Contacts of the helix formed by residues 469 - 484 (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 SER 469 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461E GLU* 2.4 32.0 + - - -
467E TYR 3.1 0.6 - - - -
468E SER* 1.3 80.0 + - - +
470E VAL* 1.3 60.9 - - - +
471E GLN 3.5 1.8 - - - -
472E ASN* 3.7 17.0 - - - +
473E TYR* 3.0 44.0 + - - -
21F GLN* 3.5 27.4 + - - -
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Residues in contact with VAL 470 (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* 4.1 24.7 - - + +
461E GLU* 6.5 0.4 - - + -
462E MET* 4.3 6.7 - - + -
466E ASP 4.8 0.9 - - - +
467E TYR* 3.4 44.5 + - + +
468E SER 3.7 0.2 - - - -
469E SER* 1.3 74.8 - - - +
471E GLN* 1.3 63.0 + - - +
472E ASN 3.3 0.2 + - - -
473E TYR* 3.3 3.5 + - - +
474E LEU* 2.9 51.1 + - + +
511E LEU* 3.9 20.4 - - + -
514E TYR* 4.2 15.7 - - + -
530E TRP* 4.4 3.6 - - + -
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Residues in contact with GLN 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467E TYR 5.1 0.2 + - - -
469E SER 3.5 0.2 - - - -
470E VAL* 1.3 78.7 - - - +
472E ASN* 1.3 57.5 + - - +
474E LEU* 4.2 6.3 - - - -
475E ASP* 2.9 54.6 + - - +
514E TYR* 5.8 0.2 + - - -
530E TRP* 3.4 68.4 + - + +
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Residues in contact with ASN 472 (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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468E SER 5.3 0.7 - - - +
469E SER* 3.4 22.8 + - - +
471E GLN* 1.3 80.4 - - - +
473E TYR* 1.3 64.0 + - - +
475E ASP* 3.3 6.4 + - - +
476E GLN* 3.1 35.3 + - - +
21F GLN* 3.9 21.1 - - + +
73F GLU* 3.0 27.7 + - - -
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Residues in contact with TYR 473 (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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454E LEU* 3.8 28.3 - - + +
457E GLN* 4.1 16.0 + - + -
458E ILE* 3.5 37.9 - - + -
461E GLU* 2.9 33.7 + - - -
469E SER* 3.0 32.9 + - - +
472E ASN* 1.3 80.9 - - - +
474E LEU* 1.3 56.6 - - - +
476E GLN* 3.2 13.1 + - - +
477E ILE* 2.9 34.6 + - - +
21F GLN* 4.6 5.0 + - - -
58F PHE* 4.5 8.1 - + - -
60F THR* 4.7 6.9 + - - -
71F LYS* 4.8 2.8 - - - -
73F GLU* 3.9 33.0 + - - +
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Residues in contact with LEU 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458E ILE* 3.7 20.6 - - + -
470E VAL* 2.9 36.0 + - + +
471E GLN* 3.8 4.7 - - - +
473E TYR* 1.3 77.9 - - - +
475E ASP* 1.3 61.1 + - - +
477E ILE* 3.4 8.9 + - + -
478E GLU 3.1 22.5 + - - -
496E PHE* 3.2 25.6 - - + -
499E CYS 5.9 0.2 - - - -
500E ILE* 4.3 21.1 - - + -
503E VAL* 5.2 7.0 - - + -
511E LEU* 4.8 11.7 - - + -
530E TRP* 4.3 13.2 - - + -
534E ILE* 4.2 28.9 - - + -
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Residues in contact with ASP 475 (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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471E GLN* 2.9 47.1 + - - +
472E ASN* 3.6 6.0 - - - +
474E LEU* 1.3 76.7 - - - +
476E GLN* 1.3 61.8 + - + +
478E GLU* 3.4 16.5 + - - +
479E ASP* 2.9 29.7 + - - +
496E PHE* 5.4 0.9 - - - -
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Residues in contact with GLN 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454E LEU* 3.7 25.1 - - + +
472E ASN* 3.1 35.5 + - - +
473E TYR* 3.2 16.9 + - - +
475E ASP* 1.3 75.2 - - + +
477E ILE* 1.3 63.5 + - - +
479E ASP* 3.4 8.5 + - - +
480E ILE* 3.1 27.2 + - - +
23F LYS* 4.4 19.7 + - - +
73F GLU* 2.9 31.8 + - - +
75F TRP* 4.5 8.0 + - - -
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Residues in contact with ILE 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E ILE* 3.7 21.9 - - + +
454E LEU* 3.7 28.5 - - + -
455E GLN* 3.8 32.3 - - + +
458E ILE* 4.5 11.7 - - + -
473E TYR 2.9 17.7 + - - +
474E LEU* 3.5 15.3 - - + +
475E ASP 3.3 0.2 - - - -
476E GLN* 1.3 72.1 - - - +
478E GLU* 1.3 66.4 + - - +
480E ILE* 3.1 18.9 + - - +
481E LEU* 3.2 14.9 + - + +
496E PHE* 4.1 10.3 - - + -
499E CYS* 4.1 21.8 - - + -
503E VAL* 5.1 1.3 - - + -
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Residues in contact with GLU 478 (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 3.1 6.4 + - - +
475E ASP* 3.7 16.9 - - - +
477E ILE* 1.3 79.7 - - - +
479E ASP* 1.3 61.6 + - - +
481E LEU* 3.2 14.2 + - - +
482E THR* 3.1 28.4 + - + +
492E LYS* 3.2 29.0 - - + -
496E PHE* 3.3 41.2 - - + -
533E LYS* 3.1 23.9 + - - -
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Residues in contact with ASP 479 (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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475E ASP 2.9 18.2 + - - +
476E GLN* 3.5 10.5 - - - +
477E ILE 3.1 0.2 - - - -
478E GLU* 1.3 78.7 - - - +
480E ILE* 1.3 55.1 + - + +
482E THR* 3.7 6.4 - - - +
483E VAL* 2.9 51.5 + - - +
92F ARG* 2.3 35.3 + - - +
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Residues in contact with ILE 480 (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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417E LEU* 5.4 0.9 - - + -
447E HIS* 4.1 28.0 - - + +
450E ALA* 3.9 24.5 - - + -
451E ILE* 4.1 17.0 - - + -
454E LEU* 4.0 18.2 - - + -
476E GLN 3.1 16.2 - - - +
477E ILE* 3.1 5.5 + - - +
479E ASP* 1.3 76.3 - - + +
481E LEU* 1.3 58.3 + - - +
484E ASP* 3.1 33.3 + - + +
485E ALA* 2.9 26.6 + - - +
75F TRP* 5.6 1.8 - - + -
89F MET* 4.4 10.8 - - + +
92F ARG* 5.5 1.8 - - - +
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Residues in contact with LEU 481 (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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417E LEU* 3.7 15.0 - - + -
421E LEU* 4.5 5.4 - - + -
451E ILE* 3.7 26.7 - - + -
477E ILE* 3.4 19.1 - - + +
478E GLU* 3.2 9.1 + - - +
480E ILE* 1.3 77.4 - - - +
482E THR* 1.3 56.3 + - - +
485E ALA* 3.2 20.6 - - - +
487E MET* 3.4 27.4 + - + +
492E LYS* 4.5 10.3 - - + +
495E ALA* 3.9 17.7 - - + +
496E PHE* 3.6 48.5 - - + +
499E CYS* 4.4 1.1 - - - -
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Residues in contact with THR 482 (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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478E GLU* 3.1 20.7 + - + +
479E ASP* 3.4 15.0 - - - +
481E LEU* 1.3 77.5 - - - +
483E VAL* 1.3 72.8 + - + +
486E LYS* 4.1 11.8 - - - +
487E MET* 4.6 11.4 + - - +
492E LYS* 4.3 22.5 - - - +
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Residues in contact with VAL 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479E ASP* 2.9 33.9 + - - +
482E THR* 1.3 86.9 - - + +
484E ASP* 1.3 65.8 + - - +
486E LYS* 3.5 19.3 - - - +
92F ARG* 3.6 32.1 - - - +
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Residues in contact with ASP 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447E HIS* 3.1 35.4 + - + +
480E ILE* 3.1 22.4 + - + +
483E VAL* 1.3 75.6 - - - +
485E ALA* 1.3 64.1 + - - +
486E LYS* 3.2 9.3 + - - +
88F PRO* 4.6 4.0 - - - +
89F MET* 3.3 36.5 + - - +
92F ARG* 2.4 31.6 + - - -
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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