Contacts of the helix formed by residues 377 - 391 (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 ASN 377 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344G GLN* 4.1 2.6 - - - +
347G ARG* 3.1 42.0 - - - +
372G LEU* 3.9 17.2 + - - +
373G VAL* 3.5 6.9 - - - +
374G ASN 3.0 26.9 + - - +
376G ASN* 1.3 79.5 + - - +
378G ILE* 1.3 62.1 + - - +
379G ARG 3.3 2.7 - - - -
380G GLY* 3.6 3.4 + - - +
381G MET* 3.1 49.2 + - + +
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Residues in contact with ILE 378 (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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373G VAL* 3.7 23.1 - - + -
374G ASN 3.8 7.4 - - - +
375G GLY 4.0 20.4 - - - +
376G ASN 3.3 3.1 - - - +
377G ASN* 1.3 80.3 + - - +
379G ARG* 1.3 65.2 + - + +
380G GLY 3.6 0.2 + - - -
381G MET* 5.4 0.2 - - - -
382G MET* 3.2 52.5 + - + +
407G ALA 5.0 5.6 - - - +
408G ALA* 5.2 1.8 - - - -
411G TYR 3.3 30.7 - - - +
413G PRO* 3.8 22.9 - - + -
417G TRP* 3.8 17.2 - - + -
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Residues in contact with ARG 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G ASN 4.7 3.9 + - - +
377G ASN 3.3 0.6 - - - -
378G ILE* 1.3 85.9 - - + +
380G GLY* 1.3 61.8 + - - +
382G MET* 4.2 4.2 + - - +
383G LYS* 4.1 26.8 + - - +
413G PRO* 3.3 31.6 - - + +
414G SER* 4.5 9.7 + - - -
417G TRP* 3.8 42.3 + - - +
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Residues in contact with GLY 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G ASN 5.7 0.2 + - - -
377G ASN* 3.6 4.9 + - - +
378G ILE 3.4 0.2 - - - -
379G ARG* 1.3 77.3 - - - +
381G MET* 1.3 64.4 + - - +
382G MET 3.2 2.0 - - - -
383G LYS* 3.2 24.3 + - - +
384G GLU* 3.8 3.8 + - - +
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Residues in contact with MET 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347G ARG* 3.6 32.8 - - + +
351G VAL* 5.4 9.0 - - + -
369G SER* 4.1 22.2 - - - +
372G LEU* 4.4 11.9 - - + -
373G VAL* 3.6 29.4 - - + -
377G ASN* 3.1 44.0 + - + +
378G ILE* 5.4 0.2 - - - -
380G GLY* 1.3 73.1 - - - +
382G MET* 1.3 58.7 + - + +
384G GLU* 3.2 13.8 + - + +
385G LEU* 2.9 37.9 + - + +
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Residues in contact with MET 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373G VAL* 5.3 3.6 - - + -
378G ILE* 3.2 40.6 + - + +
379G ARG 4.4 1.8 - - - +
380G GLY 3.2 0.8 - - - -
381G MET* 1.3 80.0 - - + +
383G LYS* 1.3 57.8 + - + +
385G LEU* 4.1 11.2 - - + -
386G LEU* 2.8 45.0 + - + +
404G ILE* 3.7 41.1 - - + +
407G ALA* 3.8 26.9 - - + -
408G ALA* 4.3 8.3 - - + +
417G TRP* 3.6 26.0 - - + -
421G THR* 5.3 4.5 - - + -
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Residues in contact with LYS 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379G ARG* 4.1 26.1 - - - +
380G GLY* 3.2 12.2 + - - +
382G MET* 1.3 74.5 - - + +
384G GLU* 1.3 61.1 + - - +
386G LEU* 3.8 4.9 - - - +
387G TYR* 2.9 28.6 + - - +
417G TRP* 6.1 1.6 - - - +
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Residues in contact with GLU 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351G VAL* 3.5 37.9 - - + +
354G LEU* 4.5 13.4 - - + +
355G LYS* 2.8 31.4 + - - -
380G GLY 3.8 2.5 + - - +
381G MET* 3.2 19.7 + - + +
383G LYS* 1.3 78.6 - - - +
385G LEU* 1.3 59.4 + - + +
387G TYR* 3.3 11.5 + - - +
388G PHE* 2.9 27.6 + - - +
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Residues in contact with LEU 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G LEU* 4.9 13.7 - - + -
366G MET* 5.6 2.5 - - + +
369G SER* 4.4 15.7 - - - -
370G PHE* 3.6 39.9 - - + -
373G VAL* 4.8 9.0 - - + -
381G MET* 2.9 32.1 + - + +
382G MET* 3.8 18.2 - - + +
383G LYS 3.4 0.2 - - - -
384G GLU* 1.3 76.7 - - + +
386G LEU* 1.3 58.8 + - - +
388G PHE* 3.2 12.9 + - + +
389G LEU* 2.8 27.7 + - - +
400G CYS* 4.0 5.2 - - - -
404G ILE* 3.7 20.6 - - + -
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Residues in contact with LEU 386 (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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382G MET* 2.8 34.4 + - + +
383G LYS* 4.2 4.3 - - - +
385G LEU* 1.3 74.5 - - - +
387G TYR* 1.3 62.5 + - - +
389G LEU* 4.0 10.4 - - + +
390G ASP* 3.8 15.2 + - - +
404G ILE* 3.8 37.5 - - + -
421G THR* 4.5 19.1 - - + +
424G ARG* 3.7 60.3 + - + +
425G VAL* 4.5 7.6 - - + -
428G THR* 5.8 2.9 - - - +
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Residues in contact with TYR 387 (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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355G LYS* 4.1 31.1 - - - -
383G LYS 2.9 18.0 + - - +
384G GLU* 3.6 10.8 - - - +
386G LEU* 1.3 76.6 - - - +
388G PHE* 1.3 60.1 + - - +
389G LEU 3.3 0.2 - - - -
390G ASP* 3.2 18.1 + - + +
391G SER* 3.0 46.5 + - - -
424G ARG* 5.8 0.4 - - - +
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Residues in contact with PHE 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G LEU* 4.2 51.8 - - + -
355G LYS* 6.0 2.7 - - - +
362G LYS* 4.7 15.5 - - + -
366G MET* 4.2 26.5 - - + -
384G GLU* 2.9 16.1 + - - +
385G LEU* 3.2 15.2 + - + +
387G TYR* 1.3 79.6 - - + +
389G LEU* 1.3 54.3 + - - +
391G SER* 2.7 38.4 + - - -
392G CYS* 3.0 43.4 + - - -
396G PHE* 4.6 12.3 - + + -
400G CYS* 3.8 19.7 - - + -
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Residues in contact with LEU 389 (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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385G LEU 2.8 16.3 + - - +
386G LEU* 4.3 11.9 - - + +
388G PHE* 1.3 76.1 - - - +
390G ASP* 1.3 62.1 + - - +
392G CYS* 4.1 4.3 - - - -
397G LYS* 3.5 54.8 - - + +
400G CYS* 3.9 11.9 - - + -
401G ALA* 3.9 16.6 - - + +
404G ILE* 5.0 4.0 - - + -
425G VAL* 3.8 39.0 - - + -
428G THR* 3.8 22.3 + - + +
429G ALA* 4.6 6.3 - - + -
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Residues in contact with ASP 390 (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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386G LEU 3.8 11.5 + - - +
387G TYR* 3.2 21.0 + - + +
388G PHE 3.2 0.2 - - - -
389G LEU* 1.3 80.8 - - - +
391G SER* 1.3 58.9 + - - +
392G CYS 3.6 2.9 + - - +
397G LYS* 4.1 13.3 + - - +
424G ARG* 6.2 0.4 - - - +
428G THR* 5.1 13.9 + - + +
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Residues in contact with SER 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355G LYS* 5.7 1.7 - - - +
362G LYS* 5.5 2.9 + - - -
387G TYR* 3.0 38.8 + - - -
388G PHE* 2.7 33.0 + - - +
390G ASP* 1.3 73.9 - - - +
392G CYS* 1.3 60.3 + - - +
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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