Contacts of the helix formed by residues 437 - 453 (chain F) in PDB entry 6VVT
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 THR 437 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436F VAL* 1.3 89.7 - - - +
438F ARG* 1.3 77.0 + - + +
439F GLU* 3.2 9.2 - - + +
440F ARG* 3.4 10.9 + - - -
441F ILE* 3.5 6.8 + - - +
3O T 2.5 51.1 + - + +
4O T 3.5 33.9 + - + +
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Residues in contact with ARG 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F LEU* 3.4 28.8 - - + +
428F ASP* 3.6 46.8 + - - +
436F VAL 3.7 0.2 + - - -
437F THR* 1.3 78.4 - - + +
439F GLU* 1.3 66.8 + - + +
441F ILE* 3.6 1.9 + - - +
442F ARG 3.3 14.6 + - - -
6O A 3.9 11.1 - - - +
7O C 5.3 0.2 - - - +
19P T 3.8 30.6 + - - +
20P G 2.3 58.8 + - - -
21P T 4.0 10.5 + - + +
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Residues in contact with GLU 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F THR* 3.2 2.7 - - + +
438F ARG* 1.3 80.4 - - + +
440F ARG* 1.3 65.6 + - - +
442F ARG* 2.7 29.4 + - - +
443F GLN* 2.9 42.3 + - - +
3O T 4.0 4.9 - - + +
4O T 3.8 31.2 - - + +
21P T 3.9 15.8 - - + +
22P C 2.4 44.4 + - - +
23P A 3.6 2.6 + - - -
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Residues in contact with ARG 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ARG* 4.6 4.6 - - - +
436F VAL* 3.8 16.2 - - + -
437F THR* 3.4 9.3 + - - +
438F ARG 3.4 0.4 - - - -
439F GLU* 1.3 79.1 - - - +
441F ILE* 1.3 57.3 + - - +
443F GLN* 3.0 33.2 + - - +
444F ILE* 2.9 57.4 + - + +
504F SO4 5.5 0.4 + - - -
1O G 3.3 23.7 + - - -
2O C 2.5 56.7 + - - +
3O T 3.6 30.3 - - + +
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Residues in contact with ILE 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ARG* 6.5 0.2 - - - -
412F VAL* 4.2 15.3 - - + -
416F ARG* 5.9 0.2 - - - -
427F LEU* 3.8 19.3 - - + +
430F ILE* 3.8 33.9 - - + +
431F GLY* 3.3 37.2 - - - +
434F TYR* 4.3 12.3 - - + -
436F VAL* 3.8 12.6 - - + -
437F THR 3.5 6.6 + - - +
438F ARG 3.8 7.2 - - - +
439F GLU 3.2 0.6 - - - -
440F ARG* 1.3 73.6 - - - +
442F ARG* 1.3 60.7 + - - +
444F ILE* 3.3 14.8 + - + +
445F GLU* 2.9 30.8 + - + +
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Residues in contact with ARG 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F LEU* 3.7 24.6 - - + +
438F ARG 3.3 6.0 + - - +
439F GLU* 2.7 38.8 + - - +
441F ILE* 1.3 78.9 - - - +
443F GLN* 1.3 70.8 + - - +
445F GLU* 3.8 7.4 - - - +
446F SER* 3.2 40.3 + - - +
21P T 3.6 55.5 + - - +
22P C 3.0 35.1 + - - -
23P A 6.0 0.4 + - - -
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Residues in contact with GLN 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439F GLU* 2.9 38.1 + - - +
440F ARG* 3.0 36.2 + - - +
442F ARG* 1.3 85.6 - - - +
444F ILE* 1.3 63.0 + - - +
446F SER* 3.4 6.7 + - - -
447F LYS* 3.3 33.3 + - - +
2O C 3.5 17.0 + - - +
3O T 2.8 33.6 + - - +
23P A 4.3 3.2 - - - +
24P A 4.7 2.0 - - - +
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Residues in contact with ILE 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ARG* 3.9 30.7 - - - +
409F GLU* 3.9 10.0 - - + +
412F VAL* 4.6 17.7 - - + -
436F VAL* 5.5 1.1 - - + -
440F ARG* 2.9 56.9 + - + +
441F ILE* 3.8 16.8 - - + +
443F GLN* 1.3 75.2 - - - +
445F GLU* 1.3 64.4 + - - +
447F LYS* 3.2 9.5 + - - +
448F THR* 2.9 32.8 + - + +
504F SO4 4.4 12.6 - - - +
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Residues in contact with GLU 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F VAL* 4.8 11.4 - - + +
413F VAL* 6.1 2.9 - - + -
416F ARG* 3.6 44.8 + - + +
417F PHE* 4.5 12.3 - - + -
427F LEU* 4.4 9.6 - - - +
441F ILE* 2.9 19.6 + - + +
442F ARG* 3.8 7.8 - - - +
444F ILE* 1.3 77.1 - - - +
446F SER* 1.3 65.4 + - - +
448F THR* 2.4 35.7 + - - +
449F MET* 3.0 18.4 + - + +
21P T 5.0 5.9 + - - -
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Residues in contact with SER 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F ARG* 3.2 28.8 + - - +
443F GLN* 3.7 6.3 - - - -
444F ILE 3.3 0.2 - - - -
445F GLU* 1.3 81.6 + - - +
447F LYS* 1.3 71.6 + - - +
449F MET* 3.3 10.5 + - - +
450F SER* 3.1 20.6 + - - -
453F ARG* 4.9 0.7 + - - -
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Residues in contact with LYS 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F GLU* 3.9 8.1 - - - +
443F GLN* 3.3 21.4 + - + +
444F ILE* 3.2 8.9 + - - +
445F GLU 3.2 0.6 - - - -
446F SER* 1.3 79.1 - - - +
448F THR* 1.3 60.9 + - - +
450F SER* 2.4 24.9 + - - +
451F LYS* 2.8 20.5 + - + +
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Residues in contact with THR 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F LEU* 4.9 4.3 - - - -
409F GLU* 2.8 42.4 - - + +
412F VAL* 5.5 1.8 - - + -
413F VAL* 4.0 24.8 - - + +
444F ILE* 2.9 20.4 + - + +
445F GLU* 2.4 28.6 + - - +
447F LYS* 1.3 76.8 - - - +
449F MET* 1.3 60.7 + - - +
451F LYS* 3.2 4.9 + - - +
452F LEU* 2.6 43.2 + - - +
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Residues in contact with MET 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C LEU* 4.6 2.0 - - + +
814C ALA* 3.3 24.0 - - + +
815C ILE* 3.3 47.3 - - + +
413F VAL* 5.6 1.1 - - - -
417F PHE* 4.7 12.6 - - - -
445F GLU* 3.0 24.8 + - + +
446F SER* 3.3 8.7 + - - +
448F THR* 1.3 90.3 + - - +
450F SER* 1.3 50.8 + - - +
452F LEU* 2.9 11.2 + - + +
453F ARG* 2.7 64.8 + - - +
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Residues in contact with SER 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446F SER 3.1 9.8 + - - -
447F LYS* 2.4 36.9 + - - +
449F MET* 1.3 73.8 - - - +
451F LYS* 1.3 61.8 + - - +
453F ARG* 3.2 20.9 + - - +
454F HIS* 3.0 24.6 + - - -
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Residues in contact with LYS 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F THR 5.8 1.3 - - - -
405F LEU* 4.2 8.3 - - + +
406F SER 6.2 0.2 - - - +
409F GLU* 4.1 24.4 + - - +
447F LYS* 2.8 18.3 + - + +
448F THR 3.4 8.5 - - - +
450F SER* 1.3 72.9 + - - +
452F LEU* 1.3 61.8 + - - +
454F HIS* 3.3 25.1 + - + +
457F ARG* 2.9 58.1 - - - +
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Residues in contact with LEU 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811C LEU* 4.2 11.2 - - + -
815C ILE* 3.6 45.4 - - + +
401F VAL* 4.5 16.4 - - + -
402F LEU* 6.2 1.3 - - + -
405F LEU* 3.5 41.7 - - + -
413F VAL* 4.7 4.9 - - + -
448F THR* 2.6 25.1 + - - +
449F MET* 2.9 21.3 + - - +
451F LYS* 1.3 75.3 - - - +
453F ARG* 1.3 58.8 + - - +
454F HIS 3.1 2.0 + - - +
457F ARG* 4.2 5.7 - - - +
458F SER* 3.0 28.4 + - - -
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Residues in contact with ARG 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814C ALA* 3.0 22.9 + - - +
815C ILE* 3.1 24.8 + - - +
816C PHE 5.2 0.6 - - - -
817C GLY* 4.9 7.3 - - - +
446F SER 4.9 1.0 + - - -
449F MET* 2.7 59.3 + - - +
450F SER* 3.2 12.4 + - - +
452F LEU* 1.3 69.6 - - - +
454F HIS* 1.3 68.1 + - - +
455F PRO* 3.5 2.6 - - - +
458F SER* 3.3 10.4 + - - -
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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