Contacts of the helix formed by residues 429 - 445 (chain M) in PDB entry 6FF7
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 VAL 429 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424M VAL* 5.6 7.0 - - + +
427M LYS* 3.0 9.6 + - - +
428M GLN* 1.3 80.7 + - - +
430M ASP* 1.3 60.6 + - - +
431M ASP* 4.1 10.8 - - + +
432M LEU* 4.2 20.9 + - + +
433M ALA* 4.7 3.6 + - - +
468M GLU* 5.2 6.5 - - - +
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Residues in contact with ASP 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429M VAL* 1.3 71.8 - - - +
431M ASP* 1.3 62.5 - - - +
432M LEU 3.4 0.9 - - - -
433M ALA* 4.1 3.4 + - - +
434M SER* 3.3 22.4 + - - -
482M LYS* 5.1 12.8 - - + +
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Residues in contact with ASP 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391M THR* 5.6 0.2 - - - -
392M GLY* 3.6 26.7 - - - +
395M HIS* 3.5 25.8 - - + +
429M VAL* 3.4 6.6 - - + +
430M ASP* 1.3 77.5 - - - +
432M LEU* 1.3 59.7 + - - +
434M SER* 3.7 6.5 - - - -
435M VAL* 2.9 31.2 + - - +
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Residues in contact with LEU 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M HIS* 5.6 0.2 - - - -
421M ALA 5.2 7.9 - - - +
422M THR* 4.5 17.4 - - - +
424M VAL* 5.9 8.3 - - + +
427M LYS* 5.9 6.1 - - - +
429M VAL* 4.2 19.2 + - + +
430M ASP 3.4 0.6 - - - -
431M ASP* 1.3 76.1 - - - +
433M ALA* 1.3 58.7 + - - +
435M VAL* 3.0 8.9 + - - +
436M TRP* 2.9 27.4 + - - +
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Residues in contact with ALA 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429M VAL 4.7 3.5 + - - +
430M ASP 4.1 3.8 + - - +
432M LEU* 1.3 79.2 - - - +
434M SER* 1.3 57.0 + - - +
435M VAL 3.3 0.2 - - - -
436M TRP* 3.9 9.0 - - - +
437M CYS* 2.9 30.0 + - - +
463M PRO* 6.0 5.8 - - + -
482M LYS* 3.6 35.8 - - + +
483M SER* 5.2 0.7 - - - +
486M VAL* 5.4 5.9 - - + +
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Residues in contact with SER 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M HIS* 6.1 0.4 - - - -
430M ASP 3.3 20.0 + - - -
431M ASP* 3.4 8.3 + - - -
432M LEU 3.1 1.0 - - - -
433M ALA* 1.3 79.0 - - - +
435M VAL* 1.3 58.6 + - - +
437M CYS* 3.8 5.0 - - - +
438M GLN* 2.9 27.4 + - - +
482M LYS* 5.2 1.3 - - - +
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Residues in contact with VAL 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M HIS* 4.2 24.9 - - + +
398M TRP* 6.1 1.3 - - + -
399M VAL* 5.4 4.5 - - + +
421M ALA* 5.2 14.6 - - + +
431M ASP 2.9 17.2 + - - +
432M LEU* 3.5 5.2 - - - +
434M SER* 1.3 75.7 - - - +
436M TRP* 1.3 61.7 + - - +
438M GLN* 3.3 7.9 + - - +
439M CYS* 2.9 27.5 + - - +
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Residues in contact with TRP 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422M THR* 6.2 4.9 - - - -
432M LEU 2.9 14.7 + - - +
433M ALA* 4.0 8.5 - - - +
435M VAL* 1.3 77.9 - - - +
437M CYS* 1.3 56.2 + - - +
439M CYS* 3.2 9.6 + - - +
440M GLY* 2.9 22.0 + - - -
459M ALA* 5.3 19.0 - - + +
486M VAL* 6.4 1.3 - - + -
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Residues in contact with CYS 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433M ALA 2.9 19.9 + - - +
434M SER* 3.9 6.3 - - - +
436M TRP* 1.3 73.4 - - - +
438M GLN* 1.3 61.6 + - - +
440M GLY* 3.0 4.4 + - - +
441M GLU* 2.9 25.5 + - - +
482M LYS 5.8 0.7 - - - +
485M LYS* 5.3 9.4 - - + +
486M VAL* 5.1 21.2 - - + +
489M MET* 5.8 2.9 - - + -
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Residues in contact with GLN 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399M VAL* 4.3 20.6 - - + -
434M SER 2.9 18.3 + - - +
435M VAL* 3.5 9.6 - - - +
436M TRP 3.3 0.2 - - - -
437M CYS* 1.3 74.7 - - - +
439M CYS* 1.3 59.8 + - - +
441M GLU* 3.1 10.3 + - - +
442M LEU* 2.9 26.9 + - - +
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Residues in contact with CYS 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418M LEU* 5.0 16.4 - - + -
435M VAL 2.9 13.3 + - - +
436M TRP* 3.5 11.9 - - - +
438M GLN* 1.3 76.6 - - - +
440M GLY* 1.3 57.5 + - - +
442M LEU* 3.5 9.2 + - - +
443M GLU* 2.9 26.2 + - - +
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Residues in contact with GLY 440 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436M TRP 2.9 13.6 + - - -
437M CYS* 3.0 7.7 + - - -
439M CYS* 1.3 75.4 - - - +
441M GLU* 1.3 58.9 + - - +
443M GLU* 3.2 9.6 + - - +
444M LEU* 2.9 24.1 + - - +
456M LEU* 5.3 11.2 - - - -
489M MET* 5.8 9.4 - - - -
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Residues in contact with GLU 441 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437M CYS 2.9 12.0 + - - +
438M GLN* 3.1 11.6 + - - +
440M GLY* 1.3 74.3 - - - +
442M LEU* 1.3 60.5 + - - +
444M LEU* 2.9 24.6 + - + +
445M ARG* 2.9 13.3 + - - +
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Residues in contact with LEU 442 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438M GLN 2.9 13.3 + - - +
439M CYS* 3.7 11.4 - - - +
441M GLU* 1.3 75.9 - - - +
443M GLU* 1.3 60.6 + - - +
445M ARG* 3.3 18.7 + - - +
446M HIS* 3.3 11.3 + - - +
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Residues in contact with GLU 443 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439M CYS 2.9 16.5 + - - +
440M GLY* 3.3 14.4 - - - +
441M GLU 3.1 0.4 - - - -
442M LEU* 1.3 74.6 - - - +
444M LEU* 1.3 58.9 + - - +
446M HIS* 3.2 25.4 + - - +
447M GLU 4.5 2.8 + - - +
452M ALA* 3.3 39.3 - - + +
455M LEU* 6.4 1.6 - - + -
456M LEU* 5.5 2.0 - - + -
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Residues in contact with LEU 444 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440M GLY 2.9 11.3 + - - +
441M GLU* 2.9 16.6 + - - +
443M GLU* 1.3 72.5 - - - +
445M ARG* 1.3 58.2 + - - +
446M HIS 3.1 6.3 + - - -
447M GLU* 3.8 11.0 + - - +
452M ALA* 5.5 0.2 - - - -
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Residues in contact with ARG 445 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441M GLU 2.9 10.2 + - - +
442M LEU* 3.3 15.4 + - - +
444M LEU* 1.3 74.1 - - - +
446M HIS* 1.3 54.6 + - - +
447M GLU* 3.2 7.7 + - - +
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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