Contacts of the helix formed by residues 266 - 278 (chain D) in PDB entry 6XAV
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 SER 266 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU 3.8 0.2 + - - -
209D ILE* 3.2 54.3 + - - +
211D GLU* 5.4 0.4 - - - -
264D LEU* 3.3 18.7 - - - +
265D ASP* 1.3 80.8 - - - +
267D ILE* 1.3 55.7 + - - +
268D THR* 3.2 3.6 - - - +
269D ARG* 3.6 13.7 - - - +
270D LEU* 2.6 37.1 + - - +
320D LEU* 5.9 1.1 - - - -
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Residues in contact with ILE 267 (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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175D LEU* 4.3 10.1 - - + -
264D LEU* 3.8 22.3 - - + +
265D ASP 3.8 0.2 - - - -
266D SER* 1.3 76.2 - - - +
268D THR* 1.3 64.9 + - - +
270D LEU* 4.0 4.9 - - + +
271D ALA* 3.1 26.2 + - - +
297D PRO* 4.9 7.0 - - + +
301D PHE* 4.3 23.3 - - + -
317D ALA* 4.0 20.2 - - + -
318D THR 3.2 29.8 + - - +
319D ALA* 4.6 4.0 - - + -
331D ILE* 5.8 0.2 - - + -
335D PHE* 3.6 36.1 - - + -
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Residues in contact with THR 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D SER* 3.2 0.8 - - - +
267D ILE* 1.3 81.3 - - - +
269D ARG* 1.3 68.0 + - - +
271D ALA* 3.3 6.8 + - - +
272D ARG* 3.1 27.9 + - - +
319D ALA* 4.7 0.9 - - - -
320D LEU* 3.5 42.9 + - + +
328D ASP* 3.3 39.4 + - + +
331D ILE* 4.8 14.7 - - + +
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Residues in contact with ARG 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C GLU 5.1 2.4 + - - -
334C GLU* 3.8 15.5 + - - +
337C GLY* 3.7 30.9 + - - +
209D ILE* 4.0 17.7 - - + +
210D ASP* 3.7 33.2 + - + +
211D GLU* 5.6 4.5 + - - +
239D HIS* 5.4 2.4 - - - -
265D ASP 5.2 1.6 - - - +
266D SER* 3.1 22.1 + - - +
268D THR* 1.3 82.6 - - - +
270D LEU* 1.3 58.1 + - - +
272D ARG* 3.1 42.6 + - - +
273D ALA* 3.0 25.8 + - - +
320D LEU* 4.8 20.6 - - + +
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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
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209D ILE* 4.3 13.0 - - + -
239D HIS* 3.8 16.2 - - + +
243D ALA* 3.8 28.3 - - + -
264D LEU* 5.2 5.4 - - + -
266D SER* 2.6 26.5 + - - +
267D ILE* 4.0 5.4 - - - +
269D ARG* 1.3 69.8 - - - +
271D ALA* 1.3 65.3 + - - +
273D ALA* 3.1 8.2 + - + +
274D TYR* 3.1 61.7 + - + -
297D PRO* 4.8 9.9 - - + -
300D PHE* 4.0 31.9 - - + -
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Residues in contact with ALA 271 (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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267D ILE 3.1 18.5 + - - +
268D THR 3.6 5.8 - - - +
269D ARG 3.3 0.2 - - - -
270D LEU* 1.3 78.4 - - - +
272D ARG* 1.3 56.7 + - - +
274D TYR* 3.6 3.1 + - - +
275D ASN* 3.0 28.2 + - - +
293D ALA* 4.6 3.9 - - - +
294D LEU* 4.6 6.8 - - + +
297D PRO* 4.3 23.7 - - + +
331D ILE* 3.7 33.3 - - + +
335D PHE* 4.7 0.7 - - + -
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Residues in contact with ARG 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C GLU* 4.3 13.1 + - - +
334C GLU* 2.9 38.1 + - - +
268D THR* 3.1 17.4 + - - +
269D ARG* 3.1 35.5 - - - +
271D ALA* 1.3 73.5 - - - +
273D ALA* 1.3 56.6 + - - +
275D ASN* 3.3 7.6 + - - +
276D THR* 2.5 40.1 + - - +
325D SER* 4.2 11.1 + - - -
327D MET* 3.4 32.1 - - + +
328D ASP* 2.8 43.2 + - - +
331D ILE* 5.0 4.5 - - + -
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Residues in contact with ALA 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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236D ALA* 3.8 17.2 - - + +
239D HIS* 3.8 32.5 - - + -
240D VAL* 4.5 4.0 - - + -
269D ARG 3.0 13.6 + - - +
270D LEU* 3.1 15.9 + - + +
272D ARG* 1.3 77.4 - - - +
274D TYR* 1.3 61.7 + - - +
276D THR* 3.2 2.5 + - - -
277D VAL* 3.1 30.6 + - - +
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Residues in contact with TYR 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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240D VAL* 3.6 42.9 + - + +
243D ALA* 4.4 8.0 - - - +
244D GLU* 5.0 2.4 + - - +
270D LEU* 3.1 55.0 + - + +
271D ALA 4.1 1.1 - - - +
273D ALA* 1.3 75.1 - - - +
275D ASN* 1.3 62.7 + - - +
277D VAL* 3.7 8.0 - - + +
278D VAL* 3.1 28.8 + - - +
292D ASN 5.7 0.2 - - - +
293D ALA* 3.8 19.9 - - - +
296D ARG* 3.5 61.7 + - + -
297D PRO* 3.9 10.8 - - + -
300D PHE* 5.9 2.4 - - + +
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Residues in contact with ASN 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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285C LEU* 5.2 12.2 - - - +
271D ALA 3.0 19.7 + - - +
272D ARG* 3.7 8.2 + - - +
274D TYR* 1.3 76.5 - - - +
276D THR* 1.3 59.7 + - - +
278D VAL* 3.2 18.7 - - - +
288D GLY 3.5 16.3 + - - +
289D VAL* 3.4 8.4 - - + -
290D ASP* 2.9 33.1 + - - +
293D ALA* 3.4 13.0 - - + +
327D MET* 4.8 12.0 - - - -
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Residues in contact with THR 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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283C LYS* 3.7 17.2 + - - +
285C LEU* 4.0 27.2 - - + +
291C ALA* 3.7 40.6 - - + +
236D ALA* 4.2 16.5 - - + +
272D ARG* 2.5 24.9 + - - +
273D ALA* 3.6 5.1 - - - -
274D TYR 3.1 0.4 - - - -
275D ASN* 1.3 81.8 + - - +
277D VAL* 1.3 61.6 + - + +
278D VAL 3.6 1.4 + - - +
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LYS* 3.9 16.4 + - - +
236D ALA* 3.7 30.7 - - + +
237D SER* 4.0 15.3 - - - +
240D VAL* 3.8 15.9 - - + -
273D ALA 3.1 18.1 + - - +
274D TYR* 3.7 15.9 - - + +
276D THR* 1.3 75.7 - - + +
278D VAL* 1.3 66.3 + - - +
279D PRO* 3.5 7.4 - - - +
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LYS* 3.5 12.1 - - - +
274D TYR 3.1 20.4 + - - +
275D ASN* 3.2 23.0 - - - +
276D THR 4.1 1.7 - - - +
277D VAL* 1.3 78.5 - - - +
279D PRO* 1.3 83.6 - - + +
280D ALA* 4.7 0.3 - - - -
281D SER* 6.0 1.1 - - - -
290D ASP* 3.6 30.5 - - + +
292D ASN* 4.7 23.1 - - + +
293D ALA* 4.7 1.3 - - + -
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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