Contacts of the helix formed by residues 319 - 337 (chain A) in PDB entry 4KXA
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 ALA 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A VAL* 4.1 11.2 - - + -
309A ILE* 4.0 25.6 - - + +
311A VAL* 4.0 20.9 - - + -
315A GLN 3.8 0.2 + - - -
316A LYS 3.2 14.3 + - - +
318A THR* 1.3 77.6 + - - +
320A GLU* 1.3 64.5 + - - +
321A TYR 3.4 1.6 - - - -
322A ALA* 3.4 8.4 + - - +
323A ALA* 3.0 22.8 + - - +
373A LEU* 4.1 8.1 - - + -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.7 24.0 - - - +
299A ARG* 3.5 21.6 + - - -
316A LYS 4.2 1.8 + - - +
317A HIS* 3.5 24.5 - - - +
318A THR 3.4 1.4 - - - -
319A ALA* 1.3 75.6 - - - +
321A TYR* 1.3 64.6 + - - +
323A ALA* 3.1 8.3 + - - +
324A ASN* 3.0 24.6 + - - +
1C NAG 4.0 19.7 + - - +
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A THR 4.7 2.2 + - - +
319A ALA 3.4 0.4 - - - -
320A GLU* 1.3 77.1 - - - +
322A ALA* 1.3 62.8 + - - +
324A ASN* 3.0 6.8 + - + +
325A ILE* 3.0 44.7 + - + +
374A TYR* 3.6 36.9 + + + +
384A GLN* 3.5 43.7 - - + -
387A VAL* 3.8 21.5 - - + -
388A ALA* 3.5 11.7 - - + +
431A GLU* 3.1 21.4 + - - -
434A TRP* 3.3 21.1 - - - -
1C NAG 3.6 33.5 + - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 3.5 7.6 - - + -
318A THR 5.2 0.6 + - - -
319A ALA* 3.4 9.1 + - - +
320A GLU 3.3 0.6 - - - -
321A TYR* 1.3 79.6 - - - +
323A ALA* 1.3 53.3 + - - +
325A ILE* 4.0 4.1 - - - +
326A THR* 2.7 38.5 + - - -
372A LEU* 3.4 46.6 + - + +
374A TYR* 5.8 0.2 - - - +
387A VAL* 4.2 13.2 - - + +
391A VAL* 4.5 4.5 - - + +
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.7 13.7 - - + +
298A LYS 5.6 0.2 - - - -
299A ARG* 3.1 46.2 - - + +
307A LEU 6.0 0.4 - - - +
309A ILE* 3.2 15.0 - - + +
319A ALA 3.0 13.5 + - - +
320A GLU 3.2 10.1 - - - +
321A TYR 3.1 0.2 - - - -
322A ALA* 1.3 76.2 - - - +
324A ASN* 1.3 63.6 + - - +
326A THR* 3.8 2.8 - - - -
327A LYS 3.2 15.6 + - - -
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Residues in contact with ASN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG* 3.2 25.1 + - - +
320A GLU 3.0 10.5 + - - +
321A TYR* 3.0 11.5 + - + +
323A ALA* 1.3 75.5 - - - +
325A ILE* 1.3 71.5 + - + +
327A LYS* 3.3 7.1 + - - +
328A SER* 3.0 23.7 + - - -
1C NAG 1.4 63.5 + - - +
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Residues in contact with ILE 325 (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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321A TYR* 3.0 57.4 + - + +
322A ALA* 4.1 5.4 - - - +
324A ASN* 1.3 80.8 - - + +
326A THR* 1.3 54.6 - - - +
328A SER* 3.2 3.8 + - - -
329A VAL* 2.8 47.2 + - + +
388A ALA* 3.9 22.7 - - + +
391A VAL* 3.5 27.4 - - + -
392A ALA 4.7 0.2 - - - +
427A VAL* 6.3 0.7 - - - -
430A ALA* 4.4 18.6 - - + -
431A GLU* 4.0 8.1 - - + +
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Residues in contact with THR 326 (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 LEU* 4.4 17.5 - - + -
309A ILE* 4.0 4.8 - - + +
322A ALA 2.7 23.5 + - - -
323A ALA* 3.8 5.8 - - - -
325A ILE* 1.3 76.8 - - - +
327A LYS* 1.3 57.7 + - - +
330A PHE* 2.8 37.1 + - + +
346A LEU* 4.0 17.0 - - + -
348A LYS* 3.3 39.2 - - + +
391A VAL* 3.5 4.5 - - - +
395A LEU* 3.9 15.2 - - + +
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Residues in contact with LYS 327 (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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299A ARG* 4.2 20.8 - - + +
300A ILE 2.6 33.4 + - - +
301A SER* 3.5 7.1 + - - -
302A ASN* 3.4 16.3 + - - +
307A LEU* 4.0 10.7 - - + +
323A ALA 3.2 10.9 + - - +
324A ASN* 3.3 10.5 - - - +
326A THR* 1.3 77.7 - - - +
328A SER* 1.3 65.0 + - - +
330A PHE* 3.7 0.2 - - - +
331A ASP* 3.0 51.7 + - - +
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Residues in contact with SER 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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324A ASN 3.0 12.9 + - - -
325A ILE* 3.8 4.3 - - - -
327A LYS* 1.3 82.6 - - - +
329A VAL* 1.3 58.9 + - - +
331A ASP* 3.6 5.6 + - - +
332A TYR* 3.1 27.5 + - - +
429A HIS* 3.6 22.9 + - - -
430A ALA* 3.9 21.3 - - - -
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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
----------------------------------------------------------
325A ILE* 2.8 39.1 + - + +
328A SER* 1.3 71.0 - - - +
330A PHE* 1.3 59.0 + - - +
332A TYR* 3.7 5.2 - - - +
333A PHE* 2.9 63.3 + - + +
392A ALA* 4.0 11.0 - - + -
395A LEU* 3.8 15.5 - - + -
426A GLY* 3.7 29.6 - - - +
427A VAL* 4.4 1.6 - - - +
429A HIS* 5.9 0.2 - - + -
430A ALA* 4.3 10.1 - - + -
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.8 21.5 - - - -
303A SER* 3.7 22.4 - - - -
305A LYS* 5.3 4.0 - - + -
307A LEU* 4.0 26.2 - - + -
326A THR* 2.8 23.7 + - + +
327A LYS 3.7 2.2 - - - +
329A VAL* 1.3 77.5 - - - +
331A ASP* 1.3 65.6 + - - +
333A PHE* 4.0 3.3 - - - +
334A GLU* 3.2 31.8 + - - +
341A TYR* 3.4 51.8 - + + -
346A LEU* 4.0 16.6 - - + -
395A LEU* 3.9 15.3 - - + +
399A TRP* 4.2 10.8 - + - -
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Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.6 12.6 - - - -
302A ASN* 3.0 56.6 + - - +
303A SER* 5.0 0.7 + - - -
327A LYS* 3.0 37.1 + - - +
328A SER* 3.8 5.2 - - - +
330A PHE* 1.3 76.5 - - - +
332A TYR* 1.3 61.1 + - - +
334A GLU* 4.2 5.0 - - - +
335A GLU* 3.5 22.7 + - - +
429A HIS* 6.1 1.1 - - - +
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Residues in contact with TYR 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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328A SER 3.1 18.4 + - - +
329A VAL* 3.7 4.5 - - - +
330A PHE 3.3 0.2 - - - -
331A ASP* 1.3 77.4 - - - +
333A PHE* 1.3 86.2 + + - +
335A GLU* 3.3 16.0 + - - +
336A TYR* 2.8 53.6 + + + +
425A LEU* 3.7 37.9 + - + +
426A GLY* 4.1 9.0 - - - -
428A ASN* 5.9 0.5 + - - -
429A HIS* 3.4 42.3 + + + +
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Residues in contact with PHE 333 (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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329A VAL* 2.9 37.3 + - + +
332A TYR* 1.3 100.7 - + - +
334A GLU* 1.3 59.3 + - - +
336A TYR* 4.2 4.0 - + + +
337A PHE* 2.8 57.0 + + + +
392A ALA 3.7 7.9 - - - -
395A LEU* 4.0 12.6 - - + -
396A VAL* 3.4 28.9 - - + -
399A TRP* 3.7 20.0 - + + -
422A PHE* 3.2 39.7 - + + -
423A GLU* 4.9 0.4 - - - -
425A LEU* 4.8 0.4 - - + -
426A GLY* 3.6 10.8 - - - -
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Residues in contact with GLU 334 (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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302A ASN* 5.9 0.7 - - - +
303A SER* 2.9 30.8 + - - -
305A LYS* 4.0 4.7 + - - -
330A PHE* 3.2 23.4 + - - +
331A ASP* 4.2 6.0 - - - +
333A PHE* 1.3 75.7 - - - +
335A GLU* 1.3 60.6 + - - +
338A ALA* 3.3 17.0 + - - -
339A MET 3.2 35.1 + - - +
340A ASN* 3.8 19.0 - - - +
341A TYR* 3.2 28.7 + - - +
399A TRP* 3.7 9.5 - - + -
1007A NAG 5.2 2.8 + - - -
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Residues in contact with GLU 335 (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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331A ASP 3.5 12.5 + - - +
332A TYR* 3.3 17.0 + - - +
333A PHE 3.1 0.4 - - - -
334A GLU* 1.3 78.2 - - - +
336A TYR* 1.3 63.7 + - - +
338A ALA* 3.5 10.9 + - - +
429A HIS* 5.9 2.3 - - - -
499A GLN* 5.1 1.0 + - - -
503A GLN* 4.8 1.0 + - - -
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Residues in contact with TYR 336 (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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332A TYR* 2.8 52.3 + + + +
333A PHE* 3.1 8.7 + + + +
335A GLU* 1.3 76.4 - - - +
337A PHE* 1.3 77.5 + + - +
338A ALA 3.2 0.2 - - - -
421A PHE* 5.7 0.2 - - - -
422A PHE* 3.7 28.9 - + - -
425A LEU* 4.2 15.5 - - + +
490A GLU* 4.4 10.4 + - - -
495A PRO* 4.6 2.4 + - - +
498A PHE* 4.4 3.6 - - - -
499A GLN* 3.3 60.5 + - + +
502A CYS* 5.7 1.1 - - + -
503A GLN* 2.8 24.1 + - - +
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Residues in contact with PHE 337 (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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333A PHE* 2.8 60.6 + + + +
336A TYR* 1.3 82.7 - + - +
338A ALA* 1.3 70.4 + - - +
339A MET* 3.1 6.5 + - - +
396A VAL* 4.6 4.7 - - + -
399A TRP* 3.8 33.2 - + + +
400A PHE* 3.4 32.5 - + - -
422A PHE* 3.8 44.2 - + + -
502A CYS* 5.0 6.5 - - + -
503A GLN* 3.4 21.0 - - + +
506A LEU* 3.8 18.4 - - + +
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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
------------------------------------------------------------
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