Contacts of the helix formed by residues 302 - 316 (chain A) in PDB entry 3Q36
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 ARG 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A HIS* 4.1 11.9 - - + +
301A LEU* 1.3 79.2 - - - +
303A HIS* 1.3 66.0 + - - +
304A GLY 3.4 2.2 - - - +
305A GLY* 3.3 4.5 + - - +
306A ARG* 3.0 22.5 + - - +
377A SER* 5.2 2.4 - - - -
378A GLN 2.7 29.7 + - - -
379A GLY* 3.3 26.2 + - - +
380A ASP* 3.4 33.8 + - - +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 1.3 74.7 - - - +
304A GLY* 1.3 69.4 + - - +
306A ARG* 3.1 32.3 + - - +
307A MET* 2.9 57.0 + - + +
348A ASN* 6.2 5.6 - - + -
374A ASN* 5.6 6.5 - - - -
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 3.4 3.8 - - - +
303A HIS* 1.3 83.6 - - - +
305A GLY* 1.3 56.5 + - - +
307A MET* 3.5 4.9 - - - +
308A GLN* 3.1 26.5 + - - +
365A PHE* 5.4 1.6 - - - -
374A ASN* 5.3 8.7 - - - -
380A ASP* 5.1 1.4 + - - -
382A HIS* 3.7 32.1 - - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 4.2 12.8 - - - -
301A LEU* 4.0 12.1 - - - +
302A ARG* 3.3 7.0 + - - +
303A HIS 3.2 0.4 - - - -
304A GLY* 1.3 73.0 - - - +
306A ARG* 1.3 65.3 + - - +
307A MET 3.0 1.8 - - - -
308A GLN 3.9 0.9 - - - -
309A TYR* 3.0 29.6 + - - +
380A ASP* 5.6 0.2 + - - -
381A TYR 5.9 0.7 - - - -
382A HIS* 3.7 21.4 + - - +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A HIS* 3.5 9.3 + - - -
301A LEU* 2.8 40.6 + - - +
302A ARG* 3.0 15.3 + - - +
303A HIS* 3.6 36.9 + - - +
305A GLY* 1.3 77.4 - - - +
307A MET* 1.3 56.8 + - - +
310A GLY* 2.8 31.5 + - - -
327A TRP* 3.7 28.5 - - + -
331A PHE* 3.9 14.8 - - + -
345A TYR* 3.2 37.9 + - - -
348A ASN* 5.8 4.4 - - - +
349A ILE* 6.1 4.7 - - - -
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A HIS* 2.9 44.3 + - + +
304A GLY* 3.5 6.5 - - - +
306A ARG* 1.3 77.2 - - + +
308A GLN* 1.3 60.4 + - - +
310A GLY* 6.4 0.2 - - - -
311A LEU* 3.0 49.0 + - + +
348A ASN* 5.6 5.6 - - + +
352A SER* 4.3 18.2 - - - +
362A TYR* 5.6 7.6 - - + -
365A PHE* 3.5 29.2 - - + -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A CYS* 3.6 17.4 - - - +
288A MET* 3.6 17.9 - - + +
291A LEU* 3.6 19.9 - - + +
304A GLY 3.1 13.4 + - - +
305A GLY 4.4 0.2 - - - +
306A ARG 3.6 0.2 - - - -
307A MET* 1.3 79.2 - - - +
309A TYR* 1.3 59.8 + - - +
311A LEU* 4.1 1.6 - - - +
312A PHE* 3.1 27.2 + - - +
365A PHE* 4.4 22.0 + - + +
370A ILE* 3.5 29.1 - - + +
382A HIS* 3.6 6.6 - - + +
383A GLY* 3.1 40.9 + - - +
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Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ILE* 3.5 8.8 - - - +
284A PHE* 3.1 30.6 - + - -
288A MET* 4.1 15.9 - - - -
291A LEU* 3.7 24.2 - - + +
292A HIS* 2.8 43.5 + - + -
295A LEU* 4.3 2.9 - - + -
301A LEU* 4.4 5.8 - - + -
305A GLY 3.0 18.2 + - - +
308A GLN* 1.3 76.3 - - - +
310A GLY* 1.3 63.7 + - - +
312A PHE* 3.9 15.9 - + - -
313A LEU* 3.0 47.0 + - + +
326A PHE* 4.0 9.7 - + - -
327A TRP* 4.1 18.8 - + + -
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ARG 2.8 23.1 + - - -
307A MET* 6.4 0.2 - - - -
308A GLN 3.3 0.2 - - - -
309A TYR* 1.3 75.7 - - - +
311A LEU* 1.3 64.6 + - - +
313A LEU* 3.2 6.5 + - - +
314A LYS* 3.1 19.9 + - - +
327A TRP* 3.7 20.9 + - - -
352A SER* 6.2 1.6 - - - -
353A PHE* 5.3 4.6 - - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A MET* 3.0 27.8 + - + +
308A GLN 4.3 1.8 - - - +
310A GLY* 1.3 74.7 - - - +
312A PHE* 1.3 58.6 + - - +
314A LYS* 3.1 12.3 + - + +
315A GLY 2.8 24.4 + - - -
352A SER* 4.1 21.1 - - - +
362A TYR* 3.4 42.4 - - + +
363A THR 3.4 13.9 - - - +
364A PRO* 3.5 20.8 - - + +
365A PHE* 3.3 36.8 - - + +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PHE* 3.9 30.1 - + - -
285A PRO* 4.2 4.7 - - + -
288A MET* 3.3 61.9 - - + -
308A GLN 3.1 9.7 + - - +
309A TYR* 3.6 15.0 - + - +
310A GLY 3.2 0.2 - - - -
311A LEU* 1.3 76.5 - - - +
313A LEU* 1.3 65.0 + - - +
315A GLY 3.1 1.7 + - - -
316A ILE* 3.0 41.1 + - + +
364A PRO* 4.9 1.5 - - - +
365A PHE 5.6 0.4 - - - +
444A PRO* 3.5 24.5 - - + -
445A ASN* 3.2 39.8 + - - +
448A PHE* 4.1 11.9 - - + -
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ILE* 4.7 7.9 - - + -
284A PHE* 4.4 6.1 - - + -
309A TYR* 3.0 55.2 + - + +
310A GLY 3.6 4.3 - - - +
312A PHE* 1.3 74.6 - - + +
314A LYS* 1.3 69.1 + - - +
316A ILE* 3.1 32.0 - - + +
318A LEU* 3.1 38.7 + - + +
323A ALA* 6.3 2.0 - - + -
326A PHE* 3.5 36.1 - - + -
327A TRP* 4.0 12.1 - - - +
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLY 3.1 12.2 + - - +
311A LEU* 3.3 15.0 - - + +
312A PHE 3.1 0.2 - - - -
313A LEU* 1.3 75.0 - - - +
315A GLY* 1.3 54.3 + - - +
317A GLY* 2.6 31.2 + - - -
318A LEU 3.4 10.1 + - - +
352A SER 3.0 26.0 + - - +
353A PHE* 3.9 41.7 - - + +
354A GLY 6.3 0.2 - - - -
362A TYR 2.5 34.1 + - - +
364A PRO* 4.5 14.0 - - - +
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU 2.8 13.6 + - - -
312A PHE 3.1 0.4 + - - -
314A LYS* 1.3 77.5 - - - +
316A ILE* 1.3 56.0 + - - +
317A GLY* 3.0 4.3 + - - -
364A PRO* 4.0 13.9 - - - +
445A ASN* 3.4 22.5 + - - +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE* 4.7 20.1 + - - +
276A ILE* 6.0 2.9 - - + -
279A LEU* 4.9 8.1 - - + -
284A PHE* 4.5 16.6 - - + -
312A PHE* 3.0 35.7 + - + +
313A LEU* 3.1 38.1 - - + +
314A LYS 3.1 0.2 + - - -
315A GLY* 1.3 74.4 - - - +
317A GLY* 1.3 57.7 + - - +
318A LEU* 4.5 10.1 - - + +
445A ASN* 3.5 11.9 - - - +
448A PHE* 3.9 35.3 - - + -
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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