Contacts of the helix formed by residues 313 - 325 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313J ASN* 3.3 26.1 + - - +
257T GLN* 5.1 0.2 - - - -
311T ASP 4.0 1.8 + - - -
312T ALA* 1.3 69.1 - - - +
314T ALA* 1.3 62.7 + - - +
315T SER* 2.9 24.8 + - - -
316T VAL* 3.2 30.1 + - + +
317T ILE* 3.4 24.4 + - - +
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Residues in contact with ALA 314 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J SER* 5.4 0.8 + - - +
249T ILE* 3.6 25.4 - - + -
257T GLN* 3.2 25.9 + - + +
258T ARG 5.6 0.2 - - - +
259T ILE* 3.7 6.7 - - + +
308T VAL* 4.2 25.1 - - + -
312T ALA 3.5 3.4 + - - -
313T ASN* 1.3 70.0 + - - +
315T SER* 1.3 59.9 + - - +
317T ILE* 3.3 5.5 + - - +
318T LEU* 2.9 28.8 + - - +
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Residues in contact with SER 315 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249J ILE* 4.8 1.7 - - - +
257J GLN* 2.4 38.8 + - - +
313J ASN* 5.4 3.2 + - - -
314J ALA* 5.5 1.9 + - - +
315J SER* 5.6 1.6 + - - -
249T ILE* 3.4 15.1 - - - +
313T ASN* 2.9 11.5 + - - -
314T ALA* 1.3 74.5 - - - +
316T VAL* 1.3 61.1 + - - +
318T LEU* 3.4 4.6 + - - +
319T ASN* 3.0 34.2 + - - +
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Residues in contact with VAL 316 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313T ASN* 3.2 32.5 + - + +
315T SER* 1.3 75.2 - - - +
317T ILE* 1.3 62.2 + - + +
319T ASN* 3.2 7.4 + - - +
320T ASN* 2.9 44.0 + - - +
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Residues in contact with ILE 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259T ILE* 3.9 16.6 - - + -
286T ILE* 4.2 4.2 - - + +
287T ASP 3.7 12.8 - - - +
288T GLY* 3.7 27.1 - - - +
289T ILE* 3.8 29.6 - - + -
308T VAL* 3.5 32.5 - - + -
312T ALA* 4.1 6.5 - - + -
313T ASN 3.4 11.4 + - - +
314T ALA 3.3 7.7 + - - +
316T VAL* 1.3 78.1 - - + +
318T LEU* 1.3 56.5 + - - +
320T ASN* 3.3 10.6 + - - +
321T LEU* 2.9 30.2 + - + +
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Residues in contact with LEU 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J GLU* 6.6 0.2 - - - -
251J GLU* 4.9 5.8 - - + +
257J GLN* 6.1 0.9 - - - +
247T ALA* 3.9 21.3 - - + +
248T VAL 5.6 0.2 - - - -
249T ILE* 4.4 20.0 - - + -
259T ILE* 3.8 31.8 - - + +
314T ALA 2.9 17.8 + - - +
315T SER* 3.6 7.2 - - - +
316T VAL 3.2 0.4 - - - -
317T ILE* 1.3 76.6 - - - +
319T ASN* 1.3 63.1 + - - +
321T LEU* 3.2 6.9 + - + +
322T TYR* 3.1 60.8 + - + +
327T LEU* 4.1 9.9 - - + -
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Residues in contact with ASN 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244T ARG* 5.6 4.2 + - - +
315T SER 3.0 20.5 + - - +
316T VAL* 3.2 7.4 + - - +
318T LEU* 1.3 77.6 - - - +
320T ASN* 1.3 63.3 + - - +
322T TYR* 3.3 20.1 + - - +
323T LYS* 3.2 33.5 + - + +
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Residues in contact with ASN 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286T ILE* 3.8 16.8 - - + +
287T ASP 5.5 3.2 + - - +
316T VAL* 2.9 33.5 + - - +
317T ILE* 3.6 12.4 - - - +
318T LEU 3.2 0.2 - - - -
319T ASN* 1.3 75.5 - - - +
321T LEU* 1.3 59.0 + - - +
323T LYS* 3.1 23.9 + - - +
324T GLN* 2.9 52.1 + - - +
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Residues in contact with LEU 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259T ILE* 4.2 17.7 - - + -
277T ILE* 3.9 37.2 - - + -
280T LEU* 5.4 0.4 - - + -
286T ILE* 3.8 20.4 - - + +
289T ILE* 4.2 6.1 - - + -
306T ILE* 3.6 28.3 - - + -
317T ILE* 2.9 22.8 + - + +
318T LEU* 3.2 9.8 + - + +
320T ASN* 1.3 75.4 - - - +
322T TYR* 1.3 57.0 + - - +
324T GLN* 4.5 0.4 - - - +
325T THR* 2.5 46.3 + - + +
327T LEU* 3.9 17.0 - - + -
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Residues in contact with TYR 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J GLU* 2.5 29.5 + - - -
244T ARG* 3.4 46.0 - - + +
245T SER* 3.7 12.9 + - - -
247T ALA* 3.9 6.6 + - - +
318T LEU* 3.1 44.0 + - + +
319T ASN* 3.6 18.6 - - - +
320T ASN 3.2 0.2 - - - -
321T LEU* 1.3 76.4 - - - +
323T LYS* 1.3 62.0 + - + +
325T THR 3.3 15.4 - - - +
327T LEU* 3.7 38.8 - - + -
328T GLN* 3.7 29.7 - - + +
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Residues in contact with LYS 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319T ASN* 3.2 21.7 + - + +
320T ASN* 3.1 30.4 + - - +
322T TYR* 1.3 78.8 - - + +
324T GLN* 1.3 69.5 + - + +
325T THR 3.7 0.6 + - - +
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Residues in contact with GLN 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276T LYS* 5.7 1.2 - - - +
280T LEU* 3.4 33.9 - - + +
285T LYS* 3.3 22.5 + - - +
286T ILE* 4.0 9.6 - - - +
320T ASN* 2.9 44.8 + - - +
321T LEU* 4.5 1.1 - - - +
323T LYS* 1.3 88.4 - - + +
325T THR* 1.3 62.5 + - + +
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Residues in contact with THR 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273T MET* 5.0 0.7 - - - -
276T LYS* 4.6 4.3 - - + -
277T ILE* 3.7 35.7 - - + +
280T LEU* 3.8 18.8 - - + -
321T LEU* 2.5 30.3 + - + +
322T TYR 3.3 10.4 - - - +
323T LYS 3.7 0.5 - - - -
324T GLN* 1.3 82.0 - - - +
326T PRO* 1.4 71.5 - - + +
327T LEU* 3.1 21.8 + - - +
328T GLN 3.1 12.6 - - - +
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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