Contacts of the helix formed by residues 373 - 387 (chain A) in PDB entry 4WHH
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 HIS 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A LEU* 1.3 63.8 + - - +
375A SER* 3.2 5.3 - - - +
376A ASP* 3.2 27.0 + - - +
377A MET* 2.9 23.6 + - - +
524A HIS* 6.3 0.2 - - - +
527A ASN 5.4 2.7 - - - -
528A GLY* 4.8 14.6 - - - -
545A PRO* 3.6 21.5 - - + +
546A LEU* 3.2 35.5 - - + +
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Residues in contact with LEU 374 (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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373A HIS* 1.3 77.3 - - - +
375A SER* 1.3 62.8 + - - +
377A MET* 3.2 7.6 + - + +
378A LEU* 3.0 22.7 + - - +
524A HIS* 3.6 33.3 + - + +
528A GLY 5.4 1.6 - - - +
530A VAL* 3.7 30.5 - - + -
545A PRO* 5.5 0.4 - - - -
587A VAL* 3.8 17.1 - - + +
590A LEU* 3.8 35.7 - - + +
591A LEU* 3.6 22.2 - - + -
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS 3.2 3.9 - - - +
374A LEU* 1.3 77.4 - - - +
376A ASP* 1.3 65.1 + - - +
378A LEU* 3.3 12.0 + - - +
379A GLN* 3.1 30.8 + - - +
591A LEU* 4.0 18.9 - - - +
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS* 3.2 34.0 + - - +
375A SER* 1.3 79.0 - - - +
377A MET* 1.3 64.5 + - - +
379A GLN* 3.2 13.7 + - - +
380A GLN* 3.0 41.2 + - - +
545A PRO* 4.5 3.8 - - + +
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Residues in contact with MET 377 (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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373A HIS 2.9 12.6 + - - +
374A LEU* 3.2 14.1 + - + +
376A ASP* 1.3 77.7 - - - +
378A LEU* 1.3 62.4 + - - +
380A GLN* 3.1 29.6 + - + +
381A LEU* 2.9 44.1 + - + +
530A VAL* 5.2 6.5 - - + -
543A LEU* 3.9 28.5 - - + -
544A CYS 4.7 0.9 - - - -
545A PRO* 3.8 25.5 - - + +
564A LEU* 3.5 24.0 - - + -
587A VAL* 4.0 14.4 - - + -
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU 3.0 12.7 + - - +
375A SER* 3.3 12.5 + - - +
377A MET* 1.3 77.3 - - - +
379A GLN* 1.4 58.4 + - + +
381A LEU* 3.9 2.7 - - - +
382A HIS* 2.6 70.8 + - + +
584A ARG* 3.9 18.4 - - + +
587A VAL* 3.7 16.1 - - + +
588A ASP* 3.9 20.6 - - - +
591A LEU* 3.7 21.3 - - + -
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Residues in contact with GLN 379 (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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375A SER* 3.1 18.0 + - - +
376A ASP* 3.7 14.9 - - - +
378A LEU* 1.4 76.2 - - + +
380A GLN* 1.3 61.2 + - + +
382A HIS* 3.4 6.5 + - - +
383A SER* 3.0 30.7 + - - -
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Residues in contact with GLN 380 (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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376A ASP* 3.0 26.9 + - - +
377A MET* 3.1 26.4 - - + +
379A GLN* 1.3 78.8 - - + +
381A LEU* 1.3 61.7 + - - +
383A SER* 3.4 5.5 + - - -
384A VAL* 3.1 24.3 + - - +
545A PRO* 3.0 38.9 + - - +
548A ALA* 3.6 24.0 - - + +
564A LEU* 3.8 13.8 - - + +
568A GLU* 5.3 0.2 - - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A MET* 2.9 34.0 + - + +
378A LEU* 3.9 3.8 - - - +
380A GLN* 1.3 71.2 - - - +
382A HIS* 1.3 60.5 + - - +
384A VAL* 2.8 27.5 - - + +
385A ASN* 2.9 20.4 + - - +
543A LEU* 4.0 15.0 - - + -
564A LEU* 4.6 4.5 - - + -
580A LEU* 4.0 33.4 - - + +
583A ALA* 4.0 7.0 - - + -
584A ARG* 3.9 35.2 - - + +
587A VAL* 3.9 22.2 - - + -
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Residues in contact with HIS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 2.6 51.7 + - + +
379A GLN* 3.6 8.1 - - - +
380A GLN 3.3 0.2 - - - -
381A LEU* 1.3 78.4 - - - +
383A SER* 1.3 56.6 + - - +
385A ASN* 3.8 3.1 - - - +
386A ALA* 2.9 32.8 + - + +
584A ARG* 3.0 57.6 + - + +
588A ASP* 4.4 4.0 + - - -
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Residues in contact with SER 383 (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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379A GLN 3.0 17.9 + - - -
380A GLN* 3.4 6.7 + - - -
382A HIS* 1.3 70.9 - - - +
384A VAL* 1.3 66.9 + - - +
386A ALA* 4.0 4.8 - - - +
387A SER* 3.4 20.6 + - - -
568A GLU* 2.6 37.0 + - - +
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Residues in contact with VAL 384 (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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380A GLN 3.1 15.8 + - - +
381A LEU* 2.8 37.9 - - + +
383A SER* 1.3 76.0 - - - +
385A ASN* 1.3 64.6 + - - +
387A SER* 2.6 25.2 + - - -
389A PRO* 3.4 21.1 - - + +
564A LEU* 4.4 20.9 - - + +
567A LEU* 4.1 25.8 - - + -
568A GLU* 4.2 11.0 + - + +
580A LEU* 4.3 15.5 - - + -
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Residues in contact with ASN 385 (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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381A LEU 2.9 24.5 + - - +
382A HIS 4.1 1.3 - - - +
384A VAL* 1.3 78.4 - - - +
386A ALA* 1.3 58.0 + - - +
388A LYS* 3.0 22.7 + - - +
389A PRO* 3.8 11.1 - - - +
577A ALA 4.6 1.6 + - - -
580A LEU* 3.2 44.4 - - - +
581A ARG* 3.5 14.8 - - + +
584A ARG* 2.7 44.4 + - - +
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Residues in contact with ALA 386 (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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382A HIS 2.9 18.8 + - - +
383A SER* 4.0 6.1 - - - +
385A ASN* 1.3 72.4 - - - +
387A SER* 1.3 60.7 + - - +
388A LYS* 3.1 17.8 + - - +
584A ARG* 5.9 0.2 - - - +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A SER 3.4 10.3 + - - -
384A VAL 2.6 21.0 + - - -
386A ALA* 1.3 77.4 - - - +
388A LYS* 1.3 69.3 + - - +
389A PRO* 4.0 8.1 - - - +
392A ARG* 4.5 10.4 - - - +
568A GLU* 3.7 34.8 + - - -
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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