Contacts of the helix formed by residues 384 - 392 (chain H) in PDB entry 5ZRV
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 GLY 384 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231H ALA* 5.3 10.1 - - - -
241H GLN* 4.5 17.2 + - - -
382H PHE 3.6 0.8 + - - -
383H SER* 1.3 71.3 - - - +
385H GLN* 1.3 52.2 + - - +
386H ILE 3.1 3.5 - - - +
387H LEU* 2.9 7.3 + - - +
388H ALA* 2.4 36.2 + - - -
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Residues in contact with GLN 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H ALA 5.9 2.2 + - - -
230H LEU 6.3 0.9 - - - -
231H ALA* 5.5 5.2 - - - +
352H LEU 5.4 6.4 - - - +
382H PHE* 3.7 7.4 + - - +
383H SER 3.0 9.1 + - - -
384H GLY* 1.3 73.4 - - - +
386H ILE* 1.3 56.7 + - - +
388H ALA* 3.4 2.6 + - - +
389H ASN* 2.8 23.6 + - - -
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Residues in contact with ILE 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379H HIS 5.8 3.4 - - - -
380H GLU* 6.0 3.6 - - - +
382H PHE 3.9 8.7 + - - -
384H GLY 3.1 2.2 - - - +
385H GLN* 1.3 75.5 - - - +
387H LEU* 1.3 58.3 + - - +
389H ASN* 3.2 5.8 - - - +
390H PHE* 2.9 17.5 + - - -
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Residues in contact with LEU 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H GLY* 2.9 13.0 + - - +
386H ILE* 1.3 75.2 - - - +
388H ALA* 1.3 56.6 + - - +
390H PHE* 3.0 5.1 + - - +
391H LYS* 2.6 31.4 + - - -
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Residues in contact with ALA 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H LEU 5.5 7.2 - - - -
231H ALA* 6.2 1.1 - - - +
234H PHE* 5.7 7.9 - - - +
384H GLY 2.4 20.5 + - - -
385H GLN* 3.6 3.1 - - - +
387H LEU* 1.3 72.0 - - - +
389H ASN* 1.3 54.8 + - - +
390H PHE 3.1 0.9 - - - -
391H LYS* 4.0 2.2 - - - +
392H ALA* 3.1 27.1 + - - +
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Residues in contact with ASN 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356H THR* 6.0 4.3 - - - +
385H GLN 2.8 14.3 + - - -
386H ILE* 3.2 10.5 - - - +
387H LEU 3.2 0.4 - - - -
388H ALA* 1.3 74.1 - - - +
390H PHE* 1.3 56.7 + - - +
392H ALA 5.0 0.4 - - - -
393H MET 5.7 1.7 + - - +
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Residues in contact with PHE 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386H ILE 2.9 11.3 + - - -
387H LEU* 3.0 6.5 + - - +
389H ASN* 1.3 79.0 - - - +
391H LYS* 1.3 63.5 + - - +
392H ALA 3.5 0.9 - - - -
393H MET 4.1 1.8 + - - -
394H ASP* 3.6 16.1 + - - -
410H GLY 5.4 0.5 - - - +
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Residues in contact with LYS 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234H PHE 5.7 5.2 - - - -
387H LEU 2.6 20.1 + - - -
388H ALA* 3.3 2.6 + - - +
390H PHE* 1.3 74.0 - - - +
392H ALA* 1.3 62.7 + - - +
393H MET 3.4 0.3 + - - -
394H ASP* 3.5 11.6 + - - -
395H SER* 4.1 3.5 + - - -
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Residues in contact with ALA 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H ALA* 3.1 15.7 + - - +
391H LYS* 1.3 76.7 - - - +
393H MET* 1.3 56.7 + - - +
395H SER* 3.5 17.7 + - - +
396H ASP 4.2 5.5 - - - +
398H PHE* 5.3 5.9 + - - -
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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