Contacts of the helix formed by residues 368 - 378 (chain B) in PDB entry 3ZVU
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 ARG 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B VAL* 3.1 50.8 + - - +
363B ASP 3.2 15.8 + - - +
364B HIS* 3.5 5.5 + - - -
365B LYS* 2.8 27.8 + - + +
367B ASP* 1.3 73.1 + - - +
369B GLU* 1.3 61.7 + - - +
370B ASP* 2.8 38.0 + - - +
371B GLU* 3.1 20.5 + - + +
372B TYR* 2.8 27.4 + - - +
398B ARG* 4.7 1.2 - - - +
414B GLU* 2.7 31.3 + - - -
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Residues in contact with GLU 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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367B ASP 3.2 6.5 + - - +
368B ARG* 1.3 75.9 - - - +
370B ASP* 1.3 61.8 + - - +
372B TYR* 3.7 5.7 - - - +
373B ALA* 3.2 23.7 + - - +
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Residues in contact with ASP 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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368B ARG* 2.8 51.4 + - - +
369B GLU* 1.3 75.5 - - - +
371B GLU* 1.3 64.7 + - - +
373B ALA* 3.6 5.8 + - - +
374B ARG* 2.9 28.1 + - - +
398B ARG* 5.4 0.9 + - - -
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B HIS* 4.3 4.5 - - - +
365B LYS 3.7 12.1 - - - +
366B PRO 4.2 1.6 - - - +
368B ARG* 3.1 33.8 + - + +
370B ASP* 1.3 82.1 + - - +
372B TYR* 1.3 65.8 + - - +
374B ARG* 2.9 33.6 + - - +
375B ILE* 2.9 30.1 + - - +
397B SER* 2.6 33.0 + - - +
398B ARG* 3.0 38.7 + - - +
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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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366B PRO 3.3 23.6 + - - +
367B ASP* 4.5 8.5 - - + +
368B ARG 2.8 18.2 + - - +
369B GLU* 3.7 8.1 - - - +
371B GLU* 1.3 73.0 - - - +
373B ALA* 1.3 67.9 + - + +
375B ILE* 3.1 1.0 + - - +
376B GLU* 3.0 60.7 + - + +
381B LYS* 4.9 3.5 + - - -
382B VAL* 3.8 35.5 + - + -
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Residues in contact with ALA 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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369B GLU 3.2 15.0 + - - +
370B ASP* 4.0 4.9 - - - +
372B TYR* 1.3 83.9 - - + +
374B ARG* 1.3 57.2 + - - +
376B GLU* 4.2 3.1 - - - +
377B ASN* 2.8 45.8 + - - +
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Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ASP 2.9 19.5 + - - +
371B GLU* 2.9 37.9 + - - +
372B TYR 3.2 0.2 - - - -
373B ALA* 1.3 76.9 - - - +
375B ILE* 1.3 72.0 + - - +
377B ASN* 3.6 9.5 - - - +
378B ALA* 3.0 26.9 + - + +
397B SER* 2.9 32.7 + - - -
398B ARG* 4.5 4.7 - - - +
407B PRO 4.4 2.2 + - - -
408B TYR* 2.8 24.2 + - - +
410B ILE* 3.8 34.9 - - - +
412B GLU* 5.9 0.4 - - - -
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Residues in contact with ILE 375 (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 PRO* 4.5 1.1 - - + -
371B GLU 2.9 19.1 + - - +
372B TYR 3.8 2.7 - - - +
374B ARG* 1.3 85.5 - - - +
376B GLU* 1.3 61.2 + - - +
378B ALA* 3.3 11.6 + - - +
379B GLY 3.6 0.2 + - - -
380B GLY* 2.9 26.0 + - - -
381B LYS 3.9 23.8 - - - +
382B VAL* 4.1 20.6 - - + -
390B VAL* 3.8 23.8 - - + -
397B SER* 3.6 32.8 - - - -
408B TYR* 3.7 31.5 - - + +
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Residues in contact with GLU 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* 3.0 56.5 + - + +
373B ALA* 4.2 3.1 - - - +
375B ILE* 1.3 75.5 - - + +
377B ASN* 1.4 61.7 + - - +
379B GLY* 3.4 11.1 + - - -
380B GLY 3.6 15.8 - - - +
381B LYS* 3.7 25.9 + - - -
382B VAL* 3.1 28.9 + - + +
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Residues in contact with ASN 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 ALA* 2.8 36.1 + - - +
374B ARG* 3.6 7.8 - - + +
376B GLU* 1.4 67.8 - - - +
378B ALA* 1.3 57.7 + - - +
379B GLY 3.0 10.7 + - - -
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Residues in contact with ALA 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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374B ARG* 3.0 18.3 + - + +
375B ILE* 3.3 8.2 + - - +
377B ASN* 1.3 77.8 - - - +
379B GLY* 1.3 56.8 + - - +
380B GLY 3.5 0.7 - - - -
407B PRO* 5.2 12.3 - - + +
408B TYR* 3.1 26.7 - - + -
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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