.3 82.4 + - - +
277G SER 3.0 1.3 - - - -
278G PHE* 2.8 24.3 + - - +
279G GLU* 3.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ASN* 3.2 15.2 + - - +
273G VAL 4.5 0.2 - - - +
275G GLU* 1.3 95.3 - - - +
277G SER* 1.3 58.1 + - - +
278G PHE 3.2 1.0 + - - -
279G GLU* 4.0 18.8 - - - +
280G GLU* 3.0 40.1 + - - +
416G ASN* 3.5 18.1 - - - +
420G ILE* 3.9 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 2.9 23.3 + - - -
274G LEU* 3.9 8.3 - - - -
275G GLU 3.0 1.6 + - - -
276G ASN* 1.3 76.6 - - - +
278G PHE* 1.3 58.7 + - - +
280G GLU 4.4 1.3 - - - -
281G THR* 3.2 10.3 + - - -
409G LEU* 3.1 22.3 - - - +
412G ASN* 4.4 9.1 - - - +
413G ILE* 3.2 42.0 - - - -
416G ASN* 3.4 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 3.3 38.3 + - + +
275G GLU* 2.8 10.2 + - - +
277G SER* 1.3 77.6 - - - +
279G GLU* 1.3 61.9 + - - +
280G GLU 3.2 1.8 - - - -
281G THR* 2.9 34.8 + - - +
282G PRO* 3.9 1.2 - - - +
284G LEU* 4.3 4.7 - - + -
285G ASN* 5.1 5.2 + - - +
288G ILE* 4.1 20.6 - - + -
322G THR* 4.8 17.9 - - + -
360G MET* 3.4 33.9 - - + -
364G LEU* 4.3 21.8 - - + -
409G LEU* 4.3 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLU* 3.0 15.0 + - - +
276G ASN* 4.0 21.7 - - - +
278G PHE* 1.3 78.3 - - - +
280G GLU* 1.3 61.6 + - + +
281G THR 3.2 3.5 + - - -
282G PRO* 3.5 13.7 - - - +
285G ASN* 5.1 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ASN* 3.0 27.5 + - - +
277G SER 5.0 0.2 - - - -
278G PHE 3.2 0.4 - - - -
279G GLU* 1.3 80.3 - - + +
281G THR* 1.3 62.0 + - - +
282G PRO* 3.3 9.7 - - - +
283G GLU* 4.5 2.1 - - - +
408G LYS* 4.7 5.2 - - - +
412G ASN* 2.9 38.9 + - + +
415G LYS* 3.2 12.4 + - - +
416G ASN* 3.4 22.5 + - - +
----------------------------------------------------------
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