Contacts of the helix formed by residues 332 - 349 (chain A) in PDB entry 4X61
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 ILE 332 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP* 3.0 6.9 + - - +
331A PRO* 1.3 101.5 - - + +
333A LYS* 1.3 62.0 + - - +
334A TYR 3.3 2.2 - - - -
335A SER* 3.3 6.9 + - - +
336A GLN* 2.8 50.6 + - + +
565A LEU* 4.8 2.0 - - + -
573A SER* 4.6 16.4 - - - -
574A PRO* 3.0 36.6 - - + +
575A GLY 4.6 0.7 - - - -
576A MET* 4.5 4.9 - - + -
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE 4.7 0.2 + - - -
330A ASP* 2.9 22.8 + - + +
332A ILE* 1.3 76.4 - - - +
334A TYR* 1.3 90.7 + - + +
336A GLN* 3.5 2.4 - - - +
337A TYR* 3.0 40.8 + - + -
371A LEU* 5.1 0.9 - - - -
435A GLU* 2.8 35.8 + - + +
565A LEU* 4.1 29.3 - - + +
576A MET* 4.7 4.2 - - - +
578A SER* 4.3 8.5 + - - +
579A TRP* 3.7 21.5 - - + -
701A SAM 2.9 20.4 + - - -
702A 3XV 3.7 11.7 - - - +
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Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE 3.2 29.2 + - - -
328A GLU* 3.4 25.9 - - - +
330A ASP* 3.7 23.7 + - + +
332A ILE 3.3 0.2 - - - -
333A LYS* 1.3 92.1 + - - +
335A SER* 1.3 56.8 + - - +
337A TYR* 3.1 5.4 + - - +
338A GLN* 2.8 35.4 + - - +
370A PRO* 3.5 29.2 - - + +
371A LEU* 3.7 20.9 - - + -
374A ALA* 4.4 5.7 - - + +
377A ARG* 4.9 14.1 - - - +
701A SAM 3.0 37.3 + - - -
702A 3XV 4.5 0.3 - - - -
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP 5.7 0.2 + - - -
331A PRO 4.4 11.2 - - - -
332A ILE* 3.3 13.9 + - - +
334A TYR* 1.3 76.4 - - - +
336A GLN* 1.3 70.7 + - - +
338A GLN* 3.3 12.3 + - - +
339A GLN* 3.0 23.6 + - - +
377A ARG* 6.0 0.2 - - - +
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 2.8 41.6 + - + +
333A LYS 3.5 5.6 - - - +
335A SER* 1.3 81.7 + - - +
337A TYR* 1.3 60.4 + - - +
339A GLN* 3.4 5.4 + - - +
340A ALA* 3.1 18.5 + - - +
559A LEU* 3.8 7.4 - - + -
563A ILE* 3.2 40.6 - - - +
564A THR 3.4 16.4 + - - +
565A LEU* 3.8 20.2 - - + -
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Residues in contact with TYR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 3.0 33.6 + - + +
334A TYR 3.1 5.6 + - - +
336A GLN* 1.3 72.8 - - - +
338A GLN* 1.3 66.5 + - - +
340A ALA* 3.2 3.2 + - - +
341A ILE* 3.2 30.9 + - + +
371A LEU* 3.7 30.5 - - + -
374A ALA* 5.0 2.2 - - + -
433A VAL* 3.9 22.4 - - + -
434A SER 2.5 29.8 + - - -
435A GLU* 3.4 29.7 - - + +
437A LEU* 4.7 3.6 - - - +
464A ILE* 4.0 19.7 - - + -
465A PRO* 4.1 5.2 - - - +
559A LEU* 3.6 30.9 - - + +
565A LEU* 4.0 9.6 - - + -
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TYR 2.8 15.8 + - - +
335A SER* 3.3 15.0 + - - +
337A TYR* 1.3 74.0 - - - +
339A GLN* 1.3 56.9 + - - +
341A ILE* 3.3 1.0 + - - -
342A TYR* 3.0 26.9 + - - +
374A ALA* 3.5 29.5 - - + +
377A ARG* 3.1 49.1 + - - +
378A ALA* 3.4 13.5 - - + +
381A GLN* 3.1 26.6 + - - +
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A SER 3.0 13.4 + - - +
336A GLN* 3.7 12.3 - - - +
337A TYR 3.3 0.2 - - - -
338A GLN* 1.3 77.2 - - - +
340A ALA* 1.3 55.8 + - - +
342A TYR* 3.2 38.2 + - - +
343A LYS* 2.9 41.6 + - + +
381A GLN* 4.1 14.8 + - - +
563A ILE* 3.8 26.5 - - + -
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN 3.1 16.0 + - - +
337A TYR 3.2 6.0 + - - +
339A GLN* 1.3 76.9 - - - +
341A ILE* 1.3 60.9 + - - +
343A LYS* 5.0 0.7 - - - -
344A CYS* 3.3 22.0 + - - +
464A ILE* 3.8 12.0 - - + +
559A LEU* 3.7 29.2 - - + -
560A TYR* 3.6 23.1 - - + +
563A ILE* 3.9 10.3 - - + +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TYR* 3.2 21.8 + - + +
338A GLN 3.7 4.5 - - - +
340A ALA* 1.3 74.7 - - - +
342A TYR* 1.3 66.1 + - - +
344A CYS* 3.0 6.3 + - - +
345A LEU* 2.9 35.7 + - + +
361A LEU* 4.0 23.6 - - + -
371A LEU* 4.8 2.2 - - + +
374A ALA* 4.3 5.2 - - + +
375A SER* 3.4 34.3 - - - +
378A ALA* 3.9 13.5 - - + -
431A ILE* 5.2 4.3 - - + -
433A VAL* 4.3 22.9 - - + -
464A ILE* 4.3 15.3 - - + -
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Residues in contact with TYR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN 3.0 14.8 + - - +
339A GLN* 3.3 39.0 - - - +
341A ILE* 1.3 78.0 - - - +
343A LYS* 1.3 70.1 + - + +
345A LEU* 3.6 3.8 + - - +
346A LEU* 3.5 45.6 + - + +
378A ALA* 3.8 12.7 - - + +
381A GLN* 3.5 60.2 + - + +
382A ALA* 3.8 11.6 - - + +
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN* 2.9 28.6 + - - +
340A ALA* 5.0 0.4 - - - -
342A TYR* 1.3 89.1 - - + +
344A CYS* 1.3 61.2 + - - +
346A LEU* 3.6 4.9 + - - +
347A ASP* 2.8 31.4 + - - +
560A TYR* 3.7 18.6 - - + -
561A GLN* 3.8 17.3 + - + +
562A ASP* 2.7 35.8 + - - +
563A ILE* 4.5 18.1 - - + +
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA 3.3 16.3 + - - +
341A ILE* 3.0 8.3 + - - +
343A LYS* 1.3 80.0 - - - +
345A LEU* 1.3 56.5 + - - +
347A ASP* 3.4 3.1 + - - +
348A ARG* 3.0 30.7 + - - +
431A ILE* 3.6 26.5 - - + -
462A VAL* 3.8 39.5 - - - -
464A ILE* 4.3 4.0 - - + -
560A TYR* 3.4 21.1 - - + -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 2.9 29.9 + - + +
342A TYR 3.9 2.9 - - - +
344A CYS* 1.3 73.6 - - - +
346A LEU* 1.3 58.6 + - - +
348A ARG* 2.8 24.4 + - - -
349A VAL* 2.8 21.3 + - + +
359A GLN* 4.2 19.3 - - + -
361A LEU* 4.3 2.9 - - + -
375A SER 5.3 0.4 - - - +
378A ALA 3.7 26.7 - - - +
379A ALA* 4.0 14.1 - - - -
382A ALA* 4.2 10.8 - - + -
384A ARG* 4.5 12.8 - - + -
386A ILE* 3.7 27.1 - - + -
431A ILE* 4.3 15.0 - - + -
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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
----------------------------------------------------------
342A TYR* 3.5 44.5 + - + +
343A LYS* 3.8 9.4 - - + +
345A LEU* 1.3 77.6 - - - +
347A ASP* 1.3 65.9 + - - +
349A VAL 3.3 17.9 - - - +
350A PRO* 4.5 2.4 - - - +
382A ALA* 3.6 31.2 - - + +
384A ARG* 4.0 18.9 + - - +
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Residues in contact with ASP 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 LYS* 2.8 19.0 + - - +
344A CYS 3.6 8.1 - - - +
345A LEU 3.1 0.6 - - - -
346A LEU* 1.3 82.7 - - - +
348A ARG* 1.3 62.3 + - + +
349A VAL 3.6 0.9 + - - -
350A PRO* 5.2 2.1 - - - +
560A TYR* 3.2 10.5 + - - +
561A GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A CYS* 3.0 25.7 + - - +
345A LEU* 2.8 9.6 + - - +
347A ASP* 1.3 76.0 - - + +
349A VAL* 1.3 64.9 + - - +
350A PRO* 4.0 5.8 - - - +
357A ASN* 4.7 3.6 + - - -
359A GLN* 3.2 31.7 + - - +
430A ASP* 3.2 26.1 + - - +
431A ILE* 4.1 19.3 - - - -
458A LYS* 4.4 2.8 - - - +
460A ASP* 2.6 58.0 + - - +
461A GLY* 4.2 3.6 - - - -
462A VAL* 3.7 16.6 - - + +
560A TYR* 5.7 0.9 - - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 2.8 22.5 + - - +
346A LEU 3.3 11.3 - - - +
348A ARG* 1.3 84.1 - - - +
350A PRO* 1.4 59.8 - - + +
353A GLU* 5.0 3.1 - - + +
357A ASN* 3.5 47.6 - - + +
359A GLN* 4.0 20.4 - - + +
384A ARG* 2.7 64.7 + - + +
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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