Contacts of the helix formed by residues 436 - 448 (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 436 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G ARG* 3.1 32.5 - - - +
435G ASP* 1.3 75.1 - - - +
437G ALA* 1.3 63.1 + - - +
438G VAL 3.2 1.1 - - - -
439G PRO* 3.3 16.7 - - - +
440G ASN* 3.9 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G SER* 6.3 0.7 - - - -
405G PHE* 4.0 21.1 - - + -
433G VAL* 3.8 20.0 - - + -
434G ARG* 3.1 19.2 + - + +
436G ASP* 1.3 79.3 - - - +
438G VAL* 1.3 58.6 + - + +
440G ASN* 3.1 10.4 + - - +
441G LEU* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 438 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G ARG 4.8 1.1 - - - +
435G ASP* 4.0 13.0 - - - +
436G ASP 3.2 0.2 - - - -
437G ALA* 1.3 78.1 - - + +
439G PRO* 1.4 63.9 - - + +
441G LEU* 3.8 7.4 - - + +
442G ILE* 2.9 48.5 + - + +
471G PRO* 3.7 35.4 - - + +
474G GLN* 3.8 33.2 - - + +
475G VAL* 4.1 9.0 - - + -
525G TYR* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 439 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ASP* 3.3 45.0 - - - +
516B ASN* 4.3 11.7 - - - +
517B PRO* 4.0 19.9 - - + +
435G ASP 3.8 6.3 - - - +
436G ASP* 3.3 21.1 - - - +
438G VAL* 1.4 91.4 - - + +
440G ASN* 1.3 57.4 + - - +
442G ILE* 3.9 1.2 - - - +
443G GLN* 2.9 29.1 + - - +
525G TYR* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ASP* 4.2 12.9 - - - +
409G GLU* 3.8 19.8 + - - +
436G ASP* 3.9 23.2 + - - -
437G ALA* 3.1 9.7 + - - +
439G PRO* 1.3 76.7 - - - +
441G LEU* 1.3 61.5 + - + +
443G GLN* 3.4 8.5 + - - +
444G LEU* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G PHE* 4.1 30.3 - - + -
409G GLU* 5.8 0.2 - - - +
422G ILE* 3.7 25.1 - - + -
426G LEU* 3.7 39.7 - - + -
437G ALA* 2.9 28.2 + - + +
438G VAL* 3.8 6.3 - - + +
440G ASN* 1.3 78.8 - - + +
442G ILE* 1.3 57.7 + - - +
444G LEU* 3.3 20.6 + - + +
445G ILE* 3.0 33.3 + - + +
475G VAL* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PRO* 3.7 32.5 - - + -
438G VAL* 2.9 36.1 + - + +
439G PRO 4.1 0.2 - - - +
441G LEU* 1.3 73.1 - - - +
443G GLN* 1.3 60.4 + - - +
445G ILE* 3.4 8.1 + - + +
446G THR* 2.9 31.1 + - + +
474G GLN 4.0 7.9 - - - +
475G VAL* 4.3 16.6 - - + +
478G TRP* 3.6 58.3 - - + -
525G TYR* 4.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ASP* 5.1 11.8 - - + +
520B ARG* 3.7 11.8 + - - +
439G PRO 2.9 19.9 + - - +
440G ASN* 3.5 11.0 - - - +
442G ILE* 1.3 78.0 - - - +
444G LEU* 1.3 57.5 + - - +
446G THR* 3.4 12.0 - - - +
447G ASN* 2.8 41.4 + - - +
587G MET* 2.4 63.9 + - - +
588G GLU 5.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G PHE* 6.2 0.7 - - + -
409G GLU* 3.6 25.4 - - + +
415G LYS* 4.5 5.3 + - - +
418G HIS* 3.4 33.0 - - + +
419G ILE* 4.8 4.9 - - + -
422G ILE* 3.7 26.9 - - + -
440G ASN 2.9 19.1 + - - +
441G LEU* 3.3 20.2 - - + +
443G GLN* 1.3 77.5 - - - +
445G ILE* 1.3 75.4 + - + +
447G ASN* 3.2 12.7 + - + +
448G SER* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419G ILE* 4.6 18.2 - - + -
422G ILE* 6.0 4.7 - - + -
441G LEU* 3.0 25.7 + - + +
442G ILE* 3.4 10.5 - - + +
444G LEU* 1.3 90.5 - - + +
446G THR* 1.3 57.3 + - - +
448G SER* 3.2 25.6 - - - +
452G HIS* 3.7 12.1 + - + -
455G THR* 5.0 16.2 - - + +
475G VAL* 5.4 5.2 - - + -
478G TRP* 3.7 29.4 - - + -
479G CYS* 3.7 26.9 - - - -
483G TYR* 4.4 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 446 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ARG* 5.3 6.3 - - - +
442G ILE* 2.9 21.9 + - + +
443G GLN* 3.4 22.0 - - - +
445G ILE* 1.3 76.4 - - - +
447G ASN* 1.3 65.2 + - - +
448G SER 3.2 6.1 - - - +
449G VAL* 5.3 2.3 - - - +
478G TRP* 3.9 23.4 - - + -
483G TYR* 3.4 18.5 + - - -
584G MET 4.8 4.7 + - - -
585G PRO 5.3 1.3 + - - +
586G VAL* 3.4 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G LYS* 5.1 7.6 - - - +
443G GLN* 2.8 45.5 + - - +
444G LEU* 3.4 11.2 - - - +
446G THR* 1.3 74.5 - - - +
448G SER* 1.3 62.8 + - - +
449G VAL* 3.3 9.5 + - - +
450G GLU* 5.0 0.2 - - - +
586G VAL* 3.2 14.0 - - - +
587G MET 3.1 19.3 + - - +
588G GLU* 4.7 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 448 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G LYS* 3.3 28.2 + - - +
418G HIS* 5.8 0.2 - - - -
419G ILE* 4.0 22.1 - - - +
444G LEU* 2.9 14.1 + - - +
445G ILE* 3.2 17.4 - - - +
446G THR 3.2 6.0 - - - +
447G ASN* 1.3 75.5 - - - +
449G VAL* 1.3 53.7 + - - +
450G GLU* 3.6 10.1 - - - -
451G MET* 4.8 7.9 - - - -
452G HIS* 2.7 28.7 + - - -
483G TYR* 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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