Contacts of the helix formed by residues 482 - 499 (chain F) in PDB entry 1K9V
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 482 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423F TRP* 3.8 11.5 - - - -
437F TYR* 3.2 32.2 - - - +
438F TYR 3.0 22.7 + - - -
478F HIS 2.9 16.0 + - - -
479F PRO 3.0 11.8 + - - -
480F GLU 3.5 0.2 - - - -
481F LYS* 1.3 76.6 - - - +
483F SER* 1.3 70.5 + - - +
484F LYS 3.4 0.3 + - - -
485F ILE* 3.3 10.2 - - - +
486F GLY* 2.9 13.9 + - - -
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Residues in contact with SER 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F TRP* 4.4 9.8 - - - -
479F PRO 4.6 0.9 + - - +
480F GLU 5.1 1.8 + - - -
481F LYS 3.5 4.8 + - - -
482F SER* 1.3 79.3 - - - +
484F LYS* 1.3 67.9 + - - -
486F GLY* 3.5 0.2 - - - -
487F ARG* 3.0 22.7 + - - +
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Residues in contact with LYS 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482F SER 3.4 0.2 + - - -
483F SER* 1.3 80.5 - - - +
485F ILE* 1.3 63.4 + - - +
486F GLY 3.1 0.2 + - - -
487F ARG* 3.3 6.0 + - - +
488F LYS* 3.1 23.0 + - - +
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Residues in contact with ILE 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F TRP* 5.5 0.7 - - + -
433F PRO* 3.4 14.5 - - + +
434F ASN 3.1 28.7 - - - +
435F GLY* 3.4 16.6 - - - -
436F TYR 3.4 21.1 - - - +
437F TYR* 3.2 31.3 + - + +
482F SER 3.3 11.4 - - - +
484F LYS* 1.3 78.0 - - - +
486F GLY* 1.3 60.0 + - - +
488F LYS* 3.5 10.2 - - + +
489F LEU* 3.0 26.0 + - - +
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Residues in contact with GLY 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F TYR* 4.4 2.7 - - - -
479F PRO* 3.5 24.0 - - - +
482F SER* 2.9 19.7 + - - -
483F SER 3.5 4.0 - - - -
484F LYS 3.0 0.2 - - - -
485F ILE* 1.3 74.1 - - - +
487F ARG* 1.3 60.6 + - - +
488F LYS 3.0 1.6 - - - -
489F LEU* 2.8 24.4 + - - +
490F LEU* 2.9 17.2 + - - +
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Residues in contact with ARG 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F GLY 5.7 1.8 - - - +
322F ARG* 6.5 1.1 - - + -
323F ALA* 4.1 7.0 - - + +
479F PRO 4.5 1.0 + - - -
483F SER 3.0 11.2 + - - +
484F LYS* 3.8 8.3 - - - +
486F GLY* 1.3 74.4 - - - +
488F LYS* 1.3 56.9 + - - +
490F LEU* 3.4 13.8 + - - +
491F GLU* 2.8 44.4 + - - +
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Residues in contact with LYS 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433F PRO* 3.7 33.0 - - + +
484F LYS 3.1 16.3 + - - +
485F ILE* 3.5 11.0 - - + +
486F GLY 3.0 0.4 - - - -
487F ARG* 1.3 76.3 - - - +
489F LEU* 1.3 58.8 + - - +
491F GLU* 3.3 14.2 + - - +
492F LYS* 2.9 28.6 + - + +
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Residues in contact with LEU 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428F PHE* 4.1 14.8 - - + -
432F PHE* 3.2 39.0 - - + -
433F PRO* 4.1 7.6 - - + +
437F TYR* 4.1 13.5 - - + +
475F PHE* 3.9 21.5 - - + -
477F PHE* 4.4 6.1 - - + -
479F PRO* 4.5 13.5 - - + -
485F ILE 3.0 14.2 + - - +
486F GLY* 2.8 13.9 + - - +
488F LYS* 1.3 72.5 - - - +
490F LEU* 1.3 69.9 + - + +
492F LYS* 3.0 7.8 + - - +
493F VAL* 2.9 36.1 + - + +
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Residues in contact with LEU 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F LEU* 4.4 5.6 - - + -
319F GLY* 3.5 37.5 - - - +
320F VAL* 3.8 18.6 - - + +
323F ALA* 3.8 11.7 - - + -
347F PHE* 4.4 17.2 - - + -
475F PHE* 6.5 0.2 - - + -
479F PRO* 3.6 32.1 - - + -
480F GLU* 4.6 9.0 - - - +
486F GLY 2.9 14.1 + - - +
487F ARG* 3.6 13.0 - - - +
489F LEU* 1.3 81.5 - - + +
491F GLU* 1.3 63.2 + - - +
493F VAL* 3.2 7.0 + - + +
494F ILE* 3.0 27.4 + - + +
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Residues in contact with GLU 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F ALA* 3.7 29.3 - - + +
326F ASN* 5.0 9.6 - - - +
327F PHE* 3.8 18.7 - - + -
487F ARG* 2.8 37.4 + - - +
488F LYS* 3.4 12.3 + - + +
490F LEU* 1.3 74.5 - - - +
492F LYS* 1.3 54.9 + - - +
494F ILE* 3.1 5.5 + - - +
495F GLU* 2.7 39.3 + - - +
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Residues in contact with LYS 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F THR* 3.5 36.3 - - + +
432F PHE* 3.6 26.9 - - + -
433F PRO* 5.1 4.3 - - + -
488F LYS* 2.9 14.5 + - + +
489F LEU* 3.0 9.2 + - - +
491F GLU* 1.3 76.0 - - - +
493F VAL* 1.3 56.9 + - - +
495F GLU* 3.1 37.4 + - - +
496F CYS* 2.9 35.5 + - - -
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Residues in contact with VAL 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F LEU* 4.1 17.7 - - + -
347F PHE* 4.2 10.3 - - + -
379F TYR* 5.2 2.4 - - + -
381F VAL* 4.0 25.4 - - + -
432F PHE* 3.8 15.3 - - + -
473F LEU* 4.4 7.2 - - + -
475F PHE* 3.9 13.5 - - + -
489F LEU* 2.9 37.7 + - + +
490F LEU* 3.4 12.8 - - + +
491F GLU 3.1 0.2 - - - -
492F LYS* 1.3 76.8 - - - +
494F ILE* 1.3 64.3 + - - +
496F CYS* 3.2 6.4 + - - +
497F SER* 3.1 20.7 + - - -
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Residues in contact with ILE 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ILE* 4.1 22.4 - - + -
320F VAL* 4.0 11.2 - - + +
323F ALA* 3.7 10.1 - - + +
324F SER* 3.5 40.2 - - - +
327F PHE* 4.2 13.7 - - + -
330F VAL* 5.0 6.3 - - + -
345F LEU* 4.2 7.6 - - + -
347F PHE* 5.5 1.8 - - + -
490F LEU* 3.0 15.7 + - + +
491F GLU* 3.5 5.8 - - - +
493F VAL* 1.3 73.7 - - + +
495F GLU* 1.3 64.9 + - - +
497F SER* 2.7 22.9 + - - +
498F LEU* 2.9 36.2 + - + +
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Residues in contact with GLU 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F PHE* 4.3 18.4 - - + -
491F GLU* 2.7 17.1 + - - +
492F LYS* 3.1 45.5 + - + +
494F ILE* 1.3 77.0 - - - +
496F CYS* 1.3 60.7 + - - +
498F LEU* 3.3 25.3 + - + +
499F SER* 3.6 8.8 + - - -
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Residues in contact with CYS 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F TYR* 3.0 31.6 + - + +
431F THR* 4.0 26.5 - - - -
432F PHE* 4.5 7.9 - - + -
473F LEU* 5.8 2.5 - - + -
492F LYS* 2.9 24.5 + - - -
493F VAL* 3.2 9.2 + - - +
495F GLU* 1.3 75.9 - - - +
497F SER* 1.3 61.2 + - - +
499F SER* 3.0 23.1 + - - -
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Residues in contact with SER 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F MET* 6.0 1.2 - - - +
303F ILE* 5.8 0.5 - - - +
344F ASP* 4.4 15.7 - - - +
345F LEU* 3.7 23.3 - - - +
379F TYR* 3.7 34.6 - - - -
493F VAL 3.1 12.3 + - - -
494F ILE* 2.7 25.3 + - - +
496F CYS* 1.3 75.3 - - - +
498F LEU* 1.3 62.9 + - - +
499F SER 3.3 6.4 + - - +
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Residues in contact with LEU 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F MET 4.0 24.2 - - - +
327F PHE* 3.2 44.4 - - + -
328F GLU 5.4 3.8 - - - +
330F VAL* 5.0 8.1 - - + -
494F ILE* 2.9 28.0 + - + +
495F GLU* 3.4 9.9 - - + +
496F CYS 3.2 0.2 - - - -
497F SER* 1.3 80.9 - - - +
499F SER* 1.3 60.4 + - - +
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Residues in contact with SER 499 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F TYR* 4.7 0.9 + - - -
495F GLU 3.6 5.9 + - - -
496F CYS* 3.0 18.8 + - - -
497F SER 3.3 6.4 - - - +
498F LEU* 1.3 83.6 - - - +
500F ARG* 1.3 82.8 + - - +
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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
------------------------------------------------------------
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