Contacts of the helix formed by residues 432 - 447 (chain F) in PDB entry 1K9A
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 THR 432 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306F GLU* 3.9 22.7 - - - +
366F LYS* 3.7 18.2 - - - +
369F VAL* 4.8 1.3 - - - -
431F PRO* 1.3 76.2 - - - +
433F PHE* 1.3 65.8 + - - +
434F LEU* 3.5 8.5 + - - +
435F GLN* 2.9 45.8 + - - +
436F LEU* 3.1 14.3 + - - +
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Residues in contact with PHE 433 (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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299F CYS* 3.6 9.7 - - - +
302F MET* 3.2 47.3 - - + -
303F GLU* 3.8 24.5 - - + +
306F GLU* 3.4 5.5 + - - +
365F THR* 3.3 38.1 - - + -
368F ASP* 3.5 15.3 - - + -
369F VAL* 3.5 28.3 - - + -
372F PHE* 3.8 23.8 - + + -
432F THR* 1.3 74.8 - - - +
434F LEU* 1.3 57.8 + - - +
436F LEU* 3.5 16.4 - - + +
437F ARG* 2.8 29.1 + - - +
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Residues in contact with LEU 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F GLU* 3.5 30.6 - - + +
306F GLU* 4.4 2.3 + - - +
432F THR* 3.0 10.1 + - - +
433F PHE* 1.3 76.0 - - - +
435F GLN* 1.3 72.7 + - + +
437F ARG* 3.2 15.1 + - - +
438F GLU* 3.0 49.9 + - + +
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Residues in contact with GLN 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F LYS* 5.2 0.3 + - - -
430F ARG 4.8 0.5 - - - +
431F PRO* 3.4 16.5 - - + +
432F THR* 2.9 45.8 + - - +
434F LEU* 1.3 82.0 - - + +
436F LEU* 1.3 56.7 + - - +
438F GLU* 3.2 10.7 + - - +
439F GLN* 2.8 38.7 + - - +
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Residues in contact with LEU 436 (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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299F CYS* 3.7 10.5 - - - -
369F VAL* 3.9 19.3 - - + -
372F PHE* 4.0 17.3 - - + -
418F VAL* 3.9 18.4 - - + +
421F ASN* 5.3 0.2 - - - +
422F CYS* 3.6 17.7 - - - -
431F PRO* 3.5 22.9 - - + -
432F THR 3.1 13.1 + - - +
433F PHE* 3.5 34.3 - - + +
434F LEU 3.2 0.2 - - - -
435F GLN* 1.3 75.9 - - - +
437F ARG* 1.3 63.8 + - - +
439F GLN* 2.9 14.1 + - - +
440F LEU* 2.9 26.8 + - + +
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Residues in contact with ARG 437 (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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296F LEU* 4.2 9.4 - - + +
299F CYS* 3.5 14.9 - - - -
300F GLU* 4.4 19.3 - - + -
303F GLU* 3.0 32.1 + - - +
433F PHE 2.8 20.9 + - - +
434F LEU* 3.5 24.0 - - - +
436F LEU* 1.3 72.6 - - - +
438F GLU* 1.3 84.3 + - - +
440F LEU* 3.3 5.1 + - - +
441F GLU* 2.9 68.2 + - + +
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Residues in contact with GLU 438 (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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434F LEU* 3.0 34.7 + - + +
435F GLN* 3.4 8.7 - - - +
437F ARG* 1.3 103.7 + - - +
439F GLN* 1.3 63.4 + - - +
441F GLU* 3.3 10.9 + - - +
442F HIS* 3.0 25.3 + - - +
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Residues in contact with GLN 439 (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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417F ASP 5.2 0.3 - - - -
418F VAL* 3.7 36.0 - - + +
421F ASN* 3.0 32.8 + - - +
431F PRO* 4.4 10.1 - - - +
435F GLN* 2.8 21.5 + - - +
436F LEU* 2.9 13.7 + - - +
438F GLU* 1.3 75.6 - - - +
440F LEU* 1.3 59.5 + - - +
442F HIS* 3.6 8.3 - - - +
443F ILE* 3.1 29.6 + - - +
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Residues in contact with LEU 440 (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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292F LEU* 4.1 15.4 - - + +
295F SER* 3.8 38.8 - - - +
296F LEU* 3.8 18.4 - - + -
299F CYS* 4.3 12.1 - - + -
372F PHE* 4.5 9.2 - - + -
376F LEU* 4.9 5.6 - - + -
415F VAL* 5.2 6.1 - - + -
418F VAL* 4.0 31.6 - - + -
436F LEU 2.9 19.3 + - - +
437F ARG 3.7 3.6 - - - +
439F GLN* 1.3 74.8 - - - +
441F GLU* 1.3 60.4 + - - +
442F HIS 3.2 1.3 - - - -
443F ILE* 3.2 13.8 + - + +
444F ARG* 2.8 26.0 + - - +
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Residues in contact with GLU 441 (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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296F LEU* 4.2 10.5 - - + +
437F ARG* 2.9 53.2 + - - +
438F GLU* 3.3 11.9 + - - +
440F LEU* 1.3 71.5 - - - +
442F HIS* 1.3 57.9 + - - +
444F ARG* 3.5 32.5 + - - +
445F THR* 2.7 42.5 + - - +
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Residues in contact with HIS 442 (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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438F GLU 3.0 16.7 + - - +
439F GLN* 3.6 10.3 - - - +
441F GLU* 1.3 77.9 - - - +
443F ILE* 1.3 63.2 + - + +
445F THR* 3.3 4.1 + - - -
446F HIS* 3.1 62.9 + + - +
448F LEU* 4.3 16.5 - - + +
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Residues in contact with ILE 443 (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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292F LEU* 4.4 4.7 - - + -
414F ALA* 3.8 18.6 - - + +
415F VAL* 3.8 40.6 - - + +
418F VAL* 3.9 11.2 - - + -
439F GLN 3.1 18.2 - - - +
440F LEU* 3.2 14.8 + - + +
441F GLU 3.1 0.2 - - - -
442F HIS* 1.3 79.4 - - + +
444F ARG* 1.3 52.2 + - - +
447F GLU* 2.7 32.2 + - - -
448F LEU* 3.0 34.7 + - + +
449F HIS* 3.9 23.3 - - + +
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Residues in contact with ARG 444 (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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289F ASP* 5.4 2.2 - - - +
292F LEU* 3.2 29.2 - - + -
293F LYS* 3.4 32.9 - - - +
296F LEU* 3.3 31.5 - - + +
440F LEU 2.8 11.2 + - - +
441F GLU* 3.0 32.9 + - - +
443F ILE* 1.3 78.4 - - - +
445F THR* 1.3 63.3 + - - +
447F GLU* 3.4 14.6 + - - +
449F HIS* 4.1 6.6 - - + -
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Residues in contact with THR 445 (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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441F GLU* 2.7 25.0 + - - +
442F HIS* 3.8 6.3 - - - -
444F ARG* 1.3 77.1 + - - +
446F HIS* 1.3 78.0 + - + +
447F GLU* 3.6 5.0 + - - +
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Residues in contact with HIS 446 (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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442F HIS* 3.1 51.9 + + - +
445F THR* 1.3 90.6 - - + +
447F GLU* 1.3 73.1 + - - +
448F LEU* 3.4 24.6 + - + +
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Residues in contact with GLU 447 (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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443F ILE 2.7 11.5 + - - -
444F ARG 3.4 9.1 + - - +
445F THR 3.3 5.9 - - - +
446F HIS* 1.3 82.9 - - - +
448F LEU* 1.3 52.4 + - - +
449F HIS* 2.7 27.8 + - + -
450F LEU* 3.0 51.0 + - + +
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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