Contacts of the helix formed by residues 327 - 337 (chain G) in PDB entry 6MZL
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 ASN 327 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G TYR* 5.2 1.3 - - - -
217G TYR* 5.2 5.7 - - - -
321G LEU* 3.4 43.0 + - - +
324G LYS* 3.4 33.3 - - + +
325G GLN* 4.0 3.3 - - - +
326G ASN* 1.3 70.3 - - - +
328G GLN* 1.3 62.6 + - - +
329G ILE* 3.2 23.6 + - - +
330G TRP* 3.4 25.0 - - + +
331G ASN* 2.9 29.2 + - - +
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Residues in contact with GLN 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 3.6 36.4 + - + +
246G HIS* 5.3 5.3 + - - -
247G MET* 4.6 7.2 - - - -
250G GLU* 3.3 35.7 + - - +
326G ASN 3.1 5.9 + - - -
327G ASN* 1.3 71.0 + - - +
329G ILE* 1.3 60.3 + - + +
331G ASN* 2.9 39.1 + - - +
332G ILE* 2.9 35.1 + - + +
336G HIS* 6.1 0.4 + - - -
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Residues in contact with ILE 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 5.4 4.9 - - + +
217G TYR* 4.0 26.9 - - + +
218G TYR* 4.6 4.0 - - + +
221G LEU* 3.7 26.0 - - + -
243G LEU* 4.7 16.8 - - + -
247G MET* 5.7 6.1 - - + -
317G LEU* 5.4 1.8 - - + -
321G LEU* 3.8 15.5 - - + -
324G LYS* 3.4 27.8 - - + +
327G ASN* 3.2 14.3 + - - +
328G GLN* 1.3 78.7 - - + +
330G TRP* 1.3 56.3 + - - +
332G ILE* 3.1 14.0 + - + +
333G VAL* 2.9 32.2 + - + +
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Residues in contact with TRP 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 3.1 30.5 - + - -
317G LEU* 5.3 0.7 - - + -
318G LYS* 5.2 13.9 - - + -
321G LEU* 3.7 23.3 - - + -
327G ASN* 3.2 31.6 + - + +
329G ILE* 1.3 78.3 - - - +
331G ASN* 1.3 61.5 + - - +
333G VAL* 3.1 29.2 + - + +
334G GLN* 2.9 65.0 + - + +
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Residues in contact with ASN 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 5.5 0.2 + - - -
326G ASN 4.7 4.2 + - - -
327G ASN 2.9 24.8 + - - +
328G GLN* 2.9 43.7 + - - +
330G TRP* 1.3 79.0 - - - +
332G ILE* 1.3 59.8 + - - +
334G GLN* 3.8 23.6 + - - +
335G GLU* 3.0 23.7 - - - +
336G HIS* 3.8 8.0 + - - -
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Residues in contact with ILE 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G LEU* 3.7 30.5 - - + -
246G HIS* 3.5 32.1 - - + +
247G MET* 3.8 24.2 - - + -
305G PHE* 3.5 33.6 - - + -
328G GLN* 2.9 23.1 + - + +
329G ILE* 3.1 11.4 + - + +
331G ASN* 1.3 78.0 - - - +
333G VAL* 1.3 64.0 + - + +
334G GLN 3.2 0.2 - - - -
336G HIS* 3.3 32.3 + - + +
337G LEU 4.1 0.5 + - - -
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Residues in contact with VAL 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 4.1 13.0 - - + -
317G LEU* 3.7 22.2 - - + -
321G LEU* 3.8 13.2 - - + -
329G ILE* 2.9 20.8 + - + +
330G TRP* 3.1 38.3 + - + +
332G ILE* 1.3 78.2 - - + +
334G GLN* 1.3 63.9 + - - +
337G LEU* 3.2 42.1 - - + +
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Residues in contact with GLN 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G TRP* 2.9 53.7 + - + +
331G ASN* 3.8 15.2 + - - +
332G ILE 3.2 0.6 - - - -
333G VAL* 1.3 80.9 - - - +
335G GLU* 1.3 87.7 + - - +
336G HIS 3.8 0.2 + - - -
337G LEU* 4.8 1.2 + - - +
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Residues in contact with GLU 335 (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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303G SER* 3.6 13.9 - - - -
331G ASN* 3.0 20.2 + - - +
334G GLN* 1.3 99.4 - - - +
336G HIS* 1.3 73.6 + - + +
337G LEU 3.7 1.2 - - - +
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Residues in contact with HIS 336 (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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246G HIS* 3.3 34.0 + + - -
301G ARG 3.6 10.0 + - - -
302G THR* 4.4 3.5 - - + -
303G SER* 3.3 35.0 + - - +
305G PHE* 3.1 38.2 - + + +
328G GLN* 6.1 0.6 + - - -
331G ASN 3.8 7.9 + - - -
332G ILE* 3.3 39.4 + - + +
335G GLU* 1.3 92.5 + - + +
337G LEU* 1.3 65.3 + - - +
338G TYR 3.5 0.3 + - - -
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Residues in contact with LEU 337 (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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239G LEU* 6.4 0.4 - - + -
303G SER* 5.3 1.4 - - - -
305G PHE* 3.6 24.9 - - + -
307G LEU* 3.7 17.0 - - + -
309G ILE* 5.5 3.6 - - + -
314G TYR* 4.9 10.5 - - + -
317G LEU* 5.2 4.5 - - + -
332G ILE* 5.8 0.2 - - + -
333G VAL* 3.2 51.1 + - + +
334G GLN 4.8 1.4 + - - +
335G GLU 3.7 1.5 - - - +
336G HIS* 1.3 76.8 - - - +
338G TYR* 1.3 61.0 + - - +
339G ILE* 3.8 27.8 + - + +
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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