Contacts of the helix formed by residues 353 - 374 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 5.0 4.9 - - + +
105A LYS* 3.8 20.7 - - + +
352B ALA* 1.3 74.6 - - - +
354B TYR* 1.3 59.4 + - + +
355B ASN* 4.1 17.5 + - - +
356B ASP* 2.7 62.2 + - - +
357B LEU* 3.5 3.2 + - - -
483B ARG* 2.7 33.0 + - - +
490B GLU* 5.2 1.3 - - - +
506B THR* 3.6 12.8 - - + -
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP* 1.3 77.8 - - - +
355B ASN* 1.3 76.8 + - - +
356B ASP 3.2 0.4 - - - -
357B LEU* 2.9 23.0 + - + +
358B ILE* 2.8 56.9 + - + +
469B VAL* 4.4 18.8 - - + -
470B GLU* 4.5 8.3 + - + +
482B HIS* 4.1 15.8 + - - -
483B ARG* 5.7 0.2 - - - -
490B GLU* 3.1 57.2 + - + +
491B ARG 5.0 2.7 - - - +
492B LEU* 4.3 9.6 - - + -
505B TYR* 4.9 1.3 - - - -
506B THR* 3.2 21.0 - - + +
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Residues in contact with ASN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP* 2.8 18.5 + - - +
354B TYR* 1.3 102.2 + - - +
356B ASP* 1.3 60.1 + - - +
358B ILE* 3.9 6.5 - - - +
359B LYS* 3.0 29.8 + - - +
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 5.5 0.7 - - - +
349B TRP* 3.9 29.5 - - + -
351B TYR 4.4 1.8 - - - +
352B ALA* 3.3 12.8 - - + -
353B ASP* 2.7 40.8 + - - +
355B ASN* 1.3 79.1 - - - +
357B LEU* 1.3 55.7 + - - +
359B LYS* 3.8 6.0 - - - +
360B TRP* 2.9 27.7 + - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 4.0 30.1 - - + -
349B TRP* 4.1 13.5 - - + -
352B ALA* 5.0 2.7 - - + -
353B ASP 4.2 4.0 - - - +
354B TYR* 2.9 29.9 + - + +
356B ASP* 1.3 76.5 - - - +
358B ILE* 1.3 58.0 + - - +
360B TRP* 3.2 7.1 - - - +
361B SER* 2.8 30.6 + - - -
492B LEU* 3.8 8.7 - - + -
504B ALA* 3.9 19.5 - - + -
505B TYR 3.6 28.0 - - - +
551B GLY* 4.2 17.5 - - - -
552B GLY 3.9 6.3 - - - +
553B LEU* 4.2 3.1 - - + +
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Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR* 2.8 55.8 + - + +
355B ASN* 3.4 7.2 + - - +
357B LEU* 1.3 69.1 - - - +
359B LYS* 1.3 68.1 + - - +
360B TRP 3.0 1.1 - - - -
361B SER* 3.1 5.6 + - - -
362B GLU* 2.9 34.0 + - - +
400B LYS* 3.4 33.4 - - + -
467B PHE* 4.0 19.5 - - + -
469B VAL* 5.1 5.2 - - + -
492B LEU* 3.5 25.1 - - + -
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASN 3.0 17.1 + - - +
356B ASP* 3.9 5.8 - - - +
358B ILE* 1.3 77.2 - - - +
360B TRP* 1.3 59.0 + - - +
362B GLU* 4.5 10.5 - - - +
363B ASP* 2.9 62.1 + - - +
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Residues in contact with TRP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 4.2 11.9 - - + -
264B PHE* 3.8 23.9 - + - -
265B LEU* 3.4 34.8 - - + +
268B ARG* 4.2 19.2 - - - +
270B PHE* 4.7 3.3 - + - -
345B CYS* 6.2 0.2 - - - -
347B PHE* 3.7 28.6 - + + -
349B TRP* 4.3 19.5 - + + -
356B ASP 2.9 17.6 + - - +
357B LEU* 3.2 13.9 - - - +
358B ILE 3.0 0.2 - - - -
359B LYS* 1.3 80.2 - - - +
361B SER* 1.3 64.0 + - - +
363B ASP* 3.8 4.4 - - - +
364B PHE* 2.9 52.1 + + + +
502B LEU* 4.6 0.7 - - + -
553B LEU* 3.8 23.8 - - + -
555B LEU* 4.3 10.8 - - + -
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU 2.8 19.4 + - - -
358B ILE* 3.1 7.1 + - - -
360B TRP* 1.3 83.0 - - - +
362B GLU* 1.3 65.5 + - - +
364B PHE 3.3 0.9 + - - -
365B PHE* 3.0 32.2 + - - +
398B TYR* 5.0 0.9 - - - -
467B PHE* 3.7 22.3 - - - -
492B LEU* 4.5 1.4 - - - +
494B MET* 4.5 2.2 - - - -
502B LEU* 3.4 30.9 - - - +
553B LEU* 3.7 7.6 - - - +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE* 2.9 23.8 + - - +
359B LYS* 3.9 8.2 - - - +
361B SER* 1.3 74.7 - - - +
363B ASP* 1.3 55.7 + - - +
366B SER* 2.5 40.9 + - - -
396B PRO* 3.9 13.4 - - + +
397B PRO* 3.7 24.0 - - - +
398B TYR* 3.4 34.6 + - + +
400B LYS* 2.9 37.1 + - - -
467B PHE* 4.0 4.9 - - + -
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 4.2 8.1 - - + -
268B ARG* 4.9 6.4 + - - +
359B LYS* 2.9 55.1 + - - +
360B TRP* 3.8 4.5 - - - +
362B GLU* 1.3 78.2 - - - +
364B PHE* 1.3 66.7 + - - +
366B SER* 2.9 5.5 + - - -
367B GLN* 2.9 48.7 + - - +
396B PRO* 5.6 2.9 - - - +
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Residues in contact with PHE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 5.2 5.6 - - + -
260B PHE* 4.1 21.4 - + - -
261B LEU* 3.7 34.8 - - + -
264B PHE* 3.7 34.9 - + + -
360B TRP* 2.9 36.3 + + + +
361B SER 3.7 1.1 - - - +
363B ASP* 1.3 77.3 - - - +
365B PHE* 1.3 94.4 + + - +
367B GLN* 3.9 0.9 - - - +
368B LEU* 2.9 53.5 + - + +
555B LEU* 4.1 15.5 - - + -
557B ILE* 6.3 0.4 - - + -
560B ILE* 4.6 5.4 - - + -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B SER 3.0 28.5 + - - +
364B PHE* 1.3 94.7 - + - +
366B SER* 1.3 65.6 + - - +
368B LEU* 4.3 6.7 - - + -
369B VAL* 2.9 33.0 + - + +
394B PHE* 3.6 22.4 - + + -
398B TYR* 3.8 17.3 - - + +
494B MET* 3.6 18.8 - - + -
496B ILE* 4.0 9.2 - - + -
501B VAL* 3.4 27.4 - - + -
502B LEU* 3.5 26.0 - - + -
555B LEU* 4.4 0.7 - - + -
560B ILE* 3.5 32.3 - - + -
564B LEU* 6.1 1.3 - - + -
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Residues in contact with SER 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLU 2.5 25.4 + - - -
363B ASP* 2.9 11.6 + - - -
365B PHE* 1.3 75.5 - - - +
367B GLN* 1.3 69.4 + - - +
369B VAL* 3.9 0.3 - - - -
370B TYR 3.0 20.3 + - - -
376B TYR* 3.4 24.6 - - - -
394B PHE* 3.8 11.4 - - - -
396B PRO* 3.6 31.7 - - - +
398B TYR* 3.7 0.8 + - - -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B PHE* 4.0 12.4 - - + -
264B PHE* 3.3 21.8 - - + -
268B ARG* 4.4 10.1 + - - +
363B ASP* 2.9 35.8 + - - +
364B PHE 4.1 1.6 - - - +
366B SER* 1.3 85.1 + - - +
368B LEU* 1.3 56.8 + - - +
370B TYR* 3.6 5.8 + - - +
371B HIS* 2.9 29.1 + - - +
376B TYR* 5.2 2.9 - - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 4.2 19.1 - - + -
260B PHE* 3.5 38.0 - - + -
364B PHE* 2.9 45.3 + - + +
365B PHE* 3.7 9.0 - - + +
367B GLN* 1.3 75.2 - - - +
369B VAL* 1.3 62.9 - - + +
371B HIS* 2.9 19.2 + - + +
372B LEU* 2.9 33.4 + - + +
560B ILE* 4.8 6.5 - - + -
564B LEU* 3.7 24.7 - - + -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B PHE* 2.9 21.7 + - + +
366B SER 4.0 2.0 - - - +
368B LEU* 1.3 77.2 - - + +
370B TYR* 1.3 58.2 + - - +
373B PHE* 2.9 35.3 + - + -
375B THR 3.3 17.7 - - - +
376B TYR* 3.8 14.6 - - - +
378B ILE* 3.7 25.8 - - + -
394B PHE* 3.6 33.7 - - + -
564B LEU* 4.3 20.6 - - + -
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Residues in contact with TYR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B SER 3.0 17.0 + - - +
367B GLN* 3.9 5.4 - - - +
369B VAL* 1.3 77.3 - - - +
371B HIS* 1.3 61.9 + - - +
374B GLY* 2.9 52.1 + - - -
375B THR* 3.7 8.2 + - - +
376B TYR* 3.5 42.3 - + + +
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Residues in contact with HIS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LYS* 5.2 12.1 - - + -
260B PHE* 3.9 39.7 - + + -
367B GLN 2.9 15.9 + - - +
368B LEU* 2.9 12.9 + - - +
370B TYR* 1.3 81.8 - - - +
372B LEU* 1.3 80.7 + - + +
374B GLY 4.6 0.3 + - - -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B THR* 4.3 15.9 - - + -
256B LYS* 4.3 32.1 - - + -
257B ILE* 3.5 29.4 - - + -
368B LEU* 2.9 21.9 + - + +
371B HIS* 1.3 95.8 - - + +
373B PHE* 1.3 81.0 + - + +
374B GLY 3.8 0.2 + - - -
564B LEU* 3.7 17.5 - - + -
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR* 5.9 2.2 - - + -
369B VAL* 2.9 24.7 + - + +
372B LEU* 1.3 98.5 - - + +
374B GLY* 1.3 58.0 + - - +
375B THR* 3.0 26.5 + - + +
378B ILE* 3.6 32.1 - - + -
564B LEU* 3.0 42.8 - - + -
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 2.9 46.1 + - - -
371B HIS 4.6 0.4 + - - -
372B LEU 3.5 1.8 + - - -
373B PHE* 1.3 76.3 - - - +
375B THR* 1.3 58.9 + - - +
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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