Contacts of the helix formed by residues 353 - 374 (chain A) in PDB entry 4YCV
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 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ALA* 1.3 74.7 - - - +
354A TYR* 1.3 63.9 + - - +
355A ASN* 2.7 31.9 + - - +
356A ASP* 2.8 29.0 + - - +
357A LEU* 3.2 13.1 + - - +
483A ARG* 2.2 38.4 + - - +
490A GLU* 4.3 3.1 - - - +
506A THR* 3.6 17.3 - - + -
104B HIS 4.9 6.3 - - - +
105B LYS* 2.9 21.8 + - + +
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Residues in contact with TYR 354 (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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353A ASP* 1.3 77.0 - - - +
355A ASN* 1.3 80.2 + - - +
356A ASP 3.5 0.2 - - - -
357A LEU* 3.6 14.6 - - + -
358A ILE* 2.9 53.3 + - + +
469A VAL* 5.3 8.7 - - + -
470A GLU* 3.7 12.0 + - + -
482A HIS* 3.7 21.4 + + - -
483A ARG* 5.6 2.0 - - - -
490A GLU* 3.6 47.6 - - + +
491A ARG 4.9 7.9 - - - -
492A LEU* 3.6 21.4 - - + +
505A TYR* 5.2 0.4 - - - -
506A THR* 3.2 13.7 - - + +
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Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 2.7 28.4 + - - +
354A TYR* 1.3 102.8 + - - +
356A ASP* 1.3 59.6 + - - +
358A ILE* 3.2 9.0 + - - +
359A LYS* 2.9 29.6 + - - +
483A ARG* 4.3 7.1 + - - -
105B LYS* 5.4 0.7 - - - +
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TRP* 3.7 29.4 - - + -
351A TYR 5.5 0.2 - - - -
352A ALA* 3.4 10.0 - - + -
353A ASP* 2.8 24.2 + - - +
355A ASN* 1.3 75.8 - - - +
357A LEU* 1.3 57.2 + - - +
359A LYS* 3.9 5.8 - - - +
360A TRP* 2.9 28.1 + - - +
105B LYS* 2.6 33.6 + - - -
107B GLU* 4.7 4.5 - - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PHE* 4.3 16.4 - - + -
349A TRP* 4.0 22.2 - - + -
352A ALA* 5.2 1.1 - - + -
353A ASP 3.2 10.5 + - - +
354A TYR* 3.7 20.9 - - + +
355A ASN 3.1 0.4 - - - -
356A ASP* 1.3 76.0 - - - +
358A ILE* 1.3 60.0 + - - +
360A TRP* 3.2 6.2 - - - +
361A SER* 2.9 31.2 + - - -
492A LEU* 3.8 8.5 - - + -
504A ALA* 4.0 10.1 - - + -
505A TYR* 3.9 11.0 - - - +
551A GLY* 3.8 30.5 - - - +
552A GLY 3.2 26.9 - - - +
553A LEU* 4.1 4.3 - - + +
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 2.9 46.9 + - + +
355A ASN* 3.2 8.5 + - - +
357A LEU* 1.3 73.4 - - - +
359A LYS* 1.3 60.8 + - - +
361A SER* 3.0 9.5 + - - -
362A GLU* 2.9 48.3 + - - +
400A LYS* 3.8 32.8 - - + +
467A PHE* 4.1 11.9 - - + -
469A VAL* 4.7 4.9 - - + -
492A LEU* 3.6 24.9 - - + -
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Residues in contact with LYS 359 (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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355A ASN 2.9 16.5 + - - +
356A ASP* 4.1 6.7 - - - +
358A ILE* 1.3 77.3 - - - +
360A TRP* 1.3 56.0 + - - +
362A GLU* 4.4 12.1 - - + +
363A ASP* 2.9 64.7 + - - +
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Residues in contact with TRP 360 (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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261A LEU* 4.1 15.3 - - + -
264A PHE* 4.0 19.4 - + - -
265A LEU* 3.4 33.1 - - + +
268A ARG* 4.2 24.2 - - - +
270A PHE* 4.4 2.9 - + - -
347A PHE* 3.7 25.1 - + + -
349A TRP* 4.1 20.2 - + + -
356A ASP 2.9 19.3 + - - +
357A LEU* 3.2 10.5 - - - +
359A LYS* 1.3 78.0 - - - +
361A SER* 1.3 64.3 + - - +
363A ASP* 3.8 4.9 - - - +
364A PHE* 2.9 53.3 + + + +
502A LEU* 4.5 3.8 - - + -
553A LEU* 3.8 24.9 - - + -
555A LEU* 4.4 6.1 - - + -
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Residues in contact with SER 361 (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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357A LEU 2.9 15.4 + - - -
358A ILE 3.0 7.6 + - - -
360A TRP* 1.3 80.0 - - - +
362A GLU* 1.3 61.1 + - - +
364A PHE 3.3 0.2 + - - -
365A PHE* 2.9 38.5 + - - +
398A TYR* 4.8 1.3 - - - -
467A PHE* 3.7 20.9 - - - -
492A LEU* 4.1 0.5 - - - +
494A MET* 4.6 3.8 - - - -
502A LEU* 3.2 38.1 - - - +
553A LEU* 3.8 2.4 - - - +
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 2.9 26.2 + - - +
359A LYS* 3.9 12.4 - - - +
361A SER* 1.3 76.5 - - - +
363A ASP* 1.3 60.1 + - - +
366A SER* 2.8 35.0 + - - -
396A PRO* 3.9 15.8 - - + +
397A PRO* 3.4 37.1 - - - +
398A TYR* 3.5 33.1 + - + +
400A LYS* 3.5 21.7 + - - -
467A PHE* 4.1 5.0 - - + -
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Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 3.8 11.9 - - + -
268A ARG* 5.4 2.1 + - - +
359A LYS* 2.9 55.5 + - - +
360A TRP* 3.8 5.4 - - - +
362A GLU* 1.3 79.8 - - - +
364A PHE* 1.3 56.9 + - - +
366A SER* 2.9 19.6 + - - -
367A GLN* 2.9 35.5 + - - +
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Residues in contact with PHE 364 (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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257A ILE* 5.1 4.5 - - + -
260A PHE* 3.7 25.9 - + - -
261A LEU* 3.8 33.0 - - + -
264A PHE* 3.3 32.7 - + + -
360A TRP* 2.9 39.6 + + + +
361A SER 3.3 1.5 + - - +
363A ASP* 1.3 76.8 - - - +
365A PHE* 1.3 85.5 + + - +
368A LEU* 2.9 56.6 + - + +
555A LEU* 4.1 15.7 - - + -
560A ILE* 4.8 5.2 - - + -
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Residues in contact with PHE 365 (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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361A SER 2.9 26.5 + - - +
364A PHE* 1.3 92.6 - + - +
366A SER* 1.3 67.8 + - - +
368A LEU* 3.7 7.8 - - + +
369A VAL* 2.9 33.0 + - + +
394A PHE* 3.9 21.5 - + + -
398A TYR* 3.7 16.8 - - + +
494A MET* 3.5 35.4 - - + -
496A ILE* 3.9 11.7 - - + -
501A VAL* 3.5 15.9 - - + -
502A LEU* 3.6 22.0 - - + -
555A LEU* 4.3 1.3 - - + -
560A ILE* 3.8 29.8 - - + -
564A LEU* 6.0 0.9 - - + -
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Residues in contact with SER 366 (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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362A GLU 2.8 23.9 + - - -
363A ASP* 2.9 10.7 + - - -
365A PHE* 1.3 77.2 - - - +
367A GLN* 1.3 69.1 + - - +
369A VAL* 3.8 0.7 - - - +
370A TYR* 2.9 30.1 + - - +
376A TYR* 3.5 26.8 - - - -
394A PHE* 3.8 10.3 - - - -
396A PRO* 3.7 23.9 - - - +
398A TYR* 3.7 1.4 + - - -
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Residues in contact with GLN 367 (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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260A PHE* 3.8 16.3 - - + -
264A PHE* 3.2 24.6 - - + -
268A ARG* 4.5 6.1 + - - +
363A ASP* 2.9 32.8 + - - +
364A PHE 4.2 0.2 - - - +
366A SER* 1.3 85.9 + - - +
368A LEU* 1.3 56.2 + - - +
370A TYR* 3.8 5.8 - - - +
371A HIS* 2.8 29.8 + - - +
376A TYR* 5.2 2.0 - - - +
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Residues in contact with LEU 368 (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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257A ILE* 4.3 18.2 - - + +
260A PHE* 3.5 37.6 - - + -
364A PHE* 2.9 46.4 + - + +
365A PHE* 3.7 9.4 - - + +
367A GLN* 1.3 73.8 - - - +
369A VAL* 1.3 61.6 + - + +
371A HIS* 3.0 5.8 + - - +
372A LEU* 2.9 46.1 + - + +
560A ILE* 4.5 9.4 - - + -
564A LEU* 3.7 26.0 - - + -
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Residues in contact with VAL 369 (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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365A PHE* 2.9 23.1 + - + +
366A SER 3.8 2.9 - - - +
368A LEU* 1.3 76.2 - - + +
370A TYR* 1.3 58.0 + - - +
372A LEU* 4.8 1.8 - - - -
373A PHE* 2.9 31.7 + - + -
375A THR 3.3 19.2 - - - +
376A TYR* 3.6 20.9 - - - +
378A ILE* 3.8 19.1 - - + -
394A PHE* 3.4 35.2 - - + -
564A LEU* 4.1 17.9 - - + -
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Residues in contact with TYR 370 (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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366A SER 2.9 18.1 + - - +
367A GLN* 3.9 6.5 - - - +
369A VAL* 1.3 75.5 - - - +
371A HIS* 1.3 64.2 + - - +
374A GLY* 2.8 47.8 + - - +
375A THR* 3.8 17.5 + - - -
376A TYR* 3.6 37.7 - + + +
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Residues in contact with HIS 371 (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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256A LYS* 4.7 19.1 + - + -
260A PHE* 4.0 37.8 - + + +
367A GLN 2.8 19.7 + - - +
368A LEU* 3.0 9.8 + - - +
370A TYR* 1.3 79.6 - - - +
372A LEU* 1.3 76.0 + - + +
374A GLY 4.7 0.2 + - - -
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Residues in contact with LEU 372 (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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253A THR* 4.3 16.8 - - + -
256A LYS* 4.0 31.8 + - + +
257A ILE* 4.0 20.0 - - + +
368A LEU* 2.9 23.9 + - + +
369A VAL* 5.0 0.2 - - - -
371A HIS* 1.3 91.5 - - - +
373A PHE* 1.3 93.7 + - + +
374A GLY 3.6 0.4 + - - -
564A LEU* 3.6 32.3 - - + -
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Residues in contact with PHE 373 (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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253A THR* 5.6 2.9 - - + -
369A VAL* 2.9 26.7 + - + +
372A LEU* 1.3 101.5 - - + +
374A GLY* 1.3 61.8 + - - +
375A THR* 3.0 23.9 + - + +
378A ILE* 3.3 33.0 - - + -
564A LEU* 3.1 41.7 - - + -
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A TYR* 2.8 49.9 + - - -
371A HIS 4.7 0.2 + - - -
372A LEU 3.6 1.6 + - - -
373A PHE* 1.3 71.6 - - - +
375A THR* 1.3 59.6 + - - +
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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