Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 4Y2P
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 ASP 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A GLY* 3.6 7.4 - - - -
267A PHE* 2.8 26.0 + - - +
334A HIS* 1.3 92.7 - - + +
336A TRP* 1.3 72.7 + - - +
338A GLY 2.8 15.8 + - - -
339A MET* 3.0 5.7 + - - +
358A LEU 3.4 4.4 + - - -
360A THR* 2.7 33.1 + - - +
499A LEU* 3.7 8.3 - - - +
524A HIS* 3.1 15.1 - - + +
602A 3C5 2.6 41.9 + - - -
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Residues in contact with TRP 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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265A HIS 5.0 0.7 - - - +
266A GLY* 3.9 2.2 - - - -
267A PHE* 3.9 14.1 - - + +
296A TYR* 6.0 0.4 - - - +
310A MET* 3.3 35.2 - - + -
334A HIS 3.2 0.2 + - - -
335A ASP* 1.3 95.0 + - - +
337A GLY* 1.3 57.4 + - - +
339A MET* 3.1 27.3 + - + +
340A LEU* 3.0 26.7 + - - +
465A TRP* 3.2 54.0 - + + +
466A TYR* 3.4 51.4 - + - -
469A MET* 4.1 21.8 - - + -
472A ASN* 4.1 15.5 - - - -
602A 3C5 5.2 0.2 - - - -
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Residues in contact with GLY 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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264A CYS* 3.4 25.7 - - - +
265A HIS 3.3 10.7 + - - -
293A MET* 5.1 1.8 - - - -
333A GLY* 3.5 7.4 - - - -
334A HIS 3.0 5.4 + - - -
336A TRP* 1.3 77.0 - - - +
338A GLY* 1.4 58.5 + - - +
340A LEU* 3.4 6.9 + - - +
341A VAL* 3.0 34.0 + - - +
465A TRP* 4.7 3.1 - - - -
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Residues in contact with GLY 338 (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 GLY* 3.6 13.9 - - - -
334A HIS 3.3 7.6 - - - +
335A ASP 2.8 13.2 + - - -
337A GLY* 1.4 69.2 - - - +
339A MET* 1.3 66.7 + - - +
341A VAL* 3.4 5.5 + - - +
342A TRP* 3.2 28.0 + - - -
357A SER* 3.5 19.5 - - - -
360A THR* 4.0 6.7 - - - -
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Residues in contact with MET 339 (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 MET* 4.3 5.4 - - + -
335A ASP 3.0 7.9 + - - +
336A TRP* 3.1 37.6 + - + +
338A GLY* 1.3 78.9 - - - +
340A LEU* 1.3 62.6 + - - +
342A TRP* 3.4 21.0 + - + -
343A TYR* 3.1 63.0 + - + +
360A THR* 3.6 15.3 - - + +
361A PRO 3.9 11.2 - - - +
362A PHE* 4.5 7.2 - - + -
363A ILE 5.2 3.4 - - - +
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Residues in contact with LEU 340 (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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264A CYS* 4.4 5.2 - - - -
293A MET* 3.9 25.8 - - + -
310A MET* 3.7 16.7 - - + -
313A LEU* 3.7 41.5 - - + +
314A CYS* 3.9 8.7 - - - +
317A MET* 4.3 15.3 - - + -
331A PHE* 4.9 1.8 - - + -
336A TRP 3.0 12.7 + - - +
337A GLY* 3.5 10.5 - - - +
339A MET* 1.3 77.1 - - - +
341A VAL* 1.3 68.5 + - + +
343A TYR* 3.2 3.8 + - - +
344A MET* 2.9 47.4 + - + +
465A TRP* 4.2 7.0 - - + -
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Residues in contact with VAL 341 (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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264A CYS* 4.2 14.4 - - - -
331A PHE* 3.6 31.3 - - + +
332A ILE 4.0 3.6 - - - +
333A GLY* 3.8 16.2 - - - +
337A GLY 3.0 15.3 + - - +
338A GLY* 3.4 13.5 - - - +
340A LEU* 1.3 78.0 - - + +
342A TRP* 1.3 64.9 + - + +
344A MET* 3.3 9.1 + - - +
345A ALA* 3.0 18.2 + - - +
352A VAL* 5.3 0.3 - - - +
355A VAL* 3.4 25.4 - - + +
356A ALA 3.5 19.3 - - - +
357A SER* 4.7 2.0 - - - -
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Residues in contact with TRP 342 (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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338A GLY 3.2 19.5 + - - -
339A MET* 3.7 16.2 - - + +
340A LEU 3.2 1.0 - - - -
341A VAL* 1.3 76.8 - - - +
343A TYR* 1.3 57.5 + - + +
345A ALA* 3.3 4.6 + - - +
346A LEU* 3.1 30.2 + - - +
355A VAL* 3.9 29.2 - - + -
357A SER* 3.4 26.2 - - - -
360A THR* 3.0 19.9 + - + -
361A PRO 3.6 18.0 - - - -
362A PHE* 3.9 26.0 - - + -
484A ILE* 3.8 18.3 - - + +
488A ALA* 4.1 6.1 - - + -
489A LEU 3.7 17.5 - - - -
490A MET* 3.9 5.4 - - - -
507A MET* 3.5 24.9 - - + -
511A ILE* 3.7 17.0 - - + -
514A LEU* 4.2 7.6 - - + -
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Residues in contact with TYR 343 (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 MET* 4.4 11.2 - - + -
314A CYS* 3.9 8.5 - - - -
339A MET* 3.1 55.3 + - + +
340A LEU 3.2 7.6 + - - +
342A TRP* 1.3 72.0 - - - +
344A MET* 1.3 65.8 + - - +
346A LEU* 3.7 16.4 - - + +
347A PHE* 2.9 48.6 + + - +
362A PHE* 3.9 17.1 - + - -
363A ILE 4.4 9.2 + - - -
364A PRO* 5.1 0.2 - - - +
365A ALA* 4.8 3.6 + - - +
472A ASN 5.6 0.2 - - - -
475A TRP* 3.6 25.6 - + + -
476A ALA* 3.3 37.6 - - + +
479A SER* 4.4 1.5 + - - -
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Residues in contact with MET 344 (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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314A CYS* 3.6 35.8 - - - +
317A MET* 4.0 11.7 - - + -
318A VAL* 3.9 24.2 - - + +
321A LEU* 5.1 2.5 - - + -
331A PHE* 3.8 33.7 - - + -
340A LEU* 2.9 35.4 + - + +
341A VAL* 3.5 10.3 - - - +
343A TYR* 1.3 75.7 - - - +
345A ALA* 1.3 55.9 + - - +
348A TYR* 2.7 48.0 + - + -
351A ARG* 5.3 1.3 - - + -
352A VAL* 3.8 13.5 - - + -
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Residues in contact with ALA 345 (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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341A VAL 3.0 13.5 + - - +
342A TRP* 3.5 9.0 - - - +
343A TYR 3.3 0.4 - - - -
344A MET* 1.3 75.0 - - - +
346A LEU* 1.3 61.0 + - - +
349A PRO* 3.4 24.8 - - - +
352A VAL* 4.0 8.6 - - - +
355A VAL* 3.9 16.8 - - + -
484A ILE* 4.1 19.5 - - + +
486A ILE* 3.8 23.9 - - + +
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Residues in contact with LEU 346 (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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342A TRP 3.1 15.5 + - - +
343A TYR* 3.7 27.4 - - + +
344A MET 3.3 0.2 - - - -
345A ALA* 1.3 76.5 - - - +
347A PHE* 1.3 68.0 + - + +
349A PRO* 4.2 5.1 - - - +
362A PHE* 3.5 36.8 - - + -
479A SER* 3.7 18.2 - - - +
482A ARG* 2.7 51.8 + - + +
483A LYS 4.7 5.4 - - - +
484A ILE* 3.7 24.5 - - + -
510A TRP* 5.9 0.7 - - + -
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Residues in contact with PHE 347 (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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343A TYR* 2.9 40.9 + + - +
346A LEU* 1.3 79.6 - - + +
348A TYR* 1.3 89.4 + + + +
349A PRO* 3.4 7.6 - - - +
350A GLU* 4.5 1.9 - - - +
475A TRP* 3.5 65.5 - + + -
478A LYS* 4.3 9.4 - - + -
479A SER* 3.9 16.6 - - - -
482A ARG* 3.2 30.3 - - - +
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Residues in contact with TYR 348 (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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314A CYS* 4.1 20.4 - - + -
315A LYS* 3.3 33.1 + - + +
318A VAL* 3.6 41.3 - - + -
344A MET* 2.7 35.8 + - + +
347A PHE* 1.3 98.2 - + + +
349A PRO* 1.4 65.6 - - - +
350A GLU* 3.2 20.4 - - - -
351A ARG* 2.9 20.4 + - + -
352A VAL* 3.5 9.5 - - - +
475A TRP* 4.8 5.5 - + - -
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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