Contacts of the helix formed by residues 338 - 349 (chain G) 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 ALA 338 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335G GLU 5.1 1.6 + - - -
337G LYS* 1.3 72.0 - - - +
339G LEU* 1.3 59.3 + - - +
340G MET 3.2 2.5 - - - -
341G GLY* 3.1 6.5 + - - +
342G LEU* 2.9 22.7 + - - -
715G GLY* 5.1 20.8 - - - +
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Residues in contact with LEU 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LEU* 5.5 10.6 - - - +
335G GLU 5.2 0.6 + - - -
336G SER* 3.2 18.8 + - - +
338G ALA* 1.3 75.2 - - - +
340G MET* 1.3 59.6 + - - +
342G LEU* 3.3 4.0 + - - +
343G TYR* 2.9 23.0 + - - -
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Residues in contact with MET 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336G SER 3.8 4.8 + - - -
337G LYS 3.8 8.1 + - - -
338G ALA 3.2 0.6 - - - -
339G LEU* 1.3 78.5 - - - +
341G GLY* 1.3 55.0 + - - +
343G TYR* 3.1 3.1 + - - +
344G HIS* 2.9 24.8 + - - -
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Residues in contact with GLY 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337G LYS 4.5 1.8 + - - -
338G ALA* 3.1 11.8 + - - +
340G MET* 1.3 72.4 - - - +
342G LEU* 1.3 60.2 + - - +
344G HIS* 3.8 1.7 - - - -
345G GLY* 3.0 25.6 + - - -
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Residues in contact with LEU 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G ALA 2.9 13.5 + - - -
339G LEU* 3.3 6.2 + - - +
341G GLY* 1.3 76.8 - - - +
343G TYR* 1.3 55.5 + - - +
345G GLY* 3.4 1.8 + - - -
346G GLN* 2.8 24.8 + - - -
702G ILE* 6.1 1.1 - - - +
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Residues in contact with TYR 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339G LEU 2.9 14.2 + - - -
340G MET* 3.1 4.6 + - - +
342G LEU* 1.3 74.8 - - - +
344G HIS* 1.3 61.1 + - - +
346G GLN* 3.6 2.1 - - - +
347G VAL* 2.9 25.5 + - - -
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Residues in contact with HIS 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G MET 2.9 14.4 + - - -
341G GLY* 3.3 4.4 + - - -
343G TYR* 1.3 76.6 - - - +
345G GLY* 1.3 56.1 + - - +
347G VAL* 3.6 1.1 + - - +
348G LEU* 2.8 25.8 + - - -
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Residues in contact with GLY 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341G GLY 3.0 14.6 + - - -
342G LEU* 3.7 2.7 - - - -
344G HIS* 1.3 74.4 - - - +
346G GLN* 1.3 59.2 - - - +
348G LEU* 3.7 2.6 - - - -
349G CYS* 3.0 25.6 + - - -
698G ALA 5.9 3.1 - - - -
702G ILE* 5.8 10.4 - - - -
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Residues in contact with GLN 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342G LEU 2.8 16.3 + - - -
343G TYR* 3.2 5.8 + - - +
345G GLY* 1.3 78.9 - - - +
347G VAL* 1.3 58.5 + - - +
349G CYS 4.5 0.5 - - - -
350G LYS* 3.7 12.6 + - - -
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Residues in contact with VAL 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G TYR 2.9 14.0 + - - -
344G HIS 3.8 1.1 - - - -
346G GLN* 1.3 78.2 - - - +
348G LEU* 1.3 62.5 + - - +
349G CYS 3.3 0.7 + - - -
350G LYS* 3.4 17.1 + - - +
351G LYS* 5.3 0.3 - - - -
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Residues in contact with LEU 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G HIS 2.8 19.2 + - - -
345G GLY* 3.2 3.9 + - - -
347G VAL* 1.3 79.6 - - - +
349G CYS* 1.3 56.8 + - - +
350G LYS 3.5 0.2 - - - -
351G LYS* 4.3 8.0 + - - -
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Residues in contact with CYS 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345G GLY 3.0 13.9 + - - -
346G GLN 4.5 0.9 - - - -
348G LEU* 1.3 75.7 - - - +
350G LYS* 1.3 56.6 + - - +
351G LYS 3.1 13.9 + - - +
535G VAL* 4.3 3.8 - - - -
536G ILE* 3.6 33.9 + - - +
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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