Contacts of the helix formed by residues 366 - 376 (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 LEU 366 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F ILE* 3.8 22.7 - - + -
308F VAL* 3.8 31.6 - - + -
335F VAL* 4.0 12.8 - - + +
336F GLU 3.9 12.6 - - - +
337F SER* 3.6 37.5 - - - +
338F PRO 3.9 0.7 - - - -
361F LEU* 2.9 23.8 + - + +
364F ASN* 3.4 13.0 - - + +
365F ASP* 1.3 73.3 - - - +
367F ILE* 1.3 67.8 + - - +
368F ASP 3.5 1.6 - - - -
369F PHE* 3.2 15.5 + - + +
370F VAL* 2.9 26.1 + - - +
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Residues in contact with ILE 367 (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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358F MET* 4.2 19.5 - - + +
361F LEU* 4.1 18.4 - - + +
362F ARG* 3.6 33.9 - - + +
365F ASP* 3.7 1.0 + - - +
366F LEU* 1.3 77.3 - - - +
368F ASP* 1.3 65.5 + - + +
370F VAL* 2.9 15.6 + - - +
371F ARG* 2.9 47.0 + - - +
403F LEU* 4.2 18.6 - - + +
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Residues in contact with ASP 368 (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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365F ASP* 4.9 12.2 + - - +
366F LEU 3.5 0.4 - - - +
367F ILE* 1.3 80.7 - - - +
369F PHE* 1.3 54.0 + - - +
371F ARG* 4.2 13.7 - - - +
372F LYS* 2.6 54.8 + - - +
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Residues in contact with PHE 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ILE* 5.7 1.1 - - + -
335F VAL* 3.9 28.0 - - + -
337F SER 4.6 0.7 - - - -
338F PRO* 4.0 27.5 - - + +
340F ASN* 3.4 30.5 - - + -
341F ASP 4.6 1.1 - - - -
342F LEU* 4.3 10.8 - - + -
343F TYR* 3.8 21.3 - + - -
346F LEU* 4.5 10.1 - - + -
365F ASP 5.0 0.8 + - - -
366F LEU* 3.2 26.8 + - + +
367F ILE 3.1 0.6 - - - -
368F ASP* 1.3 78.5 + - - +
370F VAL* 1.3 62.2 + - + +
372F LYS* 3.4 18.1 - - + +
373F HIS* 2.7 56.1 + + - -
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Residues in contact with VAL 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ILE* 3.8 28.5 - - + -
346F LEU* 4.2 11.9 - - + -
348F ILE* 3.6 27.4 - - + -
361F LEU* 5.3 4.9 - - + -
366F LEU 2.9 18.3 + - - +
367F ILE* 2.9 9.7 + - - +
369F PHE* 1.3 75.0 - - + +
371F ARG* 1.3 66.4 + - + +
372F LYS 3.0 1.1 - - - -
373F HIS* 3.0 14.9 + - - +
374F VAL* 3.4 10.2 + - - +
380F VAL* 4.2 8.1 - - + -
403F LEU* 4.4 10.1 - - + -
405F LEU* 3.7 22.0 - - + -
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Residues in contact with ARG 371 (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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358F MET* 5.6 0.6 - - - +
367F ILE* 2.9 41.5 + - + +
368F ASP* 3.7 15.7 - - - +
370F VAL* 1.3 77.7 - - + +
372F LYS* 1.3 62.2 + - - +
374F VAL* 3.4 2.8 + - - +
375F GLU* 3.2 24.6 + - - +
401F LYS* 2.9 31.6 - - - +
402F GLY 3.8 6.7 + - - -
403F LEU* 3.2 27.6 + - + +
404F SER* 4.6 4.2 + - - -
405F LEU* 4.3 22.8 - - + +
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Residues in contact with LYS 372 (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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342F LEU* 4.2 24.5 - - + +
368F ASP* 2.6 35.1 + - - +
369F PHE* 3.4 19.0 - - + +
370F VAL 3.0 0.2 - - - -
371F ARG* 1.3 75.5 - - - +
373F HIS* 1.3 56.4 + - - +
375F GLU* 3.8 4.6 + - - +
376F ASP* 2.8 48.1 + - - +
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Residues in contact with HIS 373 (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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342F LEU* 3.5 14.9 - - + +
343F TYR* 2.8 54.7 + + + -
346F LEU* 3.4 25.5 - - + +
369F PHE* 2.7 54.6 - + - -
370F VAL 3.0 8.5 + - - +
372F LYS* 1.3 76.4 - - - +
374F VAL* 1.3 62.5 + - - +
376F ASP* 3.6 2.8 + - - -
378F ARG* 2.9 41.5 + - + +
380F VAL* 3.9 15.5 - - + -
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Residues in contact with VAL 374 (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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370F VAL 3.4 9.8 + - - +
371F ARG 3.8 5.2 - - - +
372F LYS 3.4 0.2 - - - -
373F HIS* 1.3 73.4 - - - +
375F GLU* 1.3 58.0 + - - +
377F GLU* 2.7 29.3 + - - -
378F ARG 4.5 6.3 - - - +
380F VAL* 3.6 22.0 - - + -
405F LEU* 3.9 28.7 - - + -
472F ILE* 3.5 30.7 - - + -
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Residues in contact with GLU 375 (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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371F ARG 3.2 14.0 + - - +
372F LYS* 4.1 3.5 - - - +
374F VAL* 1.3 79.4 - - - +
376F ASP* 1.3 69.5 + - - +
377F GLU* 2.9 8.1 + - - +
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Residues in contact with ASP 376 (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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342F LEU* 3.1 31.3 - - + +
372F LYS* 2.8 35.9 + - - +
373F HIS 3.6 4.0 - - - +
374F VAL 3.0 1.4 + - - -
375F GLU* 1.3 87.7 - - - +
377F GLU* 1.3 69.0 + - - +
378F ARG* 3.2 19.2 + - + +
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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