Contacts of the helix formed by residues 509 - 524 (chain A) in PDB entry 4KYI
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 GLY 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A ASN* 3.0 26.5 + - - -
508A GLU* 1.3 76.4 - - - +
510A LYS* 1.3 63.6 + - - +
511A LEU 3.1 4.6 + - - -
512A GLU* 3.3 13.2 + - - +
513A THR* 3.3 23.5 + - - +
603A GOL 5.1 4.6 + - - -
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Residues in contact with LYS 510 (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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462A MET* 4.2 13.9 - - + +
463A ASN* 3.2 49.2 - - - +
467A TYR* 3.8 19.9 + - - +
507A SER* 3.2 26.4 + - - +
508A GLU* 3.4 14.3 + - - +
509A GLY* 1.3 77.0 - - - +
511A LEU* 1.3 58.6 + - - +
513A THR* 3.2 19.5 + - - -
514A TYR* 3.5 13.3 - - - +
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Residues in contact with LEU 511 (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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458A ILE* 5.1 1.3 - - + -
462A MET* 4.0 17.7 - - + -
470A VAL* 4.0 26.2 - - + -
474A LEU* 4.9 11.9 - - + -
500A ILE* 4.0 32.3 - - + +
503A VAL* 3.9 22.7 - - + -
504A ASN* 4.1 11.2 - - + +
507A SER* 3.6 12.9 + - - +
509A GLY 3.1 0.8 - - - -
510A LYS* 1.3 78.1 - - - +
512A GLU* 1.3 60.0 + - - +
514A TYR* 3.3 5.4 + - + +
515A LEU* 2.8 53.4 + - + +
538A LEU* 5.9 0.4 - - + -
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Residues in contact with GLU 512 (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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355A THR 4.6 0.3 - - - +
356A SER* 3.5 14.2 - - - -
357A SER* 2.6 50.8 + - - +
358A VAL* 5.0 3.5 - - - +
504A ASN* 3.7 22.4 + - - +
509A GLY* 3.3 7.4 + - - +
511A LEU* 1.3 78.4 - - - +
513A THR* 1.3 61.1 + - + +
515A LEU* 3.2 11.0 + - - +
516A ASN* 2.9 48.5 + - - +
535A LEU* 4.2 6.3 - - + -
538A LEU* 4.0 11.2 - - + -
539A TRP* 3.5 10.6 + - - -
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Residues in contact with THR 513 (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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467A TYR* 5.5 0.9 + - - -
509A GLY* 3.3 15.6 + - - +
510A LYS* 3.2 14.8 + - - -
512A GLU* 1.3 77.4 - - + +
514A TYR* 1.3 72.6 + - - +
516A ASN* 3.1 19.0 + - - +
517A LYS* 3.1 22.0 + - - +
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Residues in contact with TYR 514 (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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467A TYR* 3.2 58.2 + + + -
470A VAL* 4.2 18.0 - - + +
471A GLN* 5.5 0.9 + - - +
510A LYS 3.5 15.5 + - - +
511A LEU* 3.3 10.4 + - + +
513A THR* 1.3 82.5 + - - +
515A LEU* 1.3 65.2 + - + +
517A LYS* 3.4 12.3 + - + +
518A VAL* 3.3 43.7 + - + +
530A TRP* 3.6 37.1 + + - -
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Residues in contact with LEU 515 (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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500A ILE* 5.0 2.7 - - + -
511A LEU* 2.8 43.5 + - + +
512A GLU* 3.2 7.2 + - - +
514A TYR* 1.3 78.5 - - + +
516A ASN* 1.3 61.2 + - - +
518A VAL* 4.9 0.7 - - - -
519A GLU* 3.4 15.6 + - - +
530A TRP* 3.6 37.9 - - + -
531A ALA* 3.5 23.4 - - + +
534A ILE* 3.6 27.8 - - + +
535A LEU* 3.3 38.8 - - + +
538A LEU* 5.0 2.7 - - + -
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Residues in contact with ASN 516 (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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355A THR 5.5 4.2 + - - -
356A SER* 6.0 1.0 - - - +
512A GLU* 2.9 41.2 + - - +
513A THR* 3.1 10.5 + - - +
515A LEU* 1.3 76.7 - - - +
517A LYS* 1.3 62.8 + - + +
519A GLU* 4.3 4.6 - - - +
520A ALA* 3.3 23.7 + - - +
535A LEU* 3.3 24.0 - - - +
539A TRP* 5.5 1.4 + - - +
601A EDO 5.0 7.9 + - - -
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Residues in contact with LYS 517 (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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513A THR* 3.1 15.8 + - - +
514A TYR* 3.8 13.7 - - + +
515A LEU 3.3 0.2 - - - -
516A ASN* 1.3 77.8 - - + +
518A VAL* 1.3 55.6 + - + +
520A ALA* 3.0 4.9 + - - +
521A GLU* 2.7 61.7 + - + +
45D GLN* 5.5 6.9 - - - +
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Residues in contact with VAL 518 (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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514A TYR* 3.3 51.0 + - + +
517A LYS* 1.3 76.4 - - + +
519A GLU* 1.3 60.8 + - - +
521A GLU* 3.4 12.4 + - - +
522A ALA* 3.1 22.8 + - + +
529A SER* 3.5 12.3 - - - +
530A TRP* 3.4 28.3 - - + +
531A ALA* 4.2 9.2 - - + -
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Residues in contact with GLU 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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338A ARG* 2.6 38.5 + - - -
342A LEU* 4.1 11.2 - - - +
515A LEU 3.4 15.3 + - - +
516A ASN* 4.3 5.4 - - - +
517A LYS 3.2 0.8 - - - -
518A VAL* 1.3 79.3 - - - +
520A ALA* 1.3 59.1 + - - +
522A ALA* 3.3 3.9 + - - +
523A LYS* 3.1 27.0 + - + +
529A SER* 4.3 9.4 - - - -
531A ALA* 4.2 7.6 - - + -
532A THR* 3.7 26.0 + - - +
535A LEU* 3.5 8.6 - - - +
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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
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516A ASN 3.3 18.8 + - - +
517A LYS* 3.0 5.9 + - - +
519A GLU* 1.3 74.5 - - - +
521A GLU* 1.3 59.3 + - + +
522A ALA 3.1 4.7 - - - -
523A LYS* 3.5 11.2 + - - +
524A ALA* 3.3 27.4 + - - +
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Residues in contact with GLU 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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517A LYS* 2.7 48.7 + - - +
518A VAL* 3.7 10.7 - - - +
519A GLU 3.3 0.4 - - - -
520A ALA* 1.3 74.1 - - + +
522A ALA* 1.3 56.9 + - - +
523A LYS 3.6 0.2 - - - -
524A ALA* 4.2 8.4 - - - +
525A ALA* 3.9 13.7 + - - +
527A GLU* 4.6 2.6 - - - +
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Residues in contact with ALA 522 (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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518A VAL* 3.1 16.4 + - + +
519A GLU 3.7 5.6 - - - +
520A ALA 3.1 0.4 - - - -
521A GLU* 1.3 79.1 - - - +
523A LYS* 1.3 59.8 + - - +
524A ALA 3.3 1.1 - - - -
525A ALA 3.8 1.6 - - - -
526A ALA 3.3 4.0 + - - -
527A GLU* 2.8 60.7 + - + +
528A PRO 4.7 0.4 - - - +
529A SER* 3.7 19.5 - - - +
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Residues in contact with LYS 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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519A GLU* 3.1 15.1 + - + +
520A ALA* 3.5 10.5 + - - +
522A ALA* 1.3 73.6 - - - +
524A ALA* 1.3 58.8 + - - +
525A ALA 3.0 9.0 + - - -
526A ALA* 3.3 13.3 + - - +
527A GLU 4.9 0.4 - - - -
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Residues in contact with ALA 524 (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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520A ALA 3.3 17.8 + - - +
521A GLU* 4.6 7.6 - - - -
522A ALA 3.3 0.2 - - - -
523A LYS* 1.3 75.4 - - - +
525A ALA* 1.3 57.7 + - - +
526A ALA 3.7 0.2 - - - -
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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