Contacts of the helix formed by residues 313 - 325 (chain j) in PDB entry 6QX2
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 ASN 313 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257j GLN* 5.7 1.6 + - - +
311j ASP 4.4 0.6 + - - -
312j ALA* 1.3 69.3 - - - +
314j ALA* 1.3 64.2 + - - +
315j SER* 4.0 12.4 + - - -
316j VAL* 2.8 47.6 + - + +
317j ILE* 3.4 24.2 + - - +
313t ASN* 3.3 28.3 + - - +
315t SER* 5.5 2.6 + - - -
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Residues in contact with ALA 314 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249j ILE* 3.6 34.9 - - + +
257j GLN* 4.4 16.2 - - + +
258j ARG 5.5 0.2 - - - +
259j ILE* 3.7 5.9 - - + +
308j VAL* 4.1 29.4 - - + -
312j ALA 3.5 3.8 + - - -
313j ASN* 1.3 72.3 + - - +
315j SER* 1.3 60.0 + - - +
317j ILE* 3.3 4.1 + - - +
318j LEU* 2.9 28.4 + - - +
315t SER* 5.5 0.6 + - - +
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Residues in contact with SER 315 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249j ILE* 3.3 15.6 - - - +
313j ASN* 3.4 13.7 + - - +
314j ALA* 1.3 73.5 - - - +
316j VAL* 1.3 60.7 + - - +
318j LEU* 3.4 4.0 + - - +
319j ASN* 3.0 34.5 + - - +
249t ILE* 4.6 1.9 - - - +
257t GLN* 2.2 40.5 + - - +
314t ALA* 5.5 1.0 + - - +
315t SER* 5.6 2.3 + - - -
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Residues in contact with VAL 316 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313j ASN* 2.8 36.9 - - + +
314j ALA 3.3 0.4 - - - -
315j SER* 1.3 74.7 - - - +
317j ILE* 1.3 61.9 + - + +
319j ASN* 3.2 6.8 + - - +
320j ASN* 2.9 44.5 + - - +
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Residues in contact with ILE 317 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259j ILE* 3.9 15.5 - - + -
286j ILE* 4.8 3.8 - - + -
287j ASP 3.6 12.8 - - - +
288j GLY* 3.7 26.5 - - - +
289j ILE* 3.7 30.7 - - + -
308j VAL* 3.5 32.5 - - + -
312j ALA* 4.3 5.8 - - + -
313j ASN 3.4 11.6 + - - +
314j ALA 3.3 6.9 + - - +
316j VAL* 1.3 78.2 - - + +
318j LEU* 1.3 57.4 + - - +
320j ASN* 3.3 10.5 + - - +
321j LEU* 2.9 30.0 + - + +
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Residues in contact with LEU 318 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247j ALA* 3.9 21.8 - - + +
248j VAL* 5.5 0.4 - - - -
249j ILE* 4.4 19.5 - - + -
259j ILE* 3.8 31.8 - - + +
314j ALA 2.9 17.3 + - - +
315j SER* 3.6 7.4 - - - +
316j VAL 3.3 0.2 - - - -
317j ILE* 1.3 75.9 - - - +
319j ASN* 1.3 62.7 + - - +
321j LEU* 3.2 7.0 + - + +
322j TYR* 3.1 57.8 + - + +
327j LEU* 4.0 13.5 - - + -
250t GLU* 6.5 0.4 - - - -
251t GLU* 5.9 8.1 - - + +
257t GLN* 6.1 0.7 - - - +
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Residues in contact with ASN 319 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244j ARG* 5.6 3.9 + - - -
315j SER 3.0 20.8 + - - +
316j VAL* 3.2 7.4 + - - +
318j LEU* 1.3 77.4 - - - +
320j ASN* 1.3 64.7 + - - +
322j TYR* 3.3 20.4 + - - +
323j LYS* 3.2 21.0 + - - +
255t GLY* 6.1 3.6 - - - -
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Residues in contact with ASN 320 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286j ILE* 3.8 16.7 - - + +
287j ASP 5.4 4.6 + - - +
316j VAL* 2.9 31.9 + - - +
317j ILE* 3.6 9.6 - - - +
319j ASN* 1.3 76.3 - - - +
321j LEU* 1.3 60.0 + - - +
323j LYS* 3.1 7.3 + - - +
324j GLN* 2.9 54.4 + - - +
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Residues in contact with LEU 321 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259j ILE* 4.2 16.2 - - + -
277j ILE* 3.9 37.7 - - + -
280j LEU* 5.3 1.3 - - + -
286j ILE* 3.8 18.6 - - + -
289j ILE* 4.1 6.1 - - + -
306j ILE* 3.6 28.5 - - + -
317j ILE* 2.9 24.1 + - + +
318j LEU* 3.2 11.0 + - + +
320j ASN* 1.3 75.1 - - - +
322j TYR* 1.3 58.9 + - - +
324j GLN* 4.5 0.9 - - - +
325j THR* 2.5 46.2 + - + -
327j LEU* 3.9 17.0 - - + -
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Residues in contact with TYR 322 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244j ARG* 3.4 59.2 - - + +
245j SER* 3.7 15.8 + - - -
247j ALA* 3.9 8.5 + - + +
318j LEU* 3.1 48.0 + - + +
319j ASN* 3.6 19.3 - - - +
320j ASN 3.2 0.2 - - - -
321j LEU* 1.3 76.6 - - - +
323j LYS* 1.3 61.3 + - - +
325j THR 3.3 15.4 - - - +
327j LEU* 3.7 37.9 - - + -
328j GLN* 3.7 31.2 - - + +
251t GLU* 5.3 7.3 - - + +
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Residues in contact with LYS 323 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319j ASN 3.2 9.7 + - - +
320j ASN* 3.1 11.0 + - - +
322j TYR* 1.3 78.8 - - - +
324j GLN* 1.3 65.9 + - + +
325j THR 4.1 0.6 + - - +
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Residues in contact with GLN 324 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276j LYS* 5.7 1.9 - - - +
280j LEU* 3.4 34.8 - - + +
285j LYS* 3.3 22.5 + - - +
286j ILE* 4.0 9.4 - - - +
320j ASN* 2.9 43.8 + - - +
321j LEU* 4.5 1.1 - - - +
323j LYS* 1.3 85.2 - - + +
325j THR* 1.3 62.8 + - - +
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Residues in contact with THR 325 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273j MET* 5.1 0.7 - - - -
276j LYS* 4.6 4.9 - - + -
277j ILE* 3.7 35.5 - - + +
280j LEU* 3.8 19.3 - - + -
321j LEU* 2.5 29.3 + - + +
322j TYR 3.3 10.9 - - - +
323j LYS 4.9 0.3 - - - +
324j GLN* 1.3 83.0 - - - +
326j PRO* 1.4 69.9 - - + +
327j LEU* 3.1 21.9 + - - +
328j GLN 3.1 11.8 - - - +
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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