Contacts of the helix formed by residues 358 - 373 (chain B) in PDB entry 3C6G
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 MET 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU* 3.1 18.5 - - - +
340B ILE* 3.8 40.8 - - + +
343B ILE* 3.7 20.0 - - + -
344B MET* 3.6 30.5 - - + +
354B ASP* 3.2 23.1 - - - +
355B LYS 3.0 12.3 + - - +
357B LYS* 1.3 82.9 - - - +
359B PRO* 1.3 64.6 - - - +
361B THR* 3.3 22.9 + - - +
362B GLU* 3.3 16.6 + - - +
459B PHE* 3.9 7.3 - - + -
463B THR* 4.5 4.3 - - + -
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Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 3.7 8.7 - - - +
356B CYS 4.6 6.1 - - - +
357B LYS 3.5 9.0 - - - +
358B MET* 1.3 89.4 - - - +
360B TYR* 1.3 59.7 + - + +
362B GLU* 3.2 15.8 + - + +
363B ALA* 2.8 28.1 + - - +
426B LEU* 3.8 6.2 - - + +
430B GLY 3.5 25.8 - - - +
431B TYR* 4.3 7.2 - - + -
432B PHE* 3.8 22.5 - - + +
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Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 3.6 31.8 - - - +
335B GLN* 3.2 59.3 + - + +
336B VAL* 3.8 13.0 - - + -
339B GLU* 3.2 20.3 + - - +
359B PRO* 1.3 82.7 - - + +
361B THR* 1.3 56.3 + - - +
363B ALA* 3.4 7.0 - - + +
364B VAL* 3.1 37.9 + - + +
422B PRO* 4.4 7.4 - - + +
423B GLU* 3.3 28.9 + - + -
426B LEU* 3.9 19.9 - - + +
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Residues in contact with THR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 3.9 22.1 - - + +
339B GLU* 2.9 21.3 + - - +
358B MET* 3.6 20.7 - - + +
359B PRO 3.2 0.2 - - - -
360B TYR* 1.3 75.8 - - - +
362B GLU* 1.3 63.1 + - - +
363B ALA 3.2 0.2 - - - -
364B VAL* 4.0 1.6 - - - +
365B LEU* 3.2 26.8 + - + +
459B PHE* 4.0 11.4 - - + -
462B PHE* 4.2 19.1 - - + -
463B THR* 4.0 26.9 - - + -
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B LYS* 3.4 48.9 + - + +
356B CYS* 3.9 10.4 - - - +
358B MET 3.3 9.1 + - - +
359B PRO* 3.2 11.2 + - - +
361B THR* 1.3 77.0 - - - +
363B ALA* 1.3 58.3 + - - +
365B LEU* 3.2 7.0 + - - -
366B HIS* 2.8 47.5 + - + +
432B PHE* 3.8 42.3 - - + +
459B PHE* 5.2 4.7 - - + -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B PRO 2.8 17.0 + - - +
360B TYR* 3.4 9.4 - - + +
361B THR 3.2 0.4 - - - -
362B GLU* 1.3 77.2 - - - +
364B VAL* 1.3 58.1 + - - +
366B HIS* 3.1 2.9 + - - +
367B GLU* 2.9 28.4 + - - +
422B PRO* 3.3 27.8 - - + +
425B PHE* 3.9 17.3 - - + -
426B LEU* 3.9 17.0 - - + -
432B PHE* 4.0 3.6 - - + -
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B MET* 3.7 28.0 - - + -
332B ILE* 3.7 13.5 - - + -
336B VAL* 3.9 8.5 - - + -
360B TYR* 3.1 39.1 + - + +
361B THR 4.0 3.8 - - - +
363B ALA* 1.3 75.1 - - - +
365B LEU* 1.3 59.0 + - - +
367B GLU* 3.1 4.1 + - - +
368B VAL* 2.9 32.7 + - + +
420B PHE* 4.5 6.9 - - + -
422B PRO* 3.7 16.8 - - + -
462B PHE* 4.1 17.0 - - + -
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B VAL* 5.0 6.3 - - + -
319B LEU* 5.5 1.1 - - + -
322B ALA* 5.0 8.5 - - + -
361B THR* 3.2 20.2 + - + +
362B GLU* 3.7 5.8 - - - +
364B VAL* 1.3 79.5 - - - +
366B HIS* 1.3 64.3 + - + +
368B VAL* 3.5 7.1 + - + +
369B LEU* 3.3 25.9 + - - +
458B MET* 3.4 36.6 - - + +
459B PHE* 3.9 40.2 - - + +
462B PHE* 3.9 37.7 - - + -
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Residues in contact with HIS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLU* 2.8 41.1 + - + +
363B ALA 3.6 4.5 - - - +
365B LEU* 1.3 76.4 - - + +
367B GLU* 1.3 59.3 + - - +
369B LEU* 3.4 12.7 + - + +
370B ARG* 3.0 27.4 + - - +
425B PHE* 3.7 21.9 - + + -
432B PHE* 3.5 33.3 - + - -
438B LEU* 3.6 25.7 - - + +
455B ARG* 2.8 32.4 + - - -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ALA 2.9 15.9 + - - +
364B VAL 3.1 5.4 + - - +
366B HIS* 1.3 76.2 - - - +
368B VAL* 1.3 64.9 + - - +
370B ARG* 2.9 43.9 + - - +
371B PHE* 3.0 23.9 + - - +
419B VAL 3.3 0.5 - - - +
420B PHE* 3.3 26.7 - - + -
421B HIS 2.6 31.2 + - - +
422B PRO* 3.9 14.4 - - + -
424B ARG* 3.2 18.2 + - - -
425B PHE* 3.4 5.3 - - + -
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 3.7 34.3 - - + +
321B TRP* 3.9 20.4 - - + +
322B ALA* 3.9 23.1 - - + +
325B PHE* 5.2 2.2 - - + -
326B MET* 5.6 0.2 - - + -
364B VAL* 2.9 25.8 + - + +
365B LEU* 3.8 10.5 - - + +
366B HIS 3.4 0.2 - - - -
367B GLU* 1.3 75.5 - - - +
369B LEU* 1.3 59.1 + - - +
372B CYS* 2.9 42.0 + - + +
373B ASN 4.0 0.3 + - - -
374B ILE* 4.5 1.2 - - + +
420B PHE* 4.1 20.0 - - + -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 3.5 35.4 - - + -
365B LEU 3.3 14.1 + - - +
366B HIS* 3.6 16.6 - - + +
367B GLU 3.3 0.6 - - - -
368B VAL* 1.3 80.1 - - - +
370B ARG* 1.3 60.1 + - - +
373B ASN* 3.5 19.9 + - - +
374B ILE* 4.9 5.2 + - + +
408B HIS* 4.3 0.5 + - - -
438B LEU* 4.9 2.9 - - + -
440B PRO* 4.1 28.8 - - + +
441B PHE* 3.9 25.4 - - + -
455B ARG* 4.9 11.2 - - - +
458B MET* 4.2 16.8 - - + -
601B HEM 4.5 15.5 - - + -
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B HIS 3.0 13.6 + - - +
367B GLU* 2.9 42.6 + - - +
368B VAL 3.3 0.2 - - - -
369B LEU* 1.3 75.7 - - - +
371B PHE* 1.3 70.1 + - - +
373B ASN* 2.8 20.6 + - - -
408B HIS* 3.1 44.8 + - + +
409B PHE* 3.9 11.3 - - - -
414B TRP* 3.4 37.4 - - + -
417B PRO* 2.9 37.1 + - - +
419B VAL 3.3 8.9 + - - -
424B ARG* 3.6 13.4 - - - +
425B PHE* 4.6 0.9 - - + -
438B LEU* 3.6 23.8 - - + +
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Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B PHE* 3.5 35.9 - + - -
367B GLU* 3.0 16.4 + - - +
370B ARG* 1.3 100.4 - - - +
372B CYS* 1.3 64.3 + - - +
373B ASN* 2.8 14.9 + - - -
405B TYR* 5.1 1.4 - - - -
409B PHE* 3.9 21.4 - + - -
417B PRO 3.8 3.8 - - - -
418B GLU* 3.5 31.4 - - - -
420B PHE* 3.9 29.6 - + + -
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Residues in contact with CYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B TRP* 3.8 43.7 + - + -
325B PHE* 3.9 24.9 - - - -
368B VAL* 2.9 28.2 + - - +
371B PHE* 1.3 83.4 - - - +
373B ASN* 1.3 73.3 + - - +
374B ILE* 3.4 8.5 + - + +
420B PHE* 5.3 0.7 - - - -
489B LEU* 3.3 19.5 - - - +
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Residues in contact with ASN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU 3.5 13.8 + - - -
370B ARG 2.8 21.4 + - - -
371B PHE 2.8 17.6 + - - -
372B CYS* 1.3 78.5 - - - +
374B ILE* 1.3 66.2 + - - +
375B VAL 3.2 4.9 + - - +
376B PRO* 3.5 17.7 - - + +
404B LEU* 4.2 1.0 - - - +
405B TYR* 3.6 36.5 + - + -
408B HIS* 2.6 31.9 + - - -
409B PHE* 3.6 5.3 - - - -
440B PRO* 6.2 0.9 - - - -
489B LEU* 3.2 20.6 - - + +
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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