Contacts of the helix formed by residues 313 - 325 (chain c) 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 c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257c GLN* 5.2 0.2 - - - -
311c ASP 4.0 1.2 + - - -
312c ALA* 1.3 70.2 - - - +
314c ALA* 1.3 60.7 + - - +
315c SER* 2.8 24.7 + - - -
316c VAL* 3.2 29.7 + - + +
317c ILE* 3.4 24.9 + - - +
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Residues in contact with ALA 314 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249c ILE* 3.6 26.6 - - + +
257c GLN* 3.2 25.9 + - + +
259c ILE* 3.7 6.3 - - + +
308c VAL* 4.1 24.9 - - + -
312c ALA 3.5 4.0 + - - -
313c ASN* 1.3 71.1 + - - +
315c SER* 1.3 59.8 + - - +
317c ILE* 3.3 6.3 + - - +
318c LEU* 2.9 28.1 + - - +
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Residues in contact with SER 315 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249c ILE* 3.4 23.2 - - - +
313c ASN* 2.8 11.5 + - - -
314c ALA* 1.3 74.9 - - - +
316c VAL* 1.3 60.9 + - - +
318c LEU* 3.4 4.4 + - - +
319c ASN* 3.0 34.8 + - - +
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Residues in contact with VAL 316 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313c ASN* 3.2 31.9 + - + +
315c SER* 1.3 75.6 - - - +
317c ILE* 1.3 61.9 + - + +
319c ASN* 3.2 7.2 + - - +
320c ASN* 2.9 44.5 + - - +
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Residues in contact with ILE 317 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259c ILE* 3.9 16.2 - - + -
286c ILE* 4.1 4.9 - - + +
287c ASP 3.7 13.5 - - - +
288c GLY* 3.7 26.5 - - - +
289c ILE* 3.8 29.6 - - + -
308c VAL* 3.5 33.0 - - + -
312c ALA* 4.1 5.6 - - + -
313c ASN 3.4 12.1 + - - +
314c ALA 3.3 7.5 + - - +
316c VAL* 1.3 77.7 - - + +
318c LEU* 1.3 56.9 + - - +
320c ASN* 3.3 10.6 + - - +
321c LEU* 2.9 29.9 + - + +
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Residues in contact with LEU 318 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247c ALA* 3.9 21.3 - - + +
248c VAL 5.6 0.2 - - - -
249c ILE* 4.5 19.5 - - + -
259c ILE* 3.9 30.5 - - + +
314c ALA 2.9 16.5 + - - +
315c SER* 3.6 7.4 - - - +
316c VAL 3.3 0.2 - - - -
317c ILE* 1.3 76.8 - - - +
319c ASN* 1.3 65.0 + - - +
321c LEU* 3.2 7.4 + - + +
322c TYR* 3.1 57.7 + - + +
327c LEU* 4.0 13.5 - - + -
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Residues in contact with ASN 319 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244c ARG* 5.6 3.1 + - - +
315c SER* 3.0 21.1 + - - +
316c VAL* 3.7 7.4 - - - +
318c LEU* 1.3 76.5 - - - +
320c ASN* 1.3 62.9 + - - +
322c TYR* 3.3 20.9 + - - +
323c LYS* 3.2 31.7 + - + +
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Residues in contact with ASN 320 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A GLN* 5.7 0.6 + - - -
286c ILE* 3.8 16.8 - - + +
287c ASP 5.6 3.4 + - - +
316c VAL* 2.9 33.4 + - - +
317c ILE* 3.6 11.6 - - - +
319c ASN* 1.3 75.5 - - - +
321c LEU* 1.3 58.7 + - - +
323c LYS* 3.1 23.5 + - - +
324c GLN* 2.9 51.4 + - - +
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Residues in contact with LEU 321 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259c ILE* 4.2 16.2 - - + -
277c ILE* 3.9 38.1 - - + -
280c LEU* 5.3 0.9 - - + -
286c ILE* 3.8 19.7 - - + -
289c ILE* 4.2 6.1 - - + -
306c ILE* 3.6 27.8 - - + -
317c ILE* 2.9 22.6 + - + +
318c LEU* 3.2 11.2 + - + +
320c ASN* 1.3 75.6 - - - +
322c TYR* 1.3 57.1 + - - +
324c GLN* 4.9 0.4 - - - -
325c THR* 2.5 46.1 + - + -
327c LEU* 3.9 16.8 - - + -
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Residues in contact with TYR 322 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244c ARG* 3.4 56.9 - - + +
245c SER* 3.7 16.3 + - - -
247c ALA* 3.9 8.4 + - + +
318c LEU* 3.1 47.3 + - + +
319c ASN* 3.6 19.3 - - - +
320c ASN 3.2 0.4 - - - -
321c LEU* 1.3 77.0 - - - +
323c LYS* 1.3 62.4 + - + +
325c THR 3.3 15.4 - - - +
327c LEU* 3.7 37.7 - - + -
328c GLN* 3.7 30.2 - - + +
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Residues in contact with LYS 323 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A GLU* 5.1 4.0 + - - -
413A GLN* 2.8 44.8 + - + +
414A ARG* 6.0 0.5 - - - -
319c ASN* 3.2 22.4 + - + +
320c ASN* 3.1 29.3 + - - +
322c TYR* 1.3 79.3 - - + +
324c GLN* 1.3 62.0 + - + +
325c THR 3.7 0.6 + - - +
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Residues in contact with GLN 324 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A GLN* 3.8 45.4 - - + +
276c LYS* 5.7 1.0 - - - +
280c LEU* 3.4 36.3 - - + +
285c LYS* 3.3 24.7 + - - +
286c ILE* 4.1 7.4 - - - +
320c ASN* 2.9 41.9 + - - +
321c LEU* 4.5 0.9 - - - +
323c LYS* 1.3 81.9 - - + +
325c THR* 1.3 62.8 + - + +
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Residues in contact with THR 325 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273c MET* 5.1 0.4 - - - -
276c LYS* 4.6 3.6 - - + -
277c ILE* 3.7 35.5 - - + +
280c LEU* 3.8 18.6 - - + -
321c LEU* 2.5 31.1 + - + +
322c TYR 3.3 10.7 - - - +
323c LYS 3.7 0.7 - - - +
324c GLN* 1.3 83.9 - - - +
326c PRO* 1.4 71.5 - - + +
327c LEU* 3.1 22.3 + - - +
328c GLN 3.1 11.6 - - - +
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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