Contacts of the helix formed by residues 314 - 334 (chain A) in PDB entry 6UZA
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 PHE 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 5.4 12.1 - + - -
270A SER* 3.8 31.6 - - - -
271A ARG* 4.9 5.6 - - + -
274A ILE* 3.7 38.6 - - + -
311A GLU* 3.8 13.7 - - - -
313A GLU* 1.3 105.0 + - + +
315A LYS* 1.3 62.0 + - - +
316A ASN 3.4 1.6 - - - -
317A ASP* 3.6 16.3 + - - -
318A TYR* 3.2 31.7 + - + -
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Residues in contact with LYS 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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308A ALA* 3.4 34.3 - - + +
309A ASN* 5.2 4.9 - - - +
311A GLU 4.5 1.1 - - - -
312A LYS* 3.4 20.2 + - - +
313A GLU* 3.2 2.5 + - - -
314A PHE* 1.3 73.9 - - - +
316A ASN* 1.3 81.9 + - - +
317A ASP 3.1 5.1 + - - -
318A TYR* 3.3 2.6 + - - +
319A LYS* 3.0 49.0 + - + +
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.4 0.6 - - - +
315A LYS* 1.3 96.6 + - - +
317A ASP* 1.3 62.2 + - - +
319A LYS* 4.2 10.7 - - - +
320A LYS* 3.3 34.2 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 3.7 28.8 - - + +
278A LYS* 6.3 2.9 - - - -
314A PHE* 3.6 18.3 + - - +
315A LYS 3.1 0.6 - - - -
316A ASN* 1.3 81.5 - - - +
318A TYR* 1.3 59.8 + - - +
319A LYS 3.2 1.3 - - - -
320A LYS* 3.2 24.8 + - - +
321A LEU* 3.0 33.9 + - + +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER 5.2 0.2 + - - -
273A ARG* 3.4 34.8 - - - +
274A ILE* 4.1 21.9 - - + +
277A TYR* 4.1 12.8 - + + -
304A LEU* 3.6 37.6 - - + +
307A LEU* 3.7 34.5 - - + +
308A ALA* 3.7 21.5 - - + -
311A GLU* 3.9 20.1 + - + -
314A PHE* 3.2 28.1 + - + +
315A LYS 3.3 1.8 + - - +
317A ASP* 1.3 74.4 - - - +
319A LYS* 1.3 59.5 + - - +
321A LEU* 3.9 8.0 - - + +
322A SER* 3.0 30.5 + - - -
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 4.9 11.4 + - + +
308A ALA* 4.0 18.2 - - + +
309A ASN* 4.4 18.4 + - - +
315A LYS* 3.0 37.4 + - + +
316A ASN* 4.3 13.9 - - - +
318A TYR* 1.3 76.6 - - - +
320A LYS* 1.3 57.6 + - + +
322A SER* 3.5 5.4 + - - -
323A MET* 2.9 29.3 + - - +
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 3.3 25.0 + - - +
317A ASP* 3.2 27.0 + - - +
319A LYS* 1.3 75.7 - - + +
321A LEU* 1.3 64.1 + - + +
323A MET* 3.3 7.6 + - - +
324A GLN* 3.0 31.4 + - - +
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Residues in contact with LEU 321 (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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274A ILE* 4.5 9.2 - - + +
277A TYR* 4.1 15.0 - - + +
278A LYS* 3.9 52.3 - - + +
281A ALA* 4.2 3.5 - - + +
304A LEU* 3.7 16.6 - - + -
317A ASP* 3.0 21.2 + - + +
318A TYR* 3.9 17.9 - - + +
319A LYS 3.4 0.2 - - - -
320A LYS* 1.3 78.8 - - + +
322A SER* 1.3 57.2 + - - +
324A GLN* 3.4 26.2 - - - +
325A CYS* 3.0 30.3 + - - -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.0 26.3 + - - +
304A LEU* 3.9 12.5 - - - +
305A ALA* 4.1 10.8 - - - +
318A TYR 3.0 18.5 + - - -
319A LYS* 3.9 7.2 - - - -
321A LEU* 1.3 75.9 - - - +
323A MET* 1.3 57.6 + - - +
325A CYS* 3.3 6.6 + - - +
326A LYS* 3.0 48.7 + - - +
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Residues in contact with MET 323 (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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319A LYS 2.9 18.4 + - - +
320A LYS* 3.3 8.9 + - - +
322A SER* 1.3 77.0 - - - +
324A GLN* 1.3 56.8 + - - +
326A LYS* 3.3 24.9 + - + +
327A ASP* 2.9 61.0 + - - +
376A LYS* 4.3 23.6 - - + +
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Residues in contact with GLN 324 (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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230A GLN* 5.3 3.2 + - - +
278A LYS* 4.6 4.6 + - - +
281A ALA 2.4 37.5 + - - +
282A SER* 3.9 9.2 - - - +
283A PRO* 4.9 12.0 - - + +
320A LYS 3.0 14.2 + - - +
321A LEU* 3.4 29.8 - - - +
323A MET* 1.3 74.8 - - - +
325A CYS* 1.3 62.4 - - - +
327A ASP* 3.7 10.6 - - + +
328A PHE* 3.0 27.4 + - - +
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Residues in contact with CYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA* 3.6 27.8 - - - -
286A LEU* 4.4 10.3 - - - -
297A ALA* 3.9 9.2 - - + +
300A LEU* 3.8 27.6 - - - -
301A SER* 3.8 17.9 - - - -
304A LEU* 4.0 4.5 - - - -
321A LEU 3.0 17.4 + - - +
322A SER 3.3 8.3 + - - +
324A GLN* 1.3 77.9 - - - +
326A LYS* 1.3 60.3 + - - +
328A PHE* 3.7 10.0 + - - +
329A VAL* 3.5 19.6 - - - +
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 6.2 0.7 - - + -
301A SER* 4.2 11.9 - - - +
305A ALA* 5.6 4.7 - - - +
322A SER* 3.0 35.4 + - - +
323A MET* 3.3 27.6 + - + +
324A GLN 3.2 0.2 - - - -
325A CYS* 1.3 74.8 - - - +
327A ASP* 1.3 60.8 + - - +
329A VAL* 3.2 6.7 + - - +
330A VAL* 3.0 32.8 + - + +
372A TYR 4.1 12.4 + - - -
373A GLU* 3.4 27.8 + - - +
374A VAL* 3.9 31.4 - - + +
375A LYS 5.4 0.7 - - - +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A MET* 2.9 46.2 + - - +
324A GLN* 3.3 11.5 + - + +
326A LYS* 1.3 74.6 - - - +
328A PHE* 1.3 60.5 + - - +
330A VAL* 4.0 7.7 - - - +
331A GLY* 2.9 26.2 + - - -
376A LYS* 5.0 7.8 - - - +
866A TYR* 5.1 1.1 + - - -
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Residues in contact with PHE 328 (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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283A PRO* 4.0 17.3 - - + -
286A LEU* 4.2 15.0 - - + -
287A SER* 4.0 22.2 - - - -
293A PRO* 3.7 42.2 - - + -
294A VAL* 5.0 0.2 - - - -
297A ALA* 3.7 17.7 - - + -
324A GLN 3.0 16.5 + - - +
325A CYS 3.8 5.2 - - - +
326A LYS 3.2 0.2 - - - -
327A ASP* 1.3 76.0 - - - +
329A VAL* 1.3 61.3 + - + +
331A GLY 3.4 0.9 + - - -
332A LEU* 2.9 46.8 + - + +
863A ILE* 6.1 0.4 - - + -
866A TYR* 3.5 51.2 - + - +
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Residues in contact with VAL 329 (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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294A VAL* 3.7 32.1 - - + +
297A ALA* 3.7 22.2 - - + -
298A LEU* 4.7 17.3 - - + -
325A CYS 3.5 17.3 - - - +
326A LYS* 3.2 8.2 + - - +
328A PHE* 1.3 75.6 - - + +
330A VAL* 1.3 61.9 + - + +
332A LEU* 3.2 6.2 + - - +
333A LEU* 3.0 28.6 + - - +
345A ILE* 5.0 1.6 - - + +
374A VAL* 5.5 1.8 - - + -
377A PHE* 3.6 31.0 - - + -
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Residues in contact with VAL 330 (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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326A LYS* 3.0 19.1 + - + +
327A ASP* 4.0 9.0 - - - +
329A VAL* 1.3 77.5 - - - +
331A GLY* 1.3 59.5 + - - +
333A LEU* 3.4 6.5 + - - +
334A ASP* 3.4 21.4 + - - +
374A VAL* 4.6 4.5 - - + -
376A LYS* 3.7 36.3 - - + +
377A PHE* 3.5 32.8 - - + +
380A HIS* 4.4 13.3 - - + +
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Residues in contact with GLY 331 (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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327A ASP 2.9 17.3 + - - -
328A PHE 3.7 1.8 - - - -
330A VAL* 1.3 76.9 - - - +
332A LEU* 1.3 58.9 + - - +
334A ASP* 3.8 12.2 + - - +
335A LEU* 3.6 21.3 - - - +
866A TYR* 4.1 12.9 - - - -
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Residues in contact with LEU 332 (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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293A PRO* 4.5 9.0 - - + -
294A VAL* 3.8 28.3 - - + -
328A PHE* 2.9 39.5 + - + +
329A VAL* 3.2 6.3 + - - +
331A GLY* 1.3 76.5 - - - +
333A LEU* 1.3 63.5 + - - +
334A ASP 3.2 0.4 - - - -
335A LEU* 3.7 15.1 + - + +
336A CYS* 3.9 9.9 - - - -
345A ILE* 4.3 16.3 - - + +
859A MET* 4.7 4.0 - - + -
862A LEU* 3.9 21.5 - - + +
863A ILE* 5.0 4.3 - - + +
866A TYR* 3.8 33.2 - - + -
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL 3.0 15.4 + - - +
330A VAL* 3.4 6.7 + - - +
332A LEU* 1.3 75.5 - - - +
334A ASP* 1.3 63.0 + - - +
335A LEU 3.3 0.2 - - - -
336A CYS* 3.3 17.4 - - - -
342A VAL* 4.9 4.0 - - + -
345A ILE* 3.8 30.0 - - + +
346A LEU* 3.9 22.2 - - + -
377A PHE* 3.7 39.3 - - + +
380A HIS* 3.8 28.7 - - + +
382A ASN* 3.3 26.8 + - + -
383A CYS* 4.8 0.9 - - + -
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 3.4 14.4 + - - +
331A GLY* 3.9 12.0 - - - +
332A LEU 3.2 0.6 - - - -
333A LEU* 1.3 79.0 - - - +
335A LEU* 1.3 61.5 + - + +
336A CYS 3.2 2.5 + - - +
380A HIS* 3.5 27.6 + - + -
382A ASN* 4.5 2.4 + - - +
271B ARG* 4.0 15.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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