Contacts of the helix formed by residues 434 - 455 (chain F) in PDB entry 6C3P
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 LEU 434 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430F TRP* 3.0 13.1 + - + +
431F PHE* 3.2 8.7 - - + +
433F PHE* 1.3 76.6 - - + +
435F CYS* 1.3 65.6 + - - +
436F PRO* 3.6 1.8 - - - -
437F ASN* 3.9 8.7 + - + +
438F LEU* 3.9 12.0 + - - +
592F LEU* 4.1 27.4 - - + -
595F SER* 3.8 11.2 - - - +
596F VAL* 3.6 54.3 - - + +
599F SER* 3.8 21.5 - - - +
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Residues in contact with CYS 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 3.7 41.1 - - + -
303F SER* 5.7 0.2 - - - -
431F PHE* 2.8 12.0 + - + +
432F PHE* 3.5 34.3 - - + +
433F PHE 3.1 2.6 - - - -
434F LEU* 1.3 79.7 - - - +
436F PRO* 1.3 71.0 - - + +
438F LEU* 3.1 6.0 + - - +
439F TRP* 3.0 45.0 - - - -
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Residues in contact with PRO 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 4.8 1.6 - - + +
302F SER* 4.0 17.9 - - - +
303F SER* 3.4 40.6 + - - +
306F ARG* 3.8 23.1 - - + +
376F SER* 4.3 2.0 - - - +
380F ALA* 4.0 12.3 - - + -
433F PHE 3.3 12.8 - - - +
435F CYS* 1.3 94.4 - - + +
437F ASN* 1.3 69.2 + - + +
438F LEU 3.0 0.5 + - - -
439F TRP* 3.3 5.4 + - + -
440F ALA* 2.9 23.1 + - - +
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Residues in contact with ASN 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ARG* 3.6 23.1 + - - +
434F LEU* 4.0 14.3 - - + +
435F CYS 3.2 0.4 + - - -
436F PRO* 1.3 82.1 - - + +
438F LEU* 1.3 64.1 + - - +
440F ALA* 3.9 4.9 - - - +
441F MET* 2.9 33.4 + - - +
444F GLN* 5.6 0.7 - - - +
589F PRO* 4.6 14.2 + - - +
592F LEU* 3.6 31.6 - - + +
593F LEU* 4.7 3.5 - - - +
596F VAL* 3.7 20.1 - - + +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F PHE* 5.6 8.7 - - + -
434F LEU 3.9 6.5 + - - +
435F CYS* 3.1 13.9 + - - +
436F PRO 3.0 0.4 + - - -
437F ASN* 1.3 78.6 - - - +
439F TRP* 1.3 89.6 - - + +
441F MET* 4.4 1.7 - - - +
442F PRO* 3.0 23.5 - - + +
593F LEU* 5.3 9.6 - - + -
596F VAL* 5.0 17.4 - - + +
600F THR* 5.4 12.6 - - + +
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Residues in contact with TRP 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 5.9 2.5 - - + -
303F SER* 4.6 14.6 - - - +
307F ILE* 4.6 4.4 - - + +
431F PHE* 5.6 9.4 - + - -
432F PHE* 6.3 0.2 - + - -
435F CYS* 3.0 55.2 - - - -
436F PRO* 3.3 6.7 + - + +
438F LEU* 1.3 100.9 - - + +
440F ALA* 1.3 61.5 + - - +
441F MET 3.6 0.2 - - - -
442F PRO* 3.8 9.3 - - - +
443F VAL* 4.1 14.0 - - - +
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Residues in contact with ALA 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ARG* 3.5 33.0 - - + -
307F ILE* 4.0 18.0 - - + +
310F ASP* 4.1 10.1 - - - +
436F PRO 2.9 17.1 + - - +
437F ASN* 3.0 7.8 + - - +
439F TRP* 1.3 77.2 - - - +
441F MET* 1.3 67.0 + - - +
443F VAL* 3.4 8.5 + - - +
444F GLN* 3.2 17.3 + - - +
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Residues in contact with MET 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F ASN* 2.9 27.3 + - - +
438F LEU* 4.4 1.1 - - - +
440F ALA* 1.3 73.7 - - - +
442F PRO* 1.3 66.6 - - + +
444F GLN* 2.8 17.5 + - + +
445F ILE* 2.7 48.1 + - + +
467F ILE* 4.9 1.8 - - + -
586F LEU* 4.9 4.0 - - + +
589F PRO* 4.2 23.8 - - + +
590F LEU* 3.5 36.6 - - + -
593F LEU* 4.0 30.7 - - + -
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Residues in contact with PRO 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438F LEU* 3.0 22.2 - - + +
439F TRP* 3.8 7.2 - - - +
440F ALA 3.6 2.9 - - - -
441F MET* 1.3 92.6 - - + +
443F VAL* 1.3 62.6 + - + +
445F ILE* 3.0 14.6 - - + +
446F ILE* 2.9 31.3 + - + +
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Residues in contact with VAL 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ILE* 4.2 30.3 - - + -
310F ASP* 6.0 0.7 - - - +
311F LEU* 6.1 4.9 - - + -
439F TRP 4.1 14.8 - - - +
440F ALA 3.4 8.0 + - - +
441F MET 3.3 0.2 - - - -
442F PRO* 1.3 77.4 - - + +
444F GLN* 1.3 62.8 + - - +
446F ILE* 3.5 5.3 + - - +
447F VAL* 3.2 33.1 + - + +
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Residues in contact with GLN 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ASP* 3.4 44.2 + - + +
311F LEU* 6.4 1.6 - - - +
314F PHE* 5.0 12.7 - - + -
437F ASN* 5.6 1.2 - - - +
440F ALA* 3.2 4.8 + - - +
441F MET* 2.8 18.4 + - + +
443F VAL* 1.3 76.2 - - - +
445F ILE* 1.3 60.9 + - - +
447F VAL* 3.3 7.7 + - - +
448F GLY* 2.9 24.8 + - - -
585F ILE* 4.2 13.7 + - - +
586F LEU* 4.7 12.6 - - + +
589F PRO* 3.2 39.3 - - - +
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Residues in contact with ILE 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F MET* 2.7 25.6 + - + +
442F PRO* 3.0 31.9 - - + +
444F GLN* 1.3 72.7 - - - +
446F ILE* 1.3 71.5 + - + +
448F GLY* 3.2 1.6 + - - +
449F VAL* 2.9 36.5 + - + +
467F ILE* 3.7 28.9 - - + -
586F LEU* 3.4 42.6 - - + -
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Residues in contact with ILE 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F PRO* 2.9 26.2 + - + +
443F VAL* 3.9 5.8 - - - +
445F ILE* 1.3 85.0 - - + +
447F VAL* 1.3 58.0 + - + +
449F VAL* 3.2 11.0 + - + +
450F ILE* 2.9 51.1 + - + +
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Residues in contact with VAL 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F LEU* 3.6 28.0 - - + -
314F PHE* 3.4 27.8 - - + -
443F VAL* 3.2 26.3 + - + +
444F GLN* 3.7 5.4 - - - +
446F ILE* 1.3 78.0 - - + +
448F GLY* 1.3 57.7 + - - +
450F ILE* 3.8 12.3 - - + +
451F LEU* 2.9 28.7 + - + +
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Residues in contact with GLY 448 (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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314F PHE* 3.3 23.1 - - - -
444F GLN 2.9 13.9 + - - -
445F ILE* 3.2 5.1 + - - -
447F VAL* 1.3 77.2 - - - +
449F VAL* 1.3 60.8 + - - +
451F LEU* 3.3 1.9 + - - +
452F LEU* 3.0 33.4 + - - +
582F LEU* 5.1 3.6 - - - -
586F LEU* 5.5 9.4 - - - -
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Residues in contact with VAL 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445F ILE* 2.9 27.6 + - + +
446F ILE* 3.2 13.4 + - + +
448F GLY* 1.3 74.6 - - - +
450F ILE* 1.3 66.4 + - + +
452F LEU* 3.1 9.4 + - - +
453F TYR* 3.0 22.6 + - + +
461F LEU* 4.7 5.5 - - + +
464F ALA* 4.9 20.2 - - + -
467F ILE* 5.8 2.5 - - + -
468F ILE* 5.3 16.4 - - + -
586F LEU* 6.3 0.7 - - + -
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Residues in contact with ILE 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 ILE* 2.9 37.9 + - + +
447F VAL* 3.8 12.1 - - + +
449F VAL* 1.3 78.4 - - + +
451F LEU* 1.3 57.4 + - - +
453F TYR* 3.2 11.6 + - + +
454F TYR* 2.9 28.6 + - + +
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Residues in contact with LEU 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F PHE* 3.3 37.9 - - + +
317F PRO* 5.8 2.2 - - + -
318F LEU* 4.1 33.0 - - + -
447F VAL* 2.9 8.0 + - + +
448F GLY 3.6 0.9 - - - +
450F ILE* 1.3 73.9 - - - +
452F LEU* 1.3 54.0 + - - +
454F TYR* 2.9 17.2 + - + +
455F ILE* 2.4 66.9 + - + +
582F LEU* 3.6 20.9 - - + -
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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
----------------------------------------------------------
448F GLY 3.0 27.8 + - - +
449F VAL* 3.5 10.3 - - - +
451F LEU* 1.3 75.8 - - - +
453F TYR* 1.3 58.4 + - - +
455F ILE* 2.7 35.9 - - + +
457F GLY* 3.1 19.1 - - - -
461F LEU* 3.3 30.5 - - + -
464F ALA* 5.7 4.5 - - + -
558F THR* 6.1 0.4 - - + -
579F SER* 3.8 23.8 - - - +
582F LEU* 3.5 39.3 - - + -
583F PHE* 4.3 13.7 - - + -
586F LEU* 6.1 0.9 - - + -
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Residues in contact with TYR 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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449F VAL* 3.0 14.3 + - + +
450F ILE* 3.5 12.3 - - + +
451F LEU 3.1 0.2 - - - -
452F LEU* 1.3 76.9 - - - +
454F TYR* 1.3 59.6 + - + +
458F VAL* 3.0 57.4 - - + +
459F SER* 5.1 6.5 - - - -
461F LEU* 3.4 10.7 - - + +
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Residues in contact with TYR 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 6.5 0.4 - - + -
450F ILE* 2.9 16.9 + - + +
451F LEU* 2.9 19.0 + - + +
453F TYR* 1.3 79.7 - - + +
455F ILE* 1.3 66.8 + - + +
458F VAL* 4.1 9.1 - - + +
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Residues in contact with ILE 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 3.9 24.7 - - + -
321F PHE* 4.8 24.2 - - + -
451F LEU* 2.4 54.8 + - + +
452F LEU* 2.7 21.6 - - + +
454F TYR* 1.3 79.8 - - + +
456F LEU* 1.3 81.3 + - + +
457F GLY 2.5 18.2 + - - +
458F VAL* 2.5 22.5 + - - +
578F ALA* 6.2 0.2 - - + -
579F SER* 6.0 1.3 - - - -
582F LEU* 5.3 1.8 - - + -
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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
------------------------------------------------------------
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