Contacts of the helix formed by residues 509 - 526 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A PHE* 4.0 14.0 - - + -
432A VAL* 3.8 36.3 - - + -
435A ILE* 6.3 2.2 - - + -
504A LEU* 3.5 12.8 + - + +
505A PHE* 3.5 39.9 - - + +
508A MET* 1.3 82.9 - - + +
510A LEU* 1.3 66.2 + - - +
511A SER 3.2 1.1 - - - -
512A LEU* 3.2 17.0 + - - +
513A PHE* 3.7 15.2 + - + -
418B LEU* 6.0 1.8 - - + -
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE 5.9 1.6 - - - +
505A PHE 2.8 17.2 + - - +
506A ILE* 3.4 33.6 + - + +
509A VAL* 1.3 73.9 - - - +
511A SER* 1.3 62.8 + - - +
513A PHE* 3.3 16.8 + - + +
514A ILE* 3.4 26.9 + - + +
510B LEU* 6.4 1.6 - - + -
514B ILE* 6.3 1.6 - - + -
506D ILE* 4.4 12.3 - - + +
507D TYR* 3.7 33.7 - - + -
510D LEU* 6.4 1.1 - - + -
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE 4.0 7.2 + - - -
507A TYR 3.6 12.8 + - - -
508A MET 4.7 3.1 - - - -
509A VAL 3.2 1.4 - - - +
510A LEU* 1.3 76.1 - - - +
512A LEU* 1.3 59.5 + - - +
514A ILE* 3.5 9.9 + - - +
515A ALA* 3.0 27.0 + - - +
513B PHE* 3.0 31.8 + - - +
514B ILE* 3.9 13.6 - - - +
517B ILE* 3.7 21.1 - - - +
518B THR* 5.0 1.2 + - - -
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Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PHE* 3.7 29.6 - - + -
508A MET 3.3 24.5 - - - +
509A VAL 3.2 10.5 + - - +
511A SER* 1.3 78.2 - - - +
513A PHE* 1.3 54.6 + - - +
515A ALA* 2.8 8.1 + - + -
516A LEU* 2.7 51.6 + - + +
414B LEU* 4.6 14.4 - - + +
417B THR* 4.6 17.0 - - + -
418B LEU* 3.7 20.4 - - + -
517B ILE* 3.7 24.7 - - + -
521B TYR* 4.9 3.1 - - + -
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Residues in contact with PHE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 3.9 38.1 - - + -
428A PHE* 3.4 34.1 - + + -
429A CYS* 4.8 15.5 - - + -
432A VAL* 5.1 4.5 - - + -
509A VAL* 3.7 18.6 + - + -
510A LEU* 3.3 13.8 + - + +
512A LEU* 1.3 76.0 - - - +
514A ILE* 1.3 57.5 + - + +
516A LEU* 4.7 5.8 - - + +
517A ILE* 3.3 21.5 + - - +
507D TYR* 3.6 59.5 - + + +
511D SER* 3.0 16.5 + - - +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LEU* 3.4 29.2 + - + +
511A SER 3.9 6.5 - - - +
512A LEU 3.1 0.6 - - - -
513A PHE* 1.3 79.1 - - + +
515A ALA* 1.3 61.4 + - - +
517A ILE* 3.7 2.1 + - - +
518A THR* 3.0 32.1 + - - +
514B ILE* 3.8 44.4 - - + -
518B THR* 5.4 1.8 - - - +
510D LEU* 6.3 1.6 - - + -
511D SER* 3.9 15.7 - - - +
514D ILE* 3.8 45.1 - - + -
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Residues in contact with ALA 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER 3.0 17.0 + - - +
512A LEU* 2.8 11.5 + - + +
514A ILE* 1.3 77.2 - - - +
516A LEU* 1.3 61.5 + - - +
518A THR* 3.8 3.3 - - - -
519A GLY* 2.8 25.6 + - - -
517B ILE* 4.5 6.7 - - + +
518B THR* 3.7 36.5 + - + +
521B TYR* 4.3 16.3 - - + -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ALA* 5.0 2.3 - - + +
424A SER* 3.7 39.7 - - - +
425A VAL* 4.5 14.8 - - + +
428A PHE* 4.6 9.6 - - + -
512A LEU* 2.7 31.2 + - + +
513A PHE* 4.8 7.4 - - + +
515A ALA* 1.3 72.2 - - - +
517A ILE* 1.3 62.4 + - + +
519A GLY* 3.3 1.9 + - - -
520A ALA* 2.8 29.1 + - - +
414B LEU* 3.9 20.6 - - + -
521B TYR* 3.4 39.7 - - + +
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Residues in contact with ILE 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A THR* 4.7 7.7 - - + +
418A LEU* 5.3 4.0 - - + -
421A ALA* 3.7 25.8 - - + -
425A VAL* 4.3 17.9 - - + -
513A PHE 3.3 18.6 + - - +
514A ILE 3.7 2.1 + - - +
515A ALA 3.3 0.2 - - - -
516A LEU* 1.3 74.1 - - + +
518A THR* 1.3 60.6 + - - +
520A ALA* 3.2 3.4 + - - +
521A TYR* 2.8 29.0 + - - +
507D TYR 4.6 3.6 - - - +
508D MET* 4.9 13.0 - - + -
511D SER* 3.7 27.8 - - - +
512D LEU* 3.7 34.5 - - + -
515D ALA* 4.5 2.7 - - + -
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Residues in contact with THR 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.0 23.8 + - - +
515A ALA* 3.9 5.4 - - - -
517A ILE* 1.3 79.0 - - - +
519A GLY* 1.3 60.8 + - - +
521A TYR* 3.2 12.1 + - + +
522A ASP* 3.3 24.0 + - - +
518B THR* 4.8 17.0 - - + -
511D SER 5.1 0.2 + - - -
514D ILE* 5.1 1.4 - - - +
515D ALA* 3.8 25.1 + - + +
518D THR* 4.8 19.9 - - + -
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Residues in contact with GLY 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ALA 2.8 19.7 + - - -
516A LEU 3.5 2.2 - - - -
517A ILE 3.3 0.2 - - - -
518A THR* 1.3 76.9 - - - +
520A ALA* 1.3 57.2 + - - +
522A ASP* 4.2 7.0 + - - +
523A THR* 3.5 21.7 + - - +
521B TYR* 4.4 18.4 - - - -
522B ASP* 5.9 2.7 - - - -
525B LYS* 5.3 5.2 + - - -
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A THR* 4.5 6.4 - - + +
420A VAL* 4.3 15.8 - - + +
421A ALA* 3.9 26.0 - - + -
516A LEU 2.8 16.6 + - - +
517A ILE* 3.8 3.8 - - - +
519A GLY* 1.3 74.1 - - - +
521A TYR* 1.3 63.8 + - - +
522A ASP 3.2 2.5 - - - -
523A THR* 2.6 25.2 + - - +
524A ILE* 3.4 9.4 + - - +
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Residues in contact with TYR 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ILE* 4.8 13.4 - - + +
414A LEU* 4.5 9.3 - - + +
417A THR* 4.0 26.2 - - + -
517A ILE 2.8 17.0 + - - +
518A THR* 3.2 7.6 + - + +
520A ALA* 1.3 74.9 - - - +
522A ASP* 1.3 69.8 + - - +
524A ILE* 3.4 17.5 - - + +
525A LYS* 3.5 38.8 - - + +
424D SER* 5.6 1.6 + - - -
512D LEU* 4.9 6.1 - - + -
515D ALA* 4.2 19.3 - - + -
516D LEU* 3.4 33.7 + - + +
519D GLY* 4.3 20.9 - - - -
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Residues in contact with ASP 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 3.3 23.0 + - - +
519A GLY* 4.4 7.6 - - - +
520A ALA 3.2 0.4 - - - -
521A TYR* 1.3 88.7 - - - +
523A THR* 1.3 63.5 + - + +
525A LYS* 4.6 5.9 - - - +
526A HIS* 3.3 35.4 + - + +
522B ASP* 5.8 0.2 - - - +
519D GLY* 5.8 2.4 - - - -
522D ASP* 5.7 1.0 - - - +
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Residues in contact with THR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A VAL* 4.7 6.6 - - - +
519A GLY 3.5 18.2 - - - +
520A ALA* 2.6 24.7 + - - +
522A ASP* 1.3 78.7 - - + +
524A ILE* 1.3 62.8 + - - +
525A LYS 3.5 0.3 + - - -
526A HIS 3.6 16.8 + - - +
525B LYS* 5.1 11.2 - - - +
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Residues in contact with ILE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 3.3 44.6 - - + +
416A ALA* 3.5 20.0 - - + +
417A THR* 3.4 31.9 - - - +
420A VAL* 5.1 7.9 - - + -
520A ALA 3.9 9.9 - - - +
521A TYR* 3.4 20.2 - - + +
523A THR* 1.3 82.3 + - - +
525A LYS* 1.3 64.4 + - + +
526A HIS 3.8 1.0 + - - +
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 5.3 8.3 - - + -
521A TYR* 3.5 49.4 - - + +
522A ASP* 4.2 4.5 - - - +
523A THR 3.3 0.2 - - - -
524A ILE* 1.3 83.5 - - + +
526A HIS* 1.3 105.9 + - + +
519D GLY* 5.2 6.1 + - - +
523D THR* 5.1 12.7 - - - +
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Residues in contact with HIS 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASP* 3.3 23.0 + - + +
523A THR* 3.7 15.0 - - - +
524A ILE 3.5 1.6 - - - +
525A LYS* 1.3 127.7 + - + +
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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