Contacts of the helix formed by residues 371 - 384 (chain B) in PDB entry 5ZR1
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 ASN 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B SER 3.2 8.4 + - - +
370B CYS* 1.3 74.7 - - - +
372B TYR* 1.3 81.6 + - - +
373B ARG* 3.4 20.9 + - - +
374B ASP* 3.5 33.5 + - + +
375B VAL* 3.3 25.8 + - - +
437B PHE* 3.8 1.6 - - - -
586B LYS* 4.3 12.9 - - - +
21C SER* 5.2 1.6 + - - -
22C HIS* 5.3 1.6 + - - -
59H A 5.8 1.6 + - - -
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Residues in contact with TYR 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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371B ASN* 1.3 82.9 + - - +
373B ARG* 1.3 106.8 + - + +
374B ASP 3.3 0.2 - - - -
375B VAL* 3.9 0.7 - - - -
376B PHE* 3.1 21.7 + - - +
398B ASN* 4.2 11.9 + - - -
400B VAL* 4.2 17.5 - - + -
401B ILE* 5.7 2.2 - - + -
436B THR* 3.6 44.4 - - + +
437B PHE* 3.5 30.9 - + + -
440B MET* 3.4 36.1 - - + +
17G T 6.1 0.7 - - - -
18G G 5.8 2.5 - - - -
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Residues in contact with ARG 373 (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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371B ASN* 3.4 14.8 + - - +
372B TYR* 1.3 119.0 + - + +
374B ASP* 1.3 62.6 + - - +
376B PHE* 3.9 5.5 - - - +
377B LYS* 3.0 26.2 + - - +
398B ASN* 3.8 17.4 + - - +
400B VAL* 3.5 26.7 - - + +
17G T 5.6 7.9 - - - -
59H A 3.5 59.4 + - - +
60H C 3.9 4.6 + - - -
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Residues in contact with ASP 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ASN* 3.5 22.7 + - + +
372B TYR 3.3 0.2 - - - -
373B ARG* 1.3 79.5 - - - +
375B VAL* 1.3 62.4 + - - +
377B LYS* 3.4 9.7 + - - +
378B GLU* 3.2 15.8 + - - +
586B LYS* 3.4 30.7 + - - +
22C HIS* 3.5 33.9 + - + +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 4.7 5.4 - - + -
363B LEU* 3.7 26.0 - - + -
370B CYS* 4.3 4.3 - - - -
371B ASN 3.3 17.5 + - - +
372B TYR 4.0 4.7 - - - +
374B ASP* 1.3 77.4 - - - +
376B PHE* 1.3 57.1 + - - +
378B GLU* 3.0 18.5 + - - +
379B ILE* 3.0 30.9 + - + +
437B PHE* 4.1 13.0 - - + -
440B MET* 4.1 13.7 - - + -
441B LEU* 5.5 1.6 - - + -
22C HIS* 3.7 32.1 - - + +
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Residues in contact with PHE 376 (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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372B TYR 3.1 19.4 + - - +
373B ARG* 4.1 4.3 - - - +
375B VAL* 1.3 73.8 - - - +
377B LYS* 1.3 65.7 + - - +
379B ILE* 4.3 16.8 - - + -
380B THR* 3.2 47.2 + - + -
399B HIS 4.6 0.2 - - - -
400B VAL* 3.8 45.1 - - + -
403B GLN* 3.6 33.7 - - + -
404B ILE* 3.6 28.3 - - + -
407B MET* 4.3 10.8 - - + -
440B MET* 3.9 11.2 - - + -
444B LEU* 5.3 2.7 - - + -
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Residues in contact with LYS 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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373B ARG 3.0 19.6 + - - +
374B ASP* 3.5 12.8 - - - +
376B PHE* 1.3 79.2 - - - +
378B GLU* 1.3 58.7 + - - +
380B THR* 3.3 13.8 + - - +
381B ASP* 2.9 38.0 + - - +
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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
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361B LEU* 3.6 29.8 - - + -
374B ASP 3.2 11.4 + - - +
375B VAL 3.0 11.3 + - - +
377B LYS* 1.3 75.9 - - - +
379B ILE* 1.3 62.5 + - - +
381B ASP* 3.3 21.5 + - - +
382B LEU* 3.4 21.0 + - + +
22C HIS* 4.3 19.5 - - + +
23C TYR* 5.9 0.2 - - - -
24C THR* 2.7 24.5 + - - +
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Residues in contact with ILE 379 (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 LEU* 3.7 18.2 - - + -
375B VAL* 3.0 32.9 + - + +
376B PHE* 3.5 16.4 + - + +
377B LYS 3.4 0.2 - - - -
378B GLU* 1.3 77.7 - - - +
380B THR* 1.3 58.1 + - + +
382B LEU* 3.0 10.0 + - - +
383B LEU* 2.9 49.2 + - + +
407B MET* 5.3 3.8 - - - -
420B LEU* 4.7 7.2 - - + -
422B LEU* 4.3 11.2 - - + -
440B MET* 5.4 1.1 - - + -
444B LEU* 3.7 41.7 - - + -
450B ILE* 5.7 1.1 - - + -
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Residues in contact with THR 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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376B PHE* 3.2 50.3 + - + +
377B LYS* 3.3 15.9 + - - +
379B ILE* 1.3 76.1 - - - +
381B ASP* 1.3 60.5 + - - +
383B LEU* 5.0 0.2 - - - -
384B VAL* 3.2 25.6 + - - +
385B PRO* 3.6 29.2 - - + +
403B GLN* 4.2 5.4 - - - +
407B MET* 4.7 1.8 - - + -
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Residues in contact with ASP 381 (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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377B LYS* 2.9 34.1 + - - +
378B GLU* 3.3 18.3 + - - +
379B ILE 3.2 1.0 - - - -
380B THR* 1.3 81.9 + - - +
382B LEU* 1.3 65.9 + - + +
384B VAL* 3.7 13.6 - - - +
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Residues in contact with LEU 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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359B PRO* 4.3 15.1 - - + +
361B LEU* 4.3 10.5 - - + -
378B GLU* 3.4 21.3 + - + +
379B ILE 3.0 6.7 + - - +
381B ASP* 1.3 83.5 - - + +
383B LEU* 1.3 63.3 - - + +
384B VAL* 4.4 2.4 - - - +
420B LEU* 3.7 29.2 - - + -
24C THR* 4.1 24.9 - - + +
26C TYR* 3.3 35.4 - - + +
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Residues in contact with LEU 383 (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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379B ILE* 2.9 24.7 + - + +
382B LEU* 1.3 78.3 - - - +
384B VAL* 1.3 71.0 + - - +
385B PRO* 4.4 10.7 - - + +
407B MET* 3.7 23.3 - - + -
411B TYR* 3.5 44.9 + - + +
419B LYS* 5.0 10.8 - - + +
420B LEU* 3.7 35.9 - - + -
447B ILE* 5.4 2.0 - - + -
450B ILE* 4.4 15.7 - - + -
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Residues in contact with VAL 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 THR 3.2 13.2 + - - +
381B ASP* 3.7 19.7 - - - +
382B LEU 4.4 2.7 - - - +
383B LEU* 1.3 81.9 - - - +
385B PRO* 1.3 69.8 - - - +
386B ALA 4.0 0.2 + - - -
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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