Contacts of the helix formed by residues 327 - 335 (chain G) in PDB entry 4HY0
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 CYS 327 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F LEU* 4.7 0.9 - - - +
336F GLN* 4.0 1.3 - - - +
340F ASN* 4.0 2.6 - - - +
300G CYS* 3.6 7.9 - - - -
302G HIS* 3.9 0.7 - - - -
303G CYS* 3.5 22.0 - - + -
320G HIS* 3.5 8.3 - - - +
324G TYR 3.4 4.5 + - - +
325G PRO 3.3 5.8 - - - +
326G GLY* 1.3 77.5 - - - +
328G LYS* 1.3 63.3 + - - +
329G TYR* 3.7 9.9 - - - -
330G LEU* 3.7 25.0 - - + +
331G LEU* 3.2 22.5 + - - +
401G ZN 2.1 37.9 - - - -
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Residues in contact with LYS 328 (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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331F LEU* 3.4 31.0 - - + -
336F GLN* 3.1 24.8 - - + +
255G ASN* 4.2 20.7 + - + +
302G HIS* 3.9 23.1 - - + +
326G GLY 3.5 0.4 + - - -
327G CYS* 1.3 71.0 - - - +
329G TYR* 1.3 61.7 + - - +
331G LEU* 3.5 3.0 + - + +
332G GLU* 3.1 53.0 + - + +
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Residues in contact with TYR 329 (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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268G ARG* 3.9 12.3 + - - -
286G ARG 2.8 19.7 + - - -
287G ALA 3.5 31.0 - - - -
288G GLY* 3.8 5.6 - - - -
300G CYS* 5.0 0.7 - - - -
301G PHE* 3.7 29.4 - + - -
302G HIS* 3.8 20.3 + - + +
317G TRP* 3.9 3.4 - + - -
320G HIS* 4.8 5.2 - + - -
327G CYS* 3.7 10.9 - - - -
328G LYS* 1.3 77.5 - - - +
330G LEU* 1.3 68.7 + - - +
332G GLU* 3.1 11.6 + - - +
333G GLN* 2.9 65.3 + - + +
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Residues in contact with LEU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 3.5 43.1 - - + +
320G HIS* 4.1 18.8 - - + +
321G ALA* 3.6 30.3 - - + +
324G TYR 3.9 16.6 - - - +
325G PRO* 4.1 6.3 - - + +
327G CYS* 3.7 19.9 - - + +
328G LYS 3.4 0.2 - - - -
329G TYR* 1.3 77.5 - - - +
331G LEU* 1.3 56.1 + - - +
334G LYS* 2.7 47.6 + - + +
338G TYR* 4.8 0.7 - - + -
339G ILE* 3.9 24.0 - - + -
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Residues in contact with LEU 331 (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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255F ASN* 3.3 13.7 + - - +
326F GLY 3.1 24.5 - - - +
328F LYS* 3.6 35.2 - - + -
331F LEU* 3.6 26.5 - - + -
327G CYS 3.2 11.8 + - - +
328G LYS* 3.5 10.8 - - + +
329G TYR 3.1 0.6 - - - -
330G LEU* 1.3 79.4 - - - +
332G GLU* 1.3 62.8 + - + +
335G GLY* 2.8 29.5 + - - +
336G GLN* 3.5 19.3 - - + +
339G ILE* 3.5 19.7 - - + -
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Residues in contact with GLU 332 (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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254F THR* 5.7 1.0 + - - -
255F ASN* 4.8 4.3 + - - +
302G HIS* 5.5 1.0 - - - -
328G LYS* 3.1 48.6 + - + +
329G TYR* 3.1 9.0 + - - +
331G LEU* 1.3 79.2 - - + +
333G GLN* 1.3 72.3 + - - +
335G GLY* 4.8 0.5 + - - -
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Residues in contact with GLN 333 (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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317G TRP* 3.5 28.1 - - + -
329G TYR* 2.9 62.0 + - + +
330G LEU 3.9 0.9 - - - +
332G GLU* 1.3 85.3 - - - +
334G LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 3.6 61.0 - - + +
330G LEU* 2.7 21.4 + - + +
333G GLN* 1.3 77.3 - - - +
335G GLY* 1.3 61.9 + - - +
338G TYR* 3.6 57.5 + - + +
339G ILE* 5.2 0.4 - - + -
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Residues in contact with GLY 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ASN* 3.3 14.8 - - - -
330G LEU 3.6 2.0 + - - -
331G LEU* 2.8 29.5 + - - -
332G GLU 5.4 0.4 - - - -
333G GLN 3.8 0.2 - - - -
334G LYS* 1.3 74.7 - - - +
336G GLN* 1.3 68.0 + - - -
337G GLU 3.3 3.3 + - - -
338G TYR 3.3 3.1 + - - -
339G ILE* 3.2 21.6 + - - +
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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