Contacts of the helix formed by residues 509 - 526 (chain B) in PDB entry 6E7P
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 509 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B PHE* 4.0 12.8 - - + -
432B VAL* 3.8 36.8 - - + -
435B ILE* 6.3 2.5 - - + -
504B LEU* 3.5 12.8 + - + +
505B PHE* 3.5 39.5 - - + +
508B MET* 1.3 83.5 - - + +
510B LEU* 1.3 67.3 + - - +
511B SER 3.2 1.3 - - - -
512B LEU* 3.2 17.0 + - - +
513B PHE* 3.7 15.3 + - + -
418C LEU* 6.0 2.2 - - + -
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE* 4.4 13.2 - - + +
507A TYR* 3.7 33.9 - - + -
510A LEU* 6.4 1.6 - - + -
468B ILE 5.9 1.3 - - - +
505B PHE 2.8 17.2 + - - +
506B ILE* 3.4 34.1 + - + +
509B VAL* 1.3 74.8 - - - +
511B SER* 1.3 60.8 + - - +
513B PHE* 3.3 16.2 + - + +
514B ILE* 3.4 27.3 + - + +
510C LEU* 6.4 1.6 - - + -
514C ILE* 6.3 1.3 - - + -
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Residues in contact with SER 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ILE 4.0 6.6 + - - -
507B TYR 3.6 13.5 + - - -
508B MET 4.7 3.4 - - - -
509B VAL 3.2 1.4 - - - +
510B LEU* 1.3 77.4 - - - +
512B LEU* 1.3 59.2 + - - +
514B ILE* 3.5 9.6 + - - +
515B ALA* 3.0 27.2 + - - +
513C PHE* 3.0 30.9 + - - +
514C ILE* 3.9 13.8 - - - +
517C ILE* 3.7 20.7 - - - +
518C THR* 5.0 1.0 + - - -
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B PHE* 3.7 29.6 - - + -
508B MET 3.3 25.6 - - - +
509B VAL 3.2 10.5 + - - +
511B SER* 1.3 79.8 - - - +
513B PHE* 1.3 54.3 + - - +
515B ALA* 2.8 8.2 + - + -
516B LEU* 2.7 51.7 + - + +
414C LEU* 4.6 14.6 - - + +
417C THR* 4.6 16.8 - - + -
418C LEU* 3.7 20.2 - - + -
517C ILE* 3.7 22.7 - - + -
521C TYR* 4.9 3.4 - - + -
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Residues in contact with PHE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE 5.8 0.2 - - - +
507A TYR* 3.6 59.7 - + + +
511A SER* 3.0 16.9 + - - +
425B VAL* 3.9 37.9 - - + -
428B PHE* 3.4 33.0 - + + -
429B CYS* 4.8 15.9 - - + -
432B VAL* 5.1 4.7 - - + -
509B VAL* 3.7 19.0 + - + -
510B LEU* 3.3 12.9 + - + +
512B LEU* 1.3 76.8 - - - +
514B ILE* 1.3 57.7 + - + +
516B LEU* 4.3 5.6 - - + -
517B ILE* 3.3 21.5 + - - +
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LEU* 6.3 1.3 - - + -
511A SER* 3.9 15.7 - - - +
514A ILE* 3.8 49.4 - - + -
510B LEU* 3.4 29.4 + - + +
511B SER 3.9 6.5 - - - +
512B LEU 3.1 0.6 - - - -
513B PHE* 1.3 80.2 - - + +
515B ALA* 1.3 59.5 + - - +
516B LEU 3.5 0.2 - - - -
517B ILE* 3.7 2.3 + - - +
518B THR* 3.0 32.5 + - - +
514C ILE* 3.8 41.3 - - + -
518C THR* 5.4 1.8 - - - +
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Residues in contact with ALA 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER 3.0 17.4 + - - +
512B LEU* 2.8 12.1 + - + +
514B ILE* 1.3 77.0 - - - +
516B LEU* 1.3 60.3 + - - +
518B THR* 3.8 3.3 - - - -
519B GLY* 2.8 26.3 + - - -
517C ILE* 4.6 7.0 - - + +
518C THR* 3.7 35.8 + - + +
521C TYR* 4.3 15.7 - - + -
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ALA* 5.0 1.4 - - + +
424B SER* 3.7 40.4 - - - +
425B VAL* 4.5 13.9 - - + +
428B PHE* 4.6 9.4 - - + -
512B LEU* 2.7 30.8 + - + +
513B PHE* 4.8 7.9 - - + +
515B ALA* 1.3 73.2 - - - +
517B ILE* 1.3 62.6 + - + +
519B GLY* 3.3 2.5 + - - +
520B ALA* 2.8 29.6 + - - +
414C LEU* 3.9 20.9 - - + -
521C TYR* 3.5 39.0 + - + +
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Residues in contact with ILE 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR 4.6 3.8 - - - +
508A MET* 4.8 13.2 - - + +
511A SER* 3.7 27.4 - - - +
512A LEU* 3.7 35.7 - - + -
515A ALA* 4.5 2.2 - - + -
417B THR* 4.7 7.0 - - + +
418B LEU* 5.3 4.3 - - + -
421B ALA* 3.7 25.1 - - + -
425B VAL* 4.3 17.9 - - + -
513B PHE 3.3 18.1 + - - +
514B ILE 3.7 1.9 + - - +
515B ALA 3.3 0.4 - - - -
516B LEU* 1.3 74.5 - - + +
518B THR* 1.3 61.5 + - - +
520B ALA* 3.2 3.6 + - - +
521B TYR* 2.8 28.6 + - - +
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Residues in contact with THR 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER 5.0 0.2 + - - -
514A ILE* 5.1 1.7 - - - +
515A ALA* 3.7 26.5 + - + +
518A THR* 4.8 18.7 - - + -
514B ILE* 3.0 23.3 + - - +
515B ALA* 3.9 5.2 - - - -
517B ILE* 1.3 78.3 - - - +
519B GLY* 1.3 61.5 + - - +
521B TYR* 3.2 12.1 + - + +
522B ASP* 3.3 24.4 + - - +
518C THR* 4.9 17.0 - - + -
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Residues in contact with GLY 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ALA 2.8 18.7 + - - -
516B LEU 3.5 3.1 - - - -
518B THR* 1.3 77.5 - - - +
520B ALA* 1.3 56.8 + - - +
522B ASP* 4.2 7.4 + - - +
523B THR* 3.5 22.0 + - - +
521C TYR* 4.5 18.5 - - - -
522C ASP* 5.9 2.0 - - - -
525C LYS* 5.4 5.4 + - - -
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B THR* 4.5 6.1 - - + +
420B VAL* 4.3 15.5 - - + +
421B ALA* 3.9 25.8 - - + -
516B LEU 2.8 18.2 + - - +
517B ILE* 3.8 3.8 - - - +
518B THR 3.2 0.2 - - - -
519B GLY* 1.3 74.8 - - - +
521B TYR* 1.3 62.9 + - - +
522B ASP 3.2 2.2 - - - -
523B THR* 2.6 25.1 + - - -
524B ILE* 3.4 10.0 + - - +
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A SER* 5.6 1.7 + - - -
512A LEU* 4.9 5.4 - - + -
515A ALA* 4.3 18.6 - - + -
516A LEU* 3.4 33.3 + - + +
519A GLY* 4.4 20.4 - - - -
413B ILE* 4.8 12.6 - - + +
414B LEU* 4.5 9.3 - - + +
417B THR* 4.0 26.2 - - + +
517B ILE* 2.8 17.5 + - + +
518B THR* 3.2 7.6 + - - +
520B ALA* 1.3 74.9 - - - +
522B ASP* 1.3 69.7 + - - +
524B ILE* 3.4 17.7 - - + +
525B LYS* 3.5 39.9 - - + +
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Residues in contact with ASP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A GLY* 5.9 2.9 - - - -
522A ASP* 5.8 0.3 - - - +
518B THR* 3.3 23.5 + - - +
519B GLY* 4.4 7.7 - - - +
520B ALA 3.2 0.6 - - - -
521B TYR* 1.3 87.1 - - - +
523B THR* 1.3 62.6 + - + +
525B LYS* 4.6 5.7 - - - +
526B HIS* 3.3 33.1 + - + +
522C ASP* 5.8 0.2 - - - +
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B VAL* 4.7 6.9 - - - +
519B GLY 3.5 17.7 - - - +
520B ALA* 2.6 24.4 + - - +
522B ASP* 1.3 80.0 - - + +
524B ILE* 1.3 63.6 + - - +
525B LYS 3.5 0.2 + - - -
526B HIS 3.6 17.2 + - - +
525C LYS* 5.2 10.8 - - - +
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Residues in contact with ILE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ILE* 3.3 43.8 - - + +
416B ALA* 3.5 20.6 - - + +
417B THR* 3.4 31.2 - - - +
420B VAL* 5.1 7.9 - - + -
520B ALA 3.9 9.4 - - - +
521B TYR* 3.4 20.9 - - + +
523B THR* 1.3 81.9 + - - +
525B LYS* 1.3 63.6 + - + +
526B HIS 3.5 1.1 - - - +
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLY* 5.3 5.2 + - - -
523A THR* 5.1 12.7 - - - +
413B ILE* 5.3 8.7 - - + -
521B TYR* 3.5 49.1 - - + +
522B ASP* 4.2 4.0 - - - +
523B THR 3.3 0.2 - - - -
524B ILE* 1.3 81.7 - - + +
526B HIS* 1.3 105.4 + - + +
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Residues in contact with HIS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ASP* 3.3 23.8 + - + +
523B THR* 3.7 14.8 - - - +
524B ILE 3.5 1.3 - - - +
525B LYS* 1.3 128.7 + - + +
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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
------------------------------------------------------------
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