Contacts of the helix formed by residues 509 - 524 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E ASN* 2.9 31.0 + - - -
508E GLU* 1.3 74.4 - - - +
510E LYS* 1.3 62.8 + - - +
511E LEU 3.3 2.6 + - - -
512E GLU* 3.7 6.5 + - - +
513E THR* 3.2 27.4 + - - +
602E GOL 5.0 5.5 + - - -
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Residues in contact with LYS 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E MET* 4.2 14.6 - - + +
463E ASN* 2.7 43.8 + - - +
467E TYR* 4.1 18.5 + - - +
504E ASN* 4.0 0.2 + - - -
507E SER* 3.1 30.3 + - - +
508E GLU* 4.5 16.7 + - - +
509E GLY* 1.3 77.2 - - - +
511E LEU* 1.3 61.3 + - - +
513E THR* 3.0 20.3 + - - -
514E TYR* 3.5 11.6 + - - +
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Residues in contact with LEU 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E ILE* 4.7 0.9 - - + -
462E MET* 3.9 23.9 - - + -
470E VAL* 3.9 27.4 - - + -
474E LEU* 4.8 9.2 - - + -
500E ILE* 3.9 34.8 - - + +
503E VAL* 3.9 21.5 - - + -
504E ASN* 3.6 19.5 + - + +
507E SER* 4.0 2.4 + - - -
509E GLY 3.3 0.2 - - - -
510E LYS* 1.3 77.8 - - - +
512E GLU* 1.3 60.1 + - - +
514E TYR* 3.2 7.1 + - + +
515E LEU* 3.0 51.4 + - + +
538E LEU* 5.6 0.9 - - + -
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Residues in contact with GLU 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E THR 5.0 0.2 - - - +
356E SER* 3.8 7.4 - - - -
357E SER* 3.1 44.3 + - - -
358E VAL* 5.5 2.1 - - - +
504E ASN* 3.2 20.0 + - - +
509E GLY* 3.7 8.0 + - - +
510E LYS 3.5 0.4 - - - -
511E LEU* 1.3 80.1 - - - +
513E THR* 1.3 57.5 + - + +
515E LEU* 4.0 9.7 - - - +
516E ASN* 3.0 51.1 + - - +
535E LEU* 4.3 6.1 - - + -
538E LEU* 4.0 14.1 - - + -
539E TRP* 3.4 20.3 + - - -
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Residues in contact with THR 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E TYR* 5.3 2.4 + - - -
509E GLY 3.2 15.9 - - - +
510E LYS* 3.0 17.1 + - - -
512E GLU* 1.3 75.0 - - + +
514E TYR* 1.3 65.3 + - - +
516E ASN* 3.9 6.4 - - - +
517E LYS* 2.9 30.5 + - - +
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Residues in contact with TYR 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E TYR* 3.4 57.9 + + + -
468E SER* 5.5 0.2 - - - -
470E VAL* 4.2 18.3 - - + +
471E GLN 5.8 0.2 + - - -
510E LYS 3.5 9.6 + - - +
511E LEU* 3.2 11.5 + - + +
513E THR* 1.3 82.8 + - - +
515E LEU* 1.3 57.7 + - + +
517E LYS* 3.2 19.0 + - + +
518E VAL* 2.8 57.2 + - + +
530E TRP* 3.6 36.0 - + - -
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Residues in contact with LEU 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474E LEU* 5.1 0.2 - - + -
511E LEU* 3.0 43.5 + - + +
512E GLU* 4.0 2.0 - - - +
514E TYR* 1.3 80.7 - - + +
516E ASN* 1.3 53.0 + - - +
518E VAL* 3.1 3.3 + - - +
519E GLU* 2.7 36.9 + - - +
530E TRP* 3.5 37.7 - - + -
531E ALA* 3.8 10.5 - - + +
534E ILE* 3.6 29.4 - - + +
535E LEU* 3.6 36.1 - - + +
538E LEU* 5.1 5.4 - - + -
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Residues in contact with ASN 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E ARG* 5.9 0.2 + - - -
355E THR 5.2 6.5 + - - -
512E GLU* 3.0 45.6 + - - +
513E THR* 3.9 6.5 - - - +
515E LEU* 1.3 77.0 - - - +
517E LYS* 1.3 57.4 + - - +
519E GLU* 3.9 6.5 - - - +
520E ALA* 3.1 29.8 + - - +
535E LEU* 3.3 26.8 - - - +
539E TRP* 5.2 2.7 + - - +
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Residues in contact with LYS 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513E THR 2.9 19.3 + - - +
514E TYR* 3.4 19.3 - - + +
516E ASN* 1.3 75.1 - - - +
518E VAL* 1.3 65.2 + - + +
520E ALA* 3.3 6.1 + - - +
521E GLU* 3.1 52.8 + - + +
45H GLN* 4.4 17.8 - - - +
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Residues in contact with VAL 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514E TYR* 2.8 59.6 + - + +
515E LEU* 3.5 4.5 - - - +
517E LYS* 1.3 73.7 - - + +
519E GLU* 1.3 61.3 + - - +
521E GLU* 3.2 24.7 + - - +
522E ALA* 3.3 12.7 + - + +
529E SER* 3.2 22.7 - - - +
530E TRP* 4.0 15.3 - - + +
531E ALA* 3.8 11.0 - - + -
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Residues in contact with GLU 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E ARG* 2.5 38.4 + - - -
515E LEU 2.7 20.4 + - - +
516E ASN* 4.1 7.4 - - - +
518E VAL* 1.3 75.1 - - - +
520E ALA* 1.3 59.2 + - - +
522E ALA* 3.6 3.3 + - + +
523E LYS* 3.5 33.3 + - + +
529E SER* 4.5 9.0 - - - -
531E ALA* 4.3 5.2 - - + -
532E THR* 3.9 27.4 + - - +
535E LEU* 3.9 12.8 - - + +
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Residues in contact with ALA 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E ASN 3.1 20.1 + - - +
517E LYS* 3.7 6.7 - - - +
518E VAL 3.1 0.4 - - - -
519E GLU* 1.3 76.6 - - - +
521E GLU* 1.3 63.8 + - + +
522E ALA 3.2 1.1 + - - -
523E LYS* 3.8 9.5 + - - +
524E ALA* 3.8 17.5 + - - +
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Residues in contact with GLU 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517E LYS* 3.1 42.8 + - + +
518E VAL* 3.2 14.5 + - - +
520E ALA* 1.3 77.5 - - + +
522E ALA* 1.3 62.1 + - - +
524E ALA* 3.9 6.8 + - - +
525E ALA* 3.5 20.3 + - - +
527E GLU* 5.1 0.8 - - - +
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Residues in contact with ALA 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E VAL 3.3 8.7 + - - +
519E GLU* 3.9 5.6 - - + +
520E ALA 3.2 0.6 - - - -
521E GLU* 1.3 78.4 - - - +
523E LYS* 1.3 63.0 + - + +
524E ALA 3.3 0.4 - - - -
525E ALA 3.4 0.6 + - - -
526E ALA 3.2 3.6 + - - -
527E GLU* 2.9 63.6 + - + +
528E PRO 4.4 0.2 - - - +
529E SER* 3.8 26.7 - - - -
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Residues in contact with LYS 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E SER 6.0 2.5 - - - -
344E GLU 5.8 8.8 - - - -
519E GLU* 3.5 25.9 + - + +
520E ALA* 3.8 10.5 + - - +
522E ALA* 1.3 76.9 - - + +
524E ALA* 1.3 61.1 + - - +
525E ALA 3.1 1.6 - - - -
526E ALA* 3.3 12.6 + - - +
527E GLU 4.9 0.4 - - - -
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Residues in contact with ALA 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E ALA 3.8 13.6 + - - +
521E GLU* 3.9 6.7 + - - +
522E ALA 3.3 0.2 - - - -
523E LYS* 1.3 78.0 - - - +
525E ALA* 1.3 58.6 + - - +
526E ALA 3.4 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