Contacts of the helix formed by residues 376 - 389 (chain B) in PDB entry 3KCZ
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 SER 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B LEU* 4.4 4.9 - - - +
373B ASP* 2.7 35.5 + - - +
374B HIS 3.4 0.7 - - - +
375B GLU* 1.3 82.7 - - - +
377B TYR* 1.3 65.7 + - - +
378B GLU* 3.5 18.2 + - - +
379B PHE* 3.2 16.8 + - - +
380B LYS* 3.1 20.4 + - - +
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Residues in contact with TYR 377 (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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375B GLU 4.0 0.4 + - - -
376B SER* 1.3 73.4 - - - +
378B GLU* 1.3 75.6 + - - +
380B LYS* 3.1 33.8 + - + +
381B VAL* 3.0 36.7 + - + +
529B VAL* 5.1 8.7 - - - +
530B THR 4.6 9.8 + - - -
531B LEU* 3.7 28.7 - - + -
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.2 22.9 - - + +
376B SER* 3.5 19.8 - - - +
377B TYR* 1.3 95.2 + - - +
379B PHE* 1.3 61.9 + - - +
381B VAL* 3.3 4.0 + - - +
382B ILE* 3.0 33.0 + - + +
404B LEU* 4.4 0.2 - - - -
531B LEU* 4.7 12.8 - - + +
532B ASN* 5.2 6.9 + - - +
571B TYR* 4.1 22.9 - - + +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU 4.8 0.7 - - - -
373B ASP 3.4 20.4 - - - +
374B HIS* 3.2 67.1 - + + +
376B SER* 3.2 9.5 + - - +
378B GLU* 1.3 78.9 - - - +
380B LYS* 1.3 56.3 + - - +
382B ILE* 3.9 0.7 - - - +
383B SER* 2.7 51.9 + - - -
401B LEU* 3.7 33.8 - - + +
403B ASP 4.7 0.2 - - - -
404B LEU* 3.7 36.5 - - + +
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Residues in contact with LYS 380 (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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374B HIS 5.2 0.4 + - - -
376B SER 3.1 12.1 + - - +
377B TYR* 3.1 33.1 + - + +
379B PHE* 1.3 79.8 - - - +
381B VAL* 1.3 82.3 + - - +
383B SER* 3.8 4.9 - - - -
384B GLN* 3.0 57.4 + - + +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.0 55.7 + - + +
378B GLU 3.9 4.0 - - - +
380B LYS* 1.3 85.0 - - - +
382B ILE* 1.3 59.6 + - + +
384B GLN* 3.3 9.0 + - - +
385B TYR* 2.8 27.7 + - - +
425B LEU* 6.2 0.2 - - + -
529B VAL* 4.3 24.0 - - + -
531B LEU* 4.3 21.5 - - + -
536B VAL* 4.3 15.3 - - + -
538B LEU* 4.1 3.9 - - + +
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Residues in contact with ILE 382 (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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378B GLU 3.0 21.3 + - - +
379B PHE 4.1 2.2 - - - +
381B VAL* 1.3 76.5 - - + +
383B SER* 1.3 54.1 + - - +
385B TYR* 3.1 6.9 + - + +
386B LEU* 2.8 34.5 + - - +
401B LEU* 4.5 2.9 - - + -
404B LEU* 3.9 17.7 - - + -
425B LEU* 5.1 1.3 - - + -
427B TRP* 4.4 1.0 - - + -
487B LEU* 3.9 20.2 - - + -
531B LEU* 4.6 10.3 - - + -
571B TYR* 3.5 50.9 - - + -
573B LEU* 3.7 32.3 - - + -
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B PHE* 2.7 46.7 + - - -
380B LYS* 3.8 4.7 - - - -
382B ILE* 1.3 75.7 - - - +
384B GLN* 1.3 64.2 + - - +
386B LEU* 3.2 7.8 + - - +
387B GLN* 3.0 33.3 + - - +
401B LEU* 3.5 14.1 - - - +
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Residues in contact with GLN 384 (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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380B LYS* 3.0 51.7 + - + +
381B VAL* 3.4 11.2 - - - +
383B SER* 1.3 75.9 - - - +
385B TYR* 1.3 53.0 + - - +
387B GLN* 4.9 2.7 - - - -
388B SER* 2.7 45.0 + - - +
538B LEU* 3.8 25.6 - - + +
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Residues in contact with TYR 385 (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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381B VAL 2.8 20.6 + - - +
382B ILE* 3.1 7.8 + - + +
384B GLN* 1.3 73.6 - - - +
386B LEU* 1.3 59.1 + - - +
388B SER* 3.9 0.4 - - - -
389B THR* 2.7 43.2 + - + -
425B LEU* 2.7 34.1 + - + -
426B LEU* 3.9 3.3 - - - -
427B TRP* 3.3 35.5 + + + -
465B ASP* 3.8 11.9 - - - -
487B LEU* 3.6 28.9 - - + -
536B VAL* 3.7 20.0 - - + -
537B PRO* 3.2 37.3 - - + +
538B LEU* 3.5 13.0 - - + -
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Residues in contact with LEU 386 (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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382B ILE 2.8 16.5 + - - +
383B SER* 3.4 10.1 - - - +
385B TYR* 1.3 73.8 - - - +
387B GLN* 1.3 79.3 + - - +
390B HIS* 3.7 5.0 + - - +
399B MET* 3.7 31.2 - - + +
401B LEU* 4.0 33.7 - - + +
427B TRP* 3.6 15.4 - - + -
467B SER* 2.7 26.3 + - - -
485B LEU* 3.6 31.0 - - + -
573B LEU* 4.2 11.9 - - + -
575B VAL* 4.7 4.0 - - + -
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Residues in contact with GLN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B SER* 3.0 21.9 + - - +
384B GLN* 4.2 3.1 - - - +
386B LEU* 1.3 91.6 - - - +
388B SER* 1.3 65.9 - - - +
390B HIS* 3.2 25.8 + - - +
398B THR* 5.5 3.5 - - - -
399B MET* 2.8 34.1 + - - +
400B THR* 4.7 2.6 - - - +
401B LEU* 5.1 1.4 - - - +
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLN* 2.7 30.8 + - - -
385B TYR* 3.7 4.7 + - - -
387B GLN* 1.3 73.9 - - - +
389B THR* 1.3 59.6 + - - +
390B HIS 3.4 3.6 + - - +
466B MET* 5.4 0.3 - - - +
538B LEU* 4.0 4.8 - - - +
539B GLY* 3.1 43.8 + - - -
540B PRO* 3.6 11.9 - - - +
541B ALA 4.4 0.9 + - - -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TYR* 2.7 28.6 + - + +
388B SER* 1.3 76.9 - - - +
390B HIS* 1.3 61.8 + - - +
391B ALA 3.4 0.7 + - - -
427B TRP* 3.5 7.8 + - - -
465B ASP 3.4 18.4 - - - +
466B MET* 3.3 24.9 - - - +
467B SER* 3.0 31.1 + - - -
468B SER 4.0 0.2 + - - -
523B PRO* 4.3 4.5 - - + -
537B PRO 3.4 25.8 - - - +
539B GLY* 3.4 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
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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