Contacts of the helix formed by residues 508 - 524 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506H PRO 4.3 1.1 + - - +
507H GLN* 1.3 76.2 - - - +
509H GLU* 1.3 65.4 + - - +
510H GLU* 3.5 6.7 + - - +
511H ILE* 3.2 35.6 + - + +
512H ALA* 2.9 22.6 + - - +
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Residues in contact with GLU 509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508H THR* 1.3 74.6 - - - +
510H GLU* 1.3 61.8 + - + +
512H ALA* 3.5 5.9 - - - +
513H ASP* 2.9 27.2 + - - +
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Residues in contact with GLU 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H ARG* 2.8 61.2 + - - +
464H ASP* 4.5 8.0 - - + +
508H THR* 3.3 7.2 + - - +
509H GLU* 1.3 78.0 - - + +
511H ILE* 1.3 66.6 + - + +
513H ASP* 3.0 10.2 + - - -
514H VAL* 3.1 6.4 + - - +
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Residues in contact with ILE 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H ARG 5.4 0.2 - - - +
464H ASP* 3.7 20.6 - - + +
465H VAL* 3.9 31.9 - - + +
468H ALA* 3.7 29.6 - - + -
505H LEU* 5.1 3.1 - - + -
506H PRO 5.1 2.5 - - - +
507H GLN* 4.1 13.0 - - + -
508H THR* 3.2 30.9 + - + +
510H GLU* 1.3 77.7 - - + +
512H ALA* 1.3 63.7 + - - +
514H VAL* 3.2 4.3 + - - +
515H ILE* 3.0 37.4 + - + +
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Residues in contact with ALA 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507H GLN* 3.2 25.3 + - + +
508H THR 2.9 20.8 + - - +
509H GLU* 3.5 6.7 - - - +
511H ILE* 1.3 77.5 - - - +
513H ASP* 1.3 53.4 + - - +
515H ILE* 3.8 0.7 - - - +
516H GLY* 2.7 34.8 + - - -
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Residues in contact with ASP 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 4.2 11.1 + - - +
297H PRO* 4.9 7.8 - - - +
299H VAL 4.1 10.9 - - - +
300H THR* 4.5 9.9 - - - +
301H PRO* 3.9 27.3 - - - +
457H GLN* 5.2 2.1 + - - -
461H ARG* 3.7 11.9 + - - +
509H GLU 2.9 14.2 + - - +
510H GLU* 3.0 10.3 + - - +
512H ALA* 1.3 76.8 - - - +
514H VAL* 1.3 61.4 + - - +
516H GLY 3.5 0.3 + - - -
517H ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 6.4 0.9 - - - +
457H GLN* 4.3 10.5 - - + +
461H ARG* 3.6 39.9 - - + +
462H HIS* 4.1 15.9 - - + +
465H VAL* 3.8 18.2 - - + -
510H GLU 3.1 13.7 + - - +
511H ILE* 3.2 6.5 + - - +
513H ASP* 1.3 73.9 - - - +
515H ILE* 1.3 67.8 + - + +
517H ALA* 3.2 15.7 + - - +
518H PHE* 3.2 40.0 + - + -
532H TYR* 4.8 2.9 - - - +
549H LEU* 5.0 1.1 - - + -
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Residues in contact with ILE 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465H VAL* 4.4 17.9 - - + -
501H LEU* 4.6 16.2 - - + -
505H LEU* 4.4 14.8 - - + -
507H GLN* 3.9 34.1 - - - +
511H ILE* 3.0 24.2 + - + +
512H ALA 3.9 2.7 - - - +
514H VAL* 1.3 75.2 - - + +
516H GLY* 1.3 62.6 + - - +
518H PHE* 3.2 11.9 + - + +
519H HIS* 3.1 45.4 + - + +
549H LEU* 6.1 0.7 - - + -
553H CYS* 4.3 12.3 - - - -
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Residues in contact with GLY 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H PRO* 3.7 14.3 - - - +
512H ALA 2.7 22.2 + - - -
513H ASP 4.0 0.9 - - - -
515H ILE* 1.3 73.1 - - - +
517H ALA* 1.3 62.6 + - - +
519H HIS* 3.2 12.4 + - - +
520H VAL* 3.0 25.8 + - - +
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Residues in contact with ALA 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 3.6 32.8 - - - +
301H PRO* 3.6 10.2 - - + +
455H ILE* 5.8 3.8 - - + -
513H ASP 3.1 14.7 + - - +
514H VAL* 3.5 10.8 - - - +
516H GLY* 1.3 75.3 - - - +
518H PHE* 1.3 65.6 + - + +
520H VAL* 3.0 6.1 + - - +
521H LEU* 2.9 30.2 + - + +
532H TYR* 5.8 5.4 - - + +
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Residues in contact with PHE 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H HIS* 4.5 3.6 - + - -
514H VAL* 3.2 39.9 + - + -
515H ILE* 3.2 3.2 + - + +
517H ALA* 1.3 78.8 - - + +
519H HIS* 1.3 58.9 + - - +
521H LEU* 3.3 13.7 + - + +
522H ALA* 2.9 23.2 + - - +
532H TYR* 3.4 39.3 - + - -
546H VAL* 4.4 8.5 - - + -
549H LEU* 3.8 27.1 - - + -
550H GLN* 3.7 31.2 - - + -
553H CYS* 3.5 36.6 - - + -
555H VAL* 3.4 13.1 - - + +
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Residues in contact with HIS 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501H LEU* 5.3 5.0 - - + +
515H ILE* 3.1 33.3 + - + +
516H GLY* 3.5 11.2 - - - +
517H ALA 3.1 0.2 - - - -
518H PHE* 1.3 77.2 - - - +
520H VAL* 1.3 62.7 + - + +
522H ALA* 3.2 7.2 + - - +
523H GLU* 3.2 37.4 + - - +
552H GLU 5.3 0.2 - - - -
553H CYS* 3.1 39.7 + - + +
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Residues in contact with VAL 520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H PRO* 3.6 38.4 - - + +
302H GLU* 5.3 0.4 - - - -
304H THR* 4.5 10.5 - - + -
305H ARG* 4.1 18.8 - - + +
516H GLY 3.0 15.0 + - - +
517H ALA* 3.0 10.5 + - - +
519H HIS* 1.3 72.2 - - + +
521H LEU* 1.3 68.1 + - + +
523H GLU* 3.0 23.7 + - - +
524H LEU* 3.3 35.2 + - + +
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Residues in contact with LEU 521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 6.2 0.2 - - - +
304H THR* 5.0 6.1 - - + -
455H ILE* 4.1 17.3 - - + -
517H ALA* 2.9 19.7 + - + +
518H PHE* 3.4 22.9 - - + +
520H VAL* 1.3 77.6 - - + +
522H ALA* 1.3 60.9 + - - +
523H GLU 3.3 0.5 + - - -
524H LEU 3.5 13.5 + - - +
529H PHE* 3.6 48.2 - - + -
532H TYR* 4.1 28.3 - - + -
550H GLN* 5.0 3.1 - - - +
555H VAL* 4.3 11.7 - - + +
559H LEU* 4.2 22.1 - - + +
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Residues in contact with ALA 522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518H PHE 2.9 13.2 + - - +
519H HIS* 3.5 10.3 - - - +
520H VAL 3.2 0.6 - - - -
521H LEU* 1.3 76.9 - - - +
523H GLU* 1.3 62.8 + - + +
524H LEU 3.7 2.8 + - - +
553H CYS 4.2 6.1 - - - +
554H GLY 3.2 34.0 - - - +
555H VAL* 3.7 10.7 - - + +
556H ARG 5.5 0.7 + - - +
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Residues in contact with GLU 523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305H ARG* 5.1 9.0 - - - -
519H HIS* 3.2 27.7 + - - +
520H VAL* 3.0 17.8 + - - +
522H ALA* 1.3 79.4 - - + +
524H LEU* 1.3 62.8 + - + +
525H PRO* 4.8 0.5 - - - +
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Residues in contact with LEU 524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H THR 5.0 0.2 - - - -
305H ARG* 4.1 28.3 - - + -
308H CYS* 4.3 19.3 - - + -
309H LEU* 4.9 16.6 - - + -
312H ARG* 5.9 1.1 - - - +
520H VAL* 3.3 33.8 + - + +
521H LEU 3.5 9.1 + - - +
522H ALA 3.4 3.9 - - - +
523H GLU* 1.3 83.5 - - + +
525H PRO* 1.3 81.0 - - + +
526H PRO* 3.5 5.5 - - - +
528H SER* 4.6 1.3 - - - +
529H PHE* 3.7 29.5 - - + -
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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) + - + + + + + -
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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