Contacts of the helix formed by residues 487 - 500 (chain A) in PDB entry 1IK2
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 GLN 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLU* 3.9 4.2 + - + +
485A LEU 2.8 4.8 + - - -
486A GLN* 1.3 75.3 - - - +
488A PHE* 1.4 67.9 + - - +
490A ASN* 3.0 20.4 + - - +
491A HIS* 3.1 14.7 + - + +
514A GLY* 3.7 27.9 + - - +
515A MET* 5.3 0.2 - - - +
517A LEU* 4.9 3.4 - - - +
518A GLN* 3.6 34.8 + - - +
521A ILE* 3.9 23.8 - - + +
657A LYS* 4.9 5.8 + - - +
658A LEU* 3.4 25.3 - - + +
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Residues in contact with PHE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.0 18.4 - - + -
483A GLU 3.1 15.7 + - - +
484A LYS* 4.1 8.7 - - + -
485A LEU 3.0 13.8 + - - +
487A GLN* 1.4 77.5 - - - +
489A PHE* 1.3 65.5 + - - +
491A HIS* 2.9 8.8 + - - +
492A HIS* 2.8 46.8 + - + -
658A LEU* 3.7 15.3 - - + +
659A MET* 3.3 37.2 - - + -
662A LEU* 4.0 22.4 - - + -
667A PRO* 4.7 9.6 - - + -
669A PHE* 3.6 30.3 - + - -
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Residues in contact with PHE 489 (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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120A LEU* 4.2 27.8 - - + +
121A PHE* 3.5 40.2 - + - -
485A LEU* 3.0 31.2 + - + +
488A PHE* 1.3 81.1 - - - +
490A ASN* 1.3 74.5 + - - +
492A HIS* 3.3 1.7 + - - +
493A MET* 2.9 65.4 + - + +
669A PHE* 4.4 16.8 - + - -
697A GLY 4.6 0.7 - - - -
700A GLU* 3.9 24.5 - - + -
701A GLY* 4.2 10.5 - - - -
704A ILE* 5.6 0.2 - - + -
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Residues in contact with ASN 490 (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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485A LEU 4.4 0.7 - - - +
486A GLN 3.2 25.0 + - - +
487A GLN* 3.0 9.5 + - - +
489A PHE* 1.3 93.6 - - - +
491A HIS* 1.3 58.5 + - - +
493A MET* 3.7 8.0 - - - -
494A PHE* 2.9 21.7 + - - +
513A PHE* 3.4 37.2 + - + +
514A GLY* 3.7 4.0 + - - +
517A LEU* 3.5 24.1 - - - +
700A GLU* 4.0 14.0 - - - +
704A ILE* 4.3 11.6 - - + +
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLN* 3.1 16.9 + - + +
488A PHE* 2.9 11.4 + - - +
490A ASN* 1.3 75.2 - - - +
492A HIS* 1.3 68.0 + - - +
494A PHE* 3.0 19.2 + + - +
495A VAL* 3.3 20.5 + - + +
512A ASP* 4.9 10.4 + - - +
514A GLY* 3.9 15.3 - - - +
658A LEU* 6.4 1.6 - - + -
659A MET* 4.0 12.9 - - + +
663A ARG* 3.4 36.3 + - - -
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Residues in contact with HIS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 4.6 18.3 - - + +
488A PHE* 2.8 41.2 + + + +
489A PHE* 3.9 3.8 - - - +
491A HIS* 1.3 77.7 - - + +
493A MET* 1.3 57.4 + - - +
495A VAL* 2.9 20.0 + - + +
496A LEU* 2.9 35.0 + - + +
659A MET* 5.8 2.0 - - + +
662A LEU 5.9 0.4 + - - -
665A THR 5.0 4.5 - - - -
667A PRO* 4.0 29.1 - - + +
669A PHE* 5.0 4.5 - + + -
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Residues in contact with MET 493 (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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120A LEU* 5.2 3.5 - - + +
489A PHE* 2.9 54.9 + - + +
490A ASN* 3.7 6.7 - - - +
492A HIS* 1.3 75.9 - - - +
494A PHE* 1.3 58.8 + - - +
496A LEU* 3.7 19.7 - - + -
497A GLU* 2.9 40.3 + - + +
513A PHE* 3.9 19.2 - - + -
701A GLY* 5.0 3.6 - - - -
704A ILE* 4.8 11.7 - - + -
705A CYS* 3.9 28.0 - - - -
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Residues in contact with PHE 494 (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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490A ASN 2.9 14.1 + - - +
491A HIS* 3.0 10.7 + + - +
493A MET* 1.3 75.3 - - - +
495A VAL* 1.3 74.9 + - + +
496A LEU 3.1 0.2 + - - -
497A GLU* 3.8 0.3 - - - -
498A GLN* 2.8 57.0 + - + +
510A PHE* 4.0 26.0 - + - -
511A ILE 3.6 12.6 - - - -
512A ASP* 3.4 51.4 - - + +
513A PHE* 3.9 15.5 - + - +
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Residues in contact with VAL 495 (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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491A HIS* 3.7 28.5 - - + +
492A HIS* 2.9 16.2 + - + +
494A PHE* 1.3 82.4 - - + +
496A LEU* 1.3 56.2 + - - +
498A GLN* 3.4 6.3 + - - +
499A GLU* 2.8 29.3 + - + +
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Residues in contact with LEU 496 (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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120A LEU* 4.1 30.3 - - + -
492A HIS* 2.9 22.2 + - + +
493A MET* 3.6 18.6 - - + +
495A VAL* 1.3 75.1 - - - +
497A GLU* 1.3 63.7 + - - +
499A GLU* 2.7 43.0 + - - +
500A GLU* 2.8 29.9 + - + +
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Residues in contact with GLU 497 (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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493A MET* 2.9 40.2 + - + +
494A PHE 4.2 0.4 - - - +
496A LEU* 1.3 77.7 - - - +
498A GLN* 1.3 56.7 + - - +
500A GLU* 3.0 16.4 + - - +
501A TYR* 2.9 27.2 + - - -
504A GLU* 3.2 33.7 - - - +
510A PHE* 3.7 28.4 - - + -
513A PHE* 3.8 17.7 - - + -
705A CYS* 4.8 11.1 - - - +
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Residues in contact with GLN 498 (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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494A PHE* 2.8 51.6 + - + +
495A VAL* 3.6 7.4 - - - +
497A GLU* 1.3 74.5 - - - +
499A GLU* 1.3 59.8 + - - +
501A TYR* 3.2 51.9 - - - +
510A PHE* 4.1 4.4 - - - +
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Residues in contact with GLU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 2.8 13.3 + - + +
496A LEU* 2.7 29.9 + - - +
498A GLN* 1.3 68.9 - - - +
500A GLU* 1.3 69.4 + - - +
501A TYR 3.1 8.9 + - - -
502A LYS* 4.7 11.6 - - - +
503A LYS* 4.0 16.1 + - - +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 2.8 31.4 + - + +
497A GLU* 3.0 28.4 + - - +
499A GLU* 1.3 97.5 - - - +
501A TYR* 1.3 56.6 + - - +
502A LYS 3.4 1.6 - - - -
503A LYS* 3.3 40.8 + - + +
504A GLU* 2.9 39.2 + - + +
762A LYS* 5.7 3.0 - - - -
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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