Contacts of the helix formed by residues 508 - 524 (chain F) in PDB entry 6V3O
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 508 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506F PRO 4.3 1.0 + - - +
507F GLN* 1.3 75.5 - - - +
509F GLU* 1.3 60.9 + - - +
510F GLU* 3.6 7.3 + - - +
511F ILE* 3.0 38.6 + - + +
512F ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F THR* 1.3 74.8 - - - +
510F GLU* 1.3 66.1 + - + +
512F ALA* 3.5 6.5 + - - +
513F ASP* 3.1 22.0 + - - +
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Residues in contact with GLU 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F ARG* 2.9 59.5 + - - +
464F ASP* 4.5 8.2 - - - +
508F THR* 3.3 7.2 + - - +
509F GLU* 1.3 77.6 - - + +
511F ILE* 1.3 67.5 + - + +
513F ASP* 3.1 9.9 + - - -
514F VAL* 3.1 7.1 + - - +
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Residues in contact with ILE 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F ASP* 3.7 21.5 - - + +
465F VAL* 4.0 29.2 - - + +
468F ALA* 3.6 27.8 - - + -
505F LEU* 4.7 5.4 - - + -
506F PRO 5.1 0.7 - - - +
507F GLN* 4.0 19.3 - - + -
508F THR* 3.0 33.8 + - + +
510F GLU* 1.3 76.7 - - + +
512F ALA* 1.3 63.8 + - - +
514F VAL* 3.2 3.9 + - - +
515F ILE* 3.1 34.4 + - + +
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Residues in contact with ALA 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F PRO* 5.4 0.2 - - - +
507F GLN* 3.1 24.6 + - + +
508F THR 2.9 20.1 + - - +
509F GLU* 3.7 7.2 - - - +
511F ILE* 1.3 76.5 - - - +
513F ASP* 1.3 52.0 + - - +
515F ILE* 3.3 1.4 + - - +
516F GLY* 2.7 34.0 + - - -
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Residues in contact with ASP 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ARG* 4.2 11.4 + - - +
297F PRO* 5.0 7.2 - - - +
299F VAL 4.0 11.7 - - - +
300F THR* 4.4 9.9 - - - +
301F PRO* 3.7 28.6 - - - +
457F GLN* 5.2 2.6 + - - -
461F ARG* 3.9 11.3 + - - +
509F GLU 3.1 14.2 + - - +
510F GLU* 3.1 9.4 + - - +
512F ALA* 1.3 76.6 - - - +
514F VAL* 1.3 56.8 + - - +
516F GLY 3.8 0.2 - - - -
517F ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ARG* 6.4 0.4 - - - +
457F GLN* 4.1 18.2 - - + +
461F ARG* 3.8 33.9 - - + +
462F HIS* 4.2 14.1 - - + +
465F VAL* 3.9 19.1 - - + -
510F GLU 3.1 15.2 + - - +
511F ILE 3.2 6.2 + - - +
513F ASP* 1.3 77.9 - - - +
515F ILE* 1.3 64.7 + - + +
517F ALA* 3.4 5.9 + - - +
518F PHE* 3.0 49.6 + - + -
532F TYR* 4.9 2.5 - - - +
549F LEU* 4.9 1.6 - - + -
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Residues in contact with ILE 515 (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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465F VAL* 4.5 17.3 - - + -
501F LEU* 4.3 27.6 - - + -
505F LEU* 4.9 2.7 - - + -
507F GLN* 3.8 35.0 - - + +
511F ILE* 3.1 24.8 + - + +
512F ALA 3.9 2.9 - - - +
514F VAL* 1.3 76.6 - - + +
516F GLY* 1.3 64.3 + - - +
518F PHE* 3.1 11.9 + - + +
519F HIS* 3.0 47.9 + - + +
549F LEU* 6.0 0.7 - - + -
553F CYS* 4.0 13.9 - - - -
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Residues in contact with GLY 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F PRO* 3.7 14.6 - - - -
512F ALA 2.7 21.8 + - - -
513F ASP 3.8 1.1 - - - -
515F ILE* 1.3 73.6 - - - +
517F ALA* 1.3 61.2 + - - +
519F HIS* 3.1 13.1 + - - +
520F VAL* 3.0 25.6 + - - +
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Residues in contact with ALA 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ARG* 3.8 33.2 - - - +
301F PRO* 3.6 10.4 - - - +
304F THR* 6.5 0.4 - - - -
455F ILE* 5.8 3.8 - - + -
513F ASP 2.9 18.2 + - - +
514F VAL* 3.6 8.1 - - - +
516F GLY* 1.3 75.3 - - - +
518F PHE* 1.3 63.7 + - + +
520F VAL* 3.0 7.9 + - - +
521F LEU* 2.9 29.6 + - + +
532F TYR* 6.0 4.3 - - + +
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Residues in contact with PHE 518 (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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462F HIS* 4.4 3.6 - + - -
514F VAL* 3.0 43.9 + - + -
515F ILE* 3.1 6.5 + - + +
517F ALA* 1.3 78.2 - - + +
519F HIS* 1.3 59.0 + - - +
521F LEU* 3.2 15.7 + - + +
522F ALA* 3.0 24.4 + - - +
532F TYR* 3.5 39.3 - + - -
546F VAL* 4.2 9.0 - - + -
549F LEU* 4.0 25.1 - - + -
550F GLN* 3.8 33.7 - - + -
553F CYS* 3.5 32.1 - - + -
555F VAL* 3.6 10.7 - - + +
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Residues in contact with HIS 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F LEU* 6.3 1.7 - - + +
515F ILE* 3.0 39.5 + - + +
516F GLY* 3.5 12.2 - - - +
517F ALA 3.1 0.2 - - - -
518F PHE* 1.3 77.3 - - - +
520F VAL* 1.3 61.8 + - + +
522F ALA* 3.4 5.0 + - + +
523F GLU* 3.2 39.8 + - - +
553F CYS* 3.3 33.5 + - + +
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Residues in contact with VAL 520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F PRO* 3.6 38.1 - - + +
302F GLU* 5.3 0.4 - - - -
304F THR* 4.5 10.5 - - + -
305F ARG* 4.1 18.2 - - + +
516F GLY 3.0 15.9 + - - +
517F ALA* 3.0 9.5 + - - +
519F HIS* 1.3 75.2 - - + +
521F LEU* 1.3 65.4 + - - +
523F GLU* 3.3 19.1 + - - +
524F LEU* 3.4 35.9 + - + +
529F PHE* 5.3 0.2 - - + -
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Residues in contact with LEU 521 (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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304F THR* 4.9 6.3 - - + -
455F ILE* 3.9 18.4 - - + -
517F ALA* 2.9 20.2 + - + +
518F PHE* 3.5 22.9 - - + +
520F VAL* 1.3 77.7 - - - +
522F ALA* 1.3 62.9 + - - +
523F GLU 3.3 0.3 + - - -
524F LEU 3.6 13.5 + - - +
529F PHE* 3.5 47.4 - - + -
532F TYR* 4.2 17.3 - - + -
550F GLN* 5.2 2.7 - - - +
555F VAL* 4.5 9.6 - - + +
557F GLN* 5.1 3.3 + - - -
559F LEU* 3.6 32.1 - - + +
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Residues in contact with ALA 522 (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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518F PHE 3.0 15.9 + - - +
519F HIS* 3.7 7.6 - - + +
520F VAL 3.2 0.4 - - - -
521F LEU* 1.3 78.4 - - - +
523F GLU* 1.3 63.5 + - + +
524F LEU 3.6 4.2 + - - +
553F CYS 4.2 6.1 - - - +
554F GLY 3.1 34.3 - - - +
555F VAL* 4.1 10.0 - - + +
556F ARG* 4.6 10.4 + - - +
557F GLN* 4.3 11.6 + - - +
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Residues in contact with GLU 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F ARG* 5.5 11.4 + - - +
519F HIS* 3.2 27.1 - - - +
520F VAL* 3.3 11.8 + - - +
521F LEU 3.2 0.6 - - - -
522F ALA* 1.3 79.2 - - + +
524F LEU* 1.3 63.1 + - + +
525F PRO* 4.7 1.0 - - - +
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Residues in contact with LEU 524 (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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305F ARG* 3.8 42.2 - - + +
308F CYS* 4.1 17.3 - - + -
309F LEU* 4.8 14.6 - - + -
312F ARG* 6.0 1.6 - - - +
520F VAL* 3.4 29.9 + - + +
521F LEU 3.6 9.6 + - - +
522F ALA 3.4 4.6 - - - +
523F GLU* 1.3 82.7 - - + +
525F PRO* 1.3 81.7 - - + +
526F PRO* 3.5 3.6 - - - +
528F SER* 4.6 1.6 - - - +
529F PHE* 3.6 32.4 - - + -
557F GLN* 5.0 4.0 + - - -
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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