Contacts of the helix formed by residues 313 - 325 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ASN* 4.0 23.6 - - - +
257L GLN* 5.1 0.2 - - - -
311L ASP 4.0 1.6 + - - -
312L ALA* 1.3 69.8 - - - +
314L ALA* 1.3 63.1 + - - +
315L SER* 2.9 24.7 + - - -
316L VAL* 3.2 30.4 + - + +
317L ILE* 3.4 24.5 + - - +
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Residues in contact with ALA 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 5.8 0.2 - - - +
249L ILE* 3.6 28.0 - - + -
257L GLN* 3.2 24.5 + - + +
258L ARG 5.6 0.4 - - - -
259L ILE* 3.7 5.7 - - + +
308L VAL* 4.2 25.6 - - + -
312L ALA 3.5 3.6 + - - -
313L ASN* 1.3 71.5 + - - +
315L SER* 1.3 59.7 + - - +
316L VAL 3.3 0.2 - - - -
317L ILE* 3.3 6.0 + - - +
318L LEU* 2.9 28.6 + - - +
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Residues in contact with SER 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 4.8 2.1 - - - +
257A GLN* 2.5 36.8 + - - +
314A ALA* 5.7 0.7 + - - +
315A SER* 5.6 1.6 + - - -
249L ILE* 3.4 15.8 - - - +
313L ASN* 2.9 10.9 + - - -
314L ALA* 1.3 74.1 - - - +
316L VAL* 1.3 60.1 - - - +
318L LEU* 3.4 5.3 + - - +
319L ASN* 3.0 34.8 + - - +
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Residues in contact with VAL 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L ASN* 3.2 33.4 + - + +
315L SER* 1.3 74.0 - - - +
317L ILE* 1.3 61.1 + - + +
319L ASN* 3.2 7.2 + - - +
320L ASN* 2.9 44.2 + - - +
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Residues in contact with ILE 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ILE* 3.9 15.3 - - + -
286L ILE* 4.2 4.0 - - + +
287L ASP 3.6 14.4 - - - +
288L GLY* 3.7 26.9 - - - +
289L ILE* 3.8 29.6 - - + -
308L VAL* 3.5 33.0 - - + -
312L ALA* 4.1 5.4 - - + -
313L ASN 3.4 11.9 + - - +
314L ALA 3.3 8.4 + - - +
316L VAL* 1.3 78.4 - - + +
318L LEU* 1.3 57.3 + - - +
320L ASN* 3.3 10.5 + - - +
321L LEU* 2.9 31.1 + - + +
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Residues in contact with LEU 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLN* 6.2 0.7 - - - +
247L ALA* 3.9 20.4 - - + +
248L VAL* 5.6 0.4 - - - -
249L ILE* 4.6 19.3 - - + -
259L ILE* 3.9 31.8 - - + +
314L ALA 2.9 16.4 + - - +
315L SER* 3.6 8.1 - - - +
316L VAL 3.2 0.2 - - - -
317L ILE* 1.3 76.3 - - - +
319L ASN* 1.3 64.0 + - - +
321L LEU* 3.2 6.4 + - + +
322L TYR* 3.1 57.8 + - + +
327L LEU* 4.0 13.9 - - + -
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Residues in contact with ASN 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244L ARG* 5.7 2.3 + - - -
315L SER 3.0 20.2 + - - +
316L VAL* 3.2 7.6 + - - +
318L LEU* 1.3 77.8 - - - +
320L ASN* 1.3 65.1 + - - +
322L TYR* 3.3 19.0 + - - +
323L LYS* 3.2 40.0 + - - +
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Residues in contact with ASN 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286L ILE* 3.8 17.5 - - + +
287L ASP 5.5 4.9 + - - +
316L VAL* 2.9 33.2 + - - +
317L ILE* 3.6 9.8 - - - +
318L LEU 3.2 0.2 - - - -
319L ASN* 1.3 75.3 - - - +
321L LEU* 1.3 57.9 + - - +
323L LYS* 3.1 15.4 + - - +
324L GLN* 2.9 54.9 + - - +
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Residues in contact with LEU 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L ILE* 4.2 17.0 - - + -
277L ILE* 3.9 38.6 - - + -
280L LEU* 5.4 0.7 - - + -
286L ILE* 3.8 19.7 - - + +
289L ILE* 4.2 4.5 - - + -
306L ILE* 3.6 28.0 - - + -
317L ILE* 2.9 24.1 + - + +
318L LEU* 3.2 10.1 + - + +
320L ASN* 1.3 74.5 - - - +
322L TYR* 1.3 58.4 + - - +
324L GLN* 4.6 0.4 - - - +
325L THR* 2.5 46.4 + - + +
327L LEU* 3.9 17.3 - - + -
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Residues in contact with TYR 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L ARG* 3.4 56.8 - - + +
245L SER* 3.7 16.6 + - - -
247L ALA* 3.9 8.4 + - + +
318L LEU* 3.1 47.9 + - + +
319L ASN* 3.6 18.6 - - - +
320L ASN 3.2 0.2 - - - -
321L LEU* 1.3 77.2 - - - +
323L LYS* 1.3 62.4 + - + +
325L THR 3.3 15.4 - - - +
327L LEU* 3.7 37.5 - - + -
328L GLN* 3.7 30.8 - - + +
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Residues in contact with LYS 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319L ASN* 3.2 27.9 + - - +
320L ASN* 3.1 19.8 + - - +
322L TYR* 1.3 79.5 - - + +
324L GLN* 1.3 65.4 + - + +
325L THR 3.7 0.7 + - - +
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Residues in contact with GLN 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L LYS* 5.5 1.6 - - - +
280L LEU* 3.5 35.3 - - + +
285L LYS* 3.3 25.5 + - - +
286L ILE* 4.1 6.6 - - - +
320L ASN* 2.9 43.0 + - - +
321L LEU* 4.5 0.9 - - - +
323L LYS* 1.3 85.5 - - + +
325L THR* 1.3 63.9 + - + +
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Residues in contact with THR 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273L MET* 4.9 0.7 - - - -
276L LYS* 4.5 4.3 - - + -
277L ILE* 3.7 36.0 - - + +
280L LEU* 3.8 18.6 - - + -
321L LEU* 2.5 29.8 + - + +
322L TYR 3.3 10.6 - - - +
323L LYS 3.7 0.7 - - - +
324L GLN* 1.3 83.5 - - - +
326L PRO* 1.4 70.5 - - + +
327L LEU* 3.1 22.0 + - - +
328L GLN 3.1 12.3 - - - +
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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