Contacts of the helix formed by residues 321 - 335 (chain G) in PDB entry 6CM9
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 ASP 321 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G ASN* 5.6 0.2 - - - +
319G ASN* 3.2 8.9 - - + +
320G ASN* 1.3 74.5 - - - +
322G LYS* 1.3 63.6 + - - +
323G ASN* 3.2 24.3 + - - +
324G ILE* 2.9 45.9 + - + +
325G ARG 3.4 6.9 + - - -
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Residues in contact with LYS 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ASN 3.1 9.2 + - - +
321G ASP* 1.3 71.2 + - - +
323G ASN* 1.3 66.1 + - - +
325G ARG* 3.3 42.8 + - - +
326G TYR* 3.0 18.5 + - - +
356G ASP* 3.3 22.9 + - - +
357G LEU* 5.2 4.9 - - - +
358G ASP* 4.9 3.4 - - + +
361G ILE* 3.9 8.8 - - + +
45S ARG* 3.0 35.0 + - + +
47S SER* 3.5 32.6 - - - +
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Residues in contact with ASN 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ASN* 5.4 6.4 + - - +
321G ASP* 3.5 24.0 + - - +
322G LYS* 1.3 76.7 - - - +
324G ILE* 1.3 61.4 + - + +
326G TYR* 3.3 5.5 + - - +
327G VAL* 2.9 31.9 + - - +
47S SER* 2.8 37.2 - - - +
48S SER* 3.6 11.2 + - - -
49S PHE* 4.4 4.5 - - + -
60S LYS* 6.2 1.6 - - - +
78S LEU* 4.3 16.3 - - + +
81S LEU* 4.8 14.8 - - - +
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Residues in contact with ILE 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ASN* 5.1 3.1 - - - +
286G ASN* 3.5 38.6 - - + +
316G PHE* 3.5 30.9 - - + +
319G ASN* 3.4 30.5 - - + +
321G ASP* 2.9 33.1 + - + +
323G ASN* 1.3 78.2 - - + +
325G ARG* 1.3 61.0 + - - +
327G VAL* 3.5 5.1 - - + +
328G ALA* 2.9 27.9 + - - +
78S LEU* 4.5 10.3 - - + -
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Residues in contact with ARG 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G PHE 4.5 4.7 - - - +
317G LEU* 4.0 19.2 + - + +
318G LEU 5.2 2.2 + - - -
319G ASN 3.0 28.7 + - - +
320G ASN* 4.1 17.5 + - - +
321G ASP 3.4 2.9 + - - +
322G LYS* 3.3 34.5 + - - +
324G ILE* 1.3 76.4 - - - +
326G TYR* 1.3 60.0 + - - +
328G ALA* 3.3 3.3 + - - +
329G LEU* 2.9 41.1 + - + +
353G CYS* 4.7 16.4 - - - -
356G ASP* 2.9 32.1 + - - +
361G ILE* 4.0 13.2 - - + -
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Residues in contact with TYR 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G LYS 3.0 13.6 + - - +
323G ASN 3.3 7.6 + - - +
325G ARG* 1.3 75.2 - - - +
327G VAL* 1.3 56.9 + - + +
329G LEU* 3.9 3.9 - - - +
330G THR* 2.7 48.8 + - - -
360G SER* 3.6 33.4 - - - -
361G ILE* 3.6 11.3 - - + +
364G ARG* 3.0 56.5 + - + -
47S SER* 4.4 3.6 - - - -
49S PHE* 3.5 48.1 - + + +
51S ASP* 4.5 6.6 + - + +
56S LYS* 3.8 19.3 - - + +
77S GLU* 4.9 5.2 - - + -
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Residues in contact with VAL 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G ASN* 5.2 0.4 - - + +
290G TYR* 3.5 43.8 - - + -
316G PHE* 4.2 17.0 - - + -
323G ASN 2.9 20.6 + - - +
324G ILE* 3.5 8.7 - - + +
325G ARG 3.2 0.2 - - - -
326G TYR* 1.3 79.0 - - + +
328G ALA* 1.3 57.4 + - - +
330G THR* 3.3 5.9 + - - -
331G SER* 2.9 32.4 + - - +
49S PHE* 5.0 5.6 - - + -
77S GLU* 5.0 4.3 - - + -
78S LEU* 3.7 35.9 - - + -
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G LEU* 4.3 8.2 - - + +
316G PHE* 3.7 22.7 - - + -
317G LEU* 3.8 30.1 - - + +
324G ILE 2.9 17.6 + - - +
325G ARG 3.8 2.0 - - - +
327G VAL* 1.3 78.4 - - - +
329G LEU* 1.3 57.5 + - - +
331G SER* 3.3 6.5 + - - -
332G LEU* 2.9 35.2 + - + +
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Residues in contact with LEU 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G LEU* 3.7 24.7 - - + -
325G ARG* 2.9 27.8 + - + +
326G TYR* 4.0 3.1 - - - +
328G ALA* 1.3 77.4 - - - +
330G THR* 1.3 57.0 + - - +
332G LEU* 3.5 1.6 + - - +
333G LEU* 2.9 28.9 + - - +
350G ILE* 5.5 5.2 - - + -
353G CYS* 4.3 16.4 - - + -
361G ILE* 3.6 23.8 - - + +
364G ARG* 3.7 16.3 - - + +
365G ALA* 3.4 36.3 - - + +
368G LEU* 4.1 21.8 - - + +
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Residues in contact with THR 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G TYR* 4.1 19.1 - - - +
294G LEU* 5.6 1.1 - - + -
326G TYR* 2.7 43.7 + - + -
327G VAL* 3.3 5.1 + - - -
329G LEU* 1.3 75.3 - - - +
331G SER* 1.3 58.3 + - - +
333G LEU* 3.3 14.5 + - + +
334G LYS* 3.0 26.8 + - + +
364G ARG* 4.5 6.4 + - - +
56S LYS* 3.9 27.6 - - + -
77S GLU* 5.5 1.6 - - + -
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Residues in contact with SER 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G TYR* 3.1 26.0 - - - -
293G VAL* 4.6 4.2 - - - +
294G LEU* 4.2 17.3 - - - +
313G LEU* 3.6 27.3 - - - +
327G VAL* 2.9 18.5 + - - +
328G ALA 3.6 4.5 - - - -
330G THR* 1.3 77.6 - - - +
332G LEU* 1.3 58.0 + - - +
334G LYS* 3.0 17.0 + - - +
335G THR* 3.1 19.1 + - - +
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Residues in contact with LEU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G ILE* 5.1 4.7 - - + -
313G LEU* 3.9 27.1 - - + -
317G LEU* 3.8 35.4 - - + -
328G ALA 2.9 20.5 + - - +
329G LEU* 4.9 0.2 - - - -
331G SER* 1.3 72.4 - - - +
333G LEU* 1.3 65.2 + - - +
334G LYS 3.4 0.2 + - - -
335G THR* 3.5 6.0 + - + +
336G VAL* 3.3 24.6 + - - +
343G VAL* 4.0 30.7 - - + +
346G HIS* 4.9 8.7 - - + -
350G ILE* 4.5 9.6 - - + -
368G LEU* 3.5 29.8 - - + +
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Residues in contact with LEU 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU 2.9 18.3 + - - +
330G THR* 3.4 12.8 - - + +
331G SER 3.2 0.2 - - - -
332G LEU* 1.3 77.7 - - - +
334G LYS* 1.3 60.5 + - - +
336G VAL* 3.4 12.5 - - - +
364G ARG* 4.0 22.4 - - - +
367G GLU* 3.7 50.9 - - + +
368G LEU* 3.7 12.7 - - + +
371G ALA* 4.5 10.8 - - + -
56S LYS* 6.3 1.1 - - - +
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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
----------------------------------------------------------
254G ARG* 4.1 23.6 - - - +
258G ARG* 6.0 2.7 - - - +
294G LEU* 3.8 22.8 - - + +
297G MET* 5.8 1.6 - - + -
298G ASP* 3.0 38.4 + - - +
330G THR* 3.0 13.4 + - + +
331G SER 3.0 9.8 + - - +
333G LEU* 1.3 79.4 - - - +
335G THR* 1.3 59.0 + - - +
336G VAL* 3.3 4.2 + - - +
337G GLN 5.1 0.7 + - - -
74S GLN* 5.8 2.8 + - - +
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Residues in contact with THR 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G MET* 3.5 52.8 - - + -
298G ASP* 5.9 1.6 - - - -
310G ILE* 5.5 1.1 - - + +
313G LEU* 4.7 4.3 - - + -
331G SER 3.1 18.8 + - - +
332G LEU* 3.6 13.0 - - + -
333G LEU 3.5 0.2 - - - -
334G LYS* 1.3 74.4 - - - +
336G VAL* 1.3 60.6 + - - +
337G GLN 3.6 1.3 - - - +
338G THR* 2.3 47.8 + - - +
339G ASP* 4.4 0.9 + - - +
343G VAL* 3.4 15.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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