Contacts of the helix formed by residues 375 - 380 (chain A) in PDB entry 4ZTZ
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 GLU 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A GLU* 3.4 24.1 + - - +
373A PRO 4.8 3.8 - - - +
374A ARG* 1.3 78.0 - - - +
376A LEU* 1.3 55.5 + - - +
377A PHE* 3.2 3.4 - - - -
378A VAL* 3.1 21.6 + - + +
379A LYS* 2.8 52.1 + - + +
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Residues in contact with LEU 376 (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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372A GLU* 3.8 19.5 - - - +
374A ARG* 3.2 46.9 - - + +
375A GLU* 1.3 75.1 - - - +
377A PHE* 1.3 58.8 + - - +
379A LYS* 5.9 0.2 - - + -
380A GLY* 3.0 31.9 + - - +
384A ASP* 3.3 43.7 - - - +
385A ILE* 4.3 7.8 - - + +
388A ASN* 3.4 24.2 - - + +
392A LEU* 4.3 22.2 - - + -
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Residues in contact with PHE 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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200A ALA* 3.5 24.0 - - + -
201A VAL 3.6 27.7 - - - +
202A CYS* 3.8 0.9 - - - -
203A LEU* 2.9 30.7 + - - +
204A ALA 4.4 1.0 + - - -
210A THR* 3.6 13.9 - - - -
211A LEU* 3.6 28.0 - - + -
372A GLU* 6.0 2.2 - - + -
375A GLU 3.1 1.6 + - - -
376A LEU* 1.3 78.0 - - - +
378A VAL* 1.3 64.9 - - + +
380A GLY 4.7 1.9 - - - +
385A ILE* 4.1 18.8 - - + -
392A LEU* 3.6 42.6 - - + -
395A TYR* 6.6 0.2 - - + -
396A CYS* 6.4 1.1 - - + -
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Residues in contact with VAL 378 (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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201A VAL 5.7 0.7 - - - +
203A LEU* 3.8 36.4 - - + +
204A ALA* 5.4 2.1 + - - -
375A GLU* 3.3 34.5 - - + +
377A PHE* 1.3 87.3 - - + +
379A LYS* 1.3 66.9 + - + +
380A GLY 3.7 1.8 - - - -
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Residues in contact with LYS 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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374A ARG 3.7 13.9 - - - +
375A GLU* 2.8 35.9 + - + +
376A LEU* 4.9 0.9 - - + -
378A VAL* 1.3 85.5 - - - +
380A GLY* 1.3 57.7 + - - +
14P C 4.6 15.9 + - - +
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Residues in contact with GLY 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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202A CYS* 4.2 3.8 - - - -
204A ALA* 3.4 18.6 + - - +
376A LEU* 3.0 22.8 + - - +
377A PHE 4.7 1.4 - - - +
378A VAL 4.8 0.3 - - - -
379A LYS* 1.3 83.5 + - - +
381A THR* 1.3 66.1 - - - -
384A ASP* 3.2 17.5 - - - -
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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