Contacts of the helix formed by residues 469 - 484 (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 SER 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 2.8 27.2 + - - -
466A ASP* 4.4 0.5 + - - -
467A TYR 3.6 0.2 - - - -
468A SER* 1.3 79.5 + - - +
470A VAL* 1.3 58.1 + - - +
471A GLN 3.4 2.0 - - - -
472A ASN* 3.6 17.7 - - - -
473A TYR* 2.8 46.7 + - - -
21B GLN* 3.2 29.8 + - - +
71B LYS* 4.4 0.7 + - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 3.9 18.7 - - + +
461A GLU* 5.3 2.4 + - + +
462A MET* 3.8 23.8 - - + -
466A ASP 4.6 2.2 - - - +
467A TYR* 3.8 32.8 - - + +
468A SER 3.3 1.6 - - - -
469A SER* 1.3 77.6 - - - +
471A GLN* 1.3 64.5 + - - +
473A TYR* 3.4 3.8 + - + +
474A LEU* 3.1 35.1 + - + +
511A LEU* 4.0 25.4 - - + -
514A TYR* 4.2 15.5 - - + -
530A TRP* 4.2 3.6 - - + -
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Residues in contact with GLN 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR 5.3 0.2 + - - -
468A SER 4.7 5.2 + - - +
469A SER* 3.4 0.4 - - - +
470A VAL* 1.3 78.4 - - - +
472A ASN* 1.3 59.2 + - - +
474A LEU* 3.4 2.3 + - - +
475A ASP* 2.8 54.3 + - - +
514A TYR* 5.5 0.6 + - - +
530A TRP* 3.3 70.0 + - + +
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Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 5.1 1.0 + - - +
469A SER* 3.2 26.3 + - - +
470A VAL 3.2 0.6 - - - -
471A GLN* 1.3 79.1 - - - +
473A TYR* 1.3 62.6 + - - +
475A ASP* 3.3 8.7 + - - +
476A GLN* 3.0 38.4 + - - +
21B GLN* 4.4 6.3 + - - +
73B GLU* 2.9 27.7 + - - -
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Residues in contact with TYR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 3.8 29.2 - - + +
457A GLN* 4.0 17.2 + - + -
458A ILE* 3.6 37.5 - - + -
461A GLU* 2.8 41.9 + - - -
469A SER* 2.8 36.2 + - - +
470A VAL* 3.9 0.9 - - - +
472A ASN* 1.3 72.1 - - - +
474A LEU* 1.3 57.8 + - - +
476A GLN* 3.2 14.1 + - - +
477A ILE* 3.0 31.2 + - - +
58B PHE* 4.7 5.6 - + - -
60B THR* 4.3 9.9 + - - -
71B LYS* 4.0 11.1 + - - -
73B GLU* 4.0 24.9 + - + +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 3.7 21.1 - - + -
470A VAL* 3.1 35.8 + - + +
471A GLN* 3.8 4.5 - - - +
473A TYR* 1.3 73.4 - - - +
475A ASP* 1.3 63.2 + - - +
477A ILE* 3.2 17.5 + - + +
478A GLU* 3.0 24.6 + - - +
496A PHE* 3.7 28.5 - - + -
499A CYS 5.6 0.7 - - - +
500A ILE* 4.7 10.3 - - + -
503A VAL* 5.3 6.3 - - + -
511A LEU* 4.9 11.4 - - + -
530A TRP* 4.2 12.3 - - + -
534A ILE* 4.1 28.9 - - + -
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Residues in contact with ASP 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLN* 2.8 48.5 + - - +
472A ASN* 3.5 8.7 - - - +
473A TYR 3.3 0.2 - - - -
474A LEU* 1.3 78.8 - - - +
476A GLN* 1.3 59.6 + - + +
478A GLU* 3.6 9.7 + - - +
479A ASP* 3.0 28.8 + - - +
530A TRP* 5.8 0.3 - - - -
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 3.7 24.7 - - + +
472A ASN* 3.0 46.0 + - - +
473A TYR* 3.5 10.7 - - - +
474A LEU 3.2 0.2 - - - -
475A ASP* 1.3 76.3 - - + +
477A ILE* 1.3 63.4 + - - +
479A ASP* 3.3 7.7 + - - +
480A ILE* 3.1 28.2 + - - +
23B LYS* 4.8 6.2 - - - +
58B PHE* 5.9 0.2 - - - -
73B GLU* 3.5 19.2 + - - +
75B TRP* 4.9 1.2 + - - -
92B ARG* 6.1 0.2 - - - +
303B EDO 3.0 29.7 + - - -
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Residues in contact with ILE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.7 25.7 - - + +
454A LEU* 3.7 24.9 - - + -
455A GLN* 4.0 27.1 - - + +
458A ILE* 4.5 6.1 - - + -
473A TYR 3.0 19.0 + - - +
474A LEU* 3.2 28.0 + - + +
476A GLN* 1.3 75.2 - - - +
478A GLU* 1.3 62.9 + - - +
480A ILE* 3.1 17.4 + - - +
481A LEU* 3.2 14.7 + - + +
496A PHE* 4.1 14.8 - - + -
499A CYS* 4.2 15.7 - - + -
503A VAL* 5.4 1.1 - - + -
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU 3.0 16.0 + - - +
475A ASP* 3.9 8.9 - - - +
477A ILE* 1.3 76.2 - - - +
479A ASP* 1.3 61.5 + - - +
481A LEU* 3.2 14.3 + - - +
482A THR* 3.1 26.9 + - + +
492A LYS* 3.5 34.6 + - - -
496A PHE* 3.2 27.1 - - + -
533A LYS* 3.3 25.8 + - - -
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Residues in contact with ASP 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASP 3.0 18.9 + - - +
476A GLN* 3.5 9.6 - - - +
478A GLU* 1.3 78.6 - - - +
480A ILE* 1.3 57.1 + - - +
482A THR* 3.8 7.8 - - - +
483A VAL* 2.9 52.6 + - - +
484A ASP* 4.1 0.2 - - - +
92B ARG* 2.4 40.3 + - - +
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 5.0 0.9 - - + -
447A HIS* 3.9 24.7 - - + +
450A ALA* 3.7 23.3 - - + -
451A ILE* 4.1 19.1 - - + +
454A LEU* 4.4 8.1 - - + -
476A GLN 3.1 15.0 + - - +
477A ILE 3.1 7.7 + - - +
479A ASP* 1.3 78.5 - - - +
481A LEU* 1.3 58.4 + - - +
484A ASP* 3.1 19.7 + - + +
485A ALA* 2.9 26.0 + - - +
89B MET* 3.8 19.5 - - + -
92B ARG* 4.6 1.8 - - - +
303B EDO 3.6 29.8 - - - -
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 3.7 25.4 - - + -
421A LEU* 4.5 5.4 - - + -
451A ILE* 3.8 13.7 - - + -
477A ILE* 3.2 18.3 + - + +
478A GLU* 3.2 9.2 + - - +
480A ILE* 1.3 78.0 - - - +
482A THR* 1.3 55.4 + - - +
485A ALA* 3.3 12.8 - - - +
486A LYS 3.4 0.7 + - - -
487A MET* 3.2 47.2 + - + +
492A LYS* 4.2 10.3 - - + +
495A ALA* 4.0 8.1 - - + +
496A PHE* 3.6 47.6 - - + +
499A CYS* 4.6 0.9 - - - -
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Residues in contact with THR 482 (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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478A GLU* 3.1 22.0 + - + +
479A ASP* 3.5 15.3 - - - +
481A LEU* 1.3 77.6 - - - +
483A VAL* 1.3 72.2 + - + +
486A LYS* 3.8 13.5 - - - +
487A MET* 4.6 8.5 + - - +
492A LYS* 4.5 19.6 + - - +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASP* 2.9 36.1 + - - +
482A THR* 1.3 86.9 - - + +
484A ASP* 1.3 66.1 + - - +
486A LYS* 3.2 21.0 + - - +
92B ARG* 3.7 27.6 - - - +
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Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A HIS* 3.3 34.9 - - + +
480A ILE* 3.1 20.9 + - + +
483A VAL* 1.3 77.4 - - - +
485A ALA* 1.3 65.1 + - - +
486A LYS* 3.2 16.3 + - - +
88B PRO* 4.5 3.5 - - - +
89B MET* 3.3 33.5 + - - +
92B ARG* 2.3 35.6 + - - -
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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
------------------------------------------------------------
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