Contacts of the helix formed by residues 313 - 325 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257R GLN* 5.5 0.2 - - - -
311R ASP 4.0 1.2 + - - -
312R ALA* 1.3 69.9 - - - +
314R ALA* 1.3 61.2 + - - +
315R SER* 2.9 25.2 + - - -
316R VAL* 3.2 29.0 + - + +
317R ILE* 3.4 24.7 + - - +
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Residues in contact with ALA 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249R ILE* 3.6 34.5 - - + -
257R GLN* 3.6 15.8 + - + +
258R ARG 5.6 0.2 - - - +
259R ILE* 3.7 5.9 - - + +
308R VAL* 4.2 27.1 - - + -
312R ALA 3.5 3.6 + - - -
313R ASN* 1.3 71.2 + - - +
315R SER* 1.3 60.0 + - - +
317R ILE* 3.3 6.0 + - - +
318R LEU* 2.9 28.4 + - - +
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Residues in contact with SER 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249R ILE* 3.4 22.8 - - - +
313R ASN* 2.9 11.8 + - - -
314R ALA* 1.3 73.8 - - - +
316R VAL* 1.3 61.0 + - - +
318R LEU* 3.4 4.9 + - - +
319R ASN* 3.0 34.6 + - - +
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Residues in contact with VAL 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313R ASN* 3.2 31.9 + - + +
315R SER* 1.3 74.9 - - - +
317R ILE* 1.3 61.9 + - + +
319R ASN* 3.2 7.7 + - - +
320R ASN* 2.9 44.4 + - - +
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Residues in contact with ILE 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259R ILE* 3.9 15.5 - - + -
286R ILE* 4.8 4.7 - - + -
287R ASP 3.6 15.0 - - - +
288R GLY* 3.7 25.8 - - - +
289R ILE* 3.8 30.7 - - + -
308R VAL* 3.5 32.8 - - + -
312R ALA* 4.3 5.6 - - + -
313R ASN 3.4 12.7 + - - +
314R ALA 3.3 6.8 + - - +
316R VAL* 1.3 78.0 - - + +
318R LEU* 1.3 57.8 + - - +
320R ASN* 3.3 10.6 + - - +
321R LEU* 2.9 29.9 + - + +
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Residues in contact with LEU 318 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247R ALA* 4.0 20.9 - - + +
248R VAL* 5.6 0.4 - - - -
249R ILE* 4.5 19.7 - - + -
259R ILE* 3.9 30.9 - - + +
314R ALA 2.9 16.9 + - - +
315R SER* 3.6 8.1 - - - +
316R VAL 3.2 0.2 - - - -
317R ILE* 1.3 76.4 - - - +
319R ASN* 1.3 63.5 + - - +
321R LEU* 3.2 7.0 + - + +
322R TYR* 3.1 58.1 + - + +
327R LEU* 4.0 13.5 - - + -
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Residues in contact with ASN 319 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244R ARG* 5.5 4.3 + - - -
315R SER* 3.0 20.7 + - - +
316R VAL* 3.7 7.4 - - - +
318R LEU* 1.3 77.3 - - - +
320R ASN* 1.3 65.0 + - - +
322R TYR* 3.3 19.7 + - - +
323R LYS* 3.2 21.0 + - - +
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Residues in contact with ASN 320 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286R ILE* 3.8 15.5 - - + +
287R ASP 5.6 3.4 + - - +
316R VAL* 2.9 33.4 + - - +
317R ILE* 3.6 11.1 - - - +
318R LEU 3.2 0.2 - - - -
319R ASN* 1.3 74.8 - - - +
321R LEU* 1.3 59.5 + - - +
323R LYS* 3.1 7.3 + - - +
324R GLN* 2.9 55.6 + - - +
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Residues in contact with LEU 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259R ILE* 4.2 16.8 - - + -
277R ILE* 4.0 36.6 - - + -
280R LEU* 5.1 1.3 - - + -
286R ILE* 3.8 19.7 - - + -
289R ILE* 4.2 6.7 - - + -
306R ILE* 3.6 28.3 - - + -
317R ILE* 2.9 23.3 + - + +
318R LEU* 3.2 10.5 + - + +
320R ASN* 1.3 75.1 - - - +
322R TYR* 1.3 57.4 + - - +
324R GLN* 4.6 0.7 - - - +
325R THR* 2.5 47.0 + - + +
327R LEU* 3.9 15.3 - - + -
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Residues in contact with TYR 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244R ARG* 3.4 55.9 - - + +
245R SER* 3.7 16.6 + - - -
247R ALA* 3.9 8.5 + - + +
318R LEU* 3.1 48.9 + - + +
319R ASN* 3.6 19.5 - - - +
320R ASN 3.2 0.4 - - - -
321R LEU* 1.3 75.5 - - - +
323R LYS* 1.3 60.9 + - - +
325R THR 3.3 15.1 - - - +
327R LEU* 3.7 38.1 - - + -
328R GLN* 3.6 30.1 - - + +
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Residues in contact with LYS 323 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319R ASN 3.2 8.8 + - - +
320R ASN* 3.1 11.7 + - - +
322R TYR* 1.3 79.1 - - - +
324R GLN* 1.3 58.8 + - + +
325R THR 3.7 0.6 - - - +
413t GLN* 2.8 25.8 + - - +
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Residues in contact with GLN 324 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276R LYS* 5.8 1.2 - - - +
280R LEU* 3.4 34.3 - - + +
285R LYS* 3.3 25.8 + - - +
286R ILE* 4.2 5.7 - - - +
320R ASN* 2.9 44.5 + - - +
321R LEU 4.5 0.4 - - - +
323R LYS* 1.3 84.8 - - + +
325R THR* 1.3 62.4 + - + +
413t GLN* 3.5 35.6 - - + +
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Residues in contact with THR 325 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273R MET* 5.2 0.2 - - - -
276R LYS* 4.6 4.0 - - + -
277R ILE* 3.7 34.1 - - + +
280R LEU* 3.8 20.2 - - + -
321R LEU* 2.5 30.1 + - + +
322R TYR 3.3 9.9 - - - +
323R LYS 4.1 0.4 + - - -
324R GLN* 1.3 82.6 - - - +
326R PRO* 1.4 70.0 - - + +
327R LEU* 3.1 20.8 + - - +
328R GLN 3.1 14.2 - - - +
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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