Contacts of the helix formed by residues 353 - 364 (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 HIS 353 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352F GLY* 1.3 83.0 - - - -
354F PHE* 1.3 67.3 + - - +
355F GLY* 4.4 4.0 - - - +
356F GLU* 3.0 19.4 + - + +
357F GLY 3.0 18.4 + - - -
385F LEU* 3.8 4.6 - - - +
396F GLU* 3.3 30.0 + - + +
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Residues in contact with PHE 354 (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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353F HIS* 1.3 70.4 - - - +
355F GLY* 1.3 63.5 + - - +
357F GLY* 3.2 2.8 + - - -
358F MET* 3.1 29.0 + - + +
385F LEU* 3.8 11.2 - - + +
388F GLN* 3.3 44.2 - - + +
389F LEU* 3.6 14.2 - - + +
391F PHE 4.1 2.0 - - - -
393F GLU* 3.9 15.9 - - - -
394F SER* 3.4 33.7 - - - +
396F GLU* 2.9 16.2 + - + +
397F ALA* 4.2 13.5 - - + -
400F VAL* 3.8 24.0 - - + -
402F GLY* 3.6 29.2 - - - -
410F VAL* 4.3 2.0 - - + -
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Residues in contact with GLY 355 (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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353F HIS* 3.1 3.2 + - - +
354F PHE* 1.3 80.4 - - - +
356F GLU* 1.3 61.2 + - - +
358F MET* 3.5 2.6 + - - +
359F ARG* 3.1 21.8 + - - +
362F ARG* 5.5 0.7 + - - -
397F ALA* 3.6 22.0 - - - +
400F VAL* 4.3 16.7 - - - +
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Residues in contact with GLU 356 (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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310F PRO* 3.3 28.2 - - + +
352F GLY* 5.3 1.0 - - - -
353F HIS* 3.0 21.5 + - + +
355F GLY* 1.3 72.2 - - - +
357F GLY* 1.3 65.5 + - - +
359F ARG* 3.0 32.2 + - - +
360F ARG* 2.7 54.9 + - - +
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Residues in contact with GLY 357 (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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309F GLY* 5.2 0.9 - - - -
310F PRO* 3.8 19.9 - - - +
353F HIS 3.0 12.8 + - - -
354F PHE 3.2 4.5 + - - -
356F GLU* 1.3 78.7 - - - +
358F MET* 1.3 59.9 + - - +
360F ARG* 3.5 2.9 + - - +
361F LEU* 3.2 24.8 + - - +
385F LEU* 4.1 10.1 - - - -
389F LEU* 4.0 14.4 - - - +
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Residues in contact with MET 358 (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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354F PHE* 3.1 24.9 + - + +
355F GLY 4.0 3.8 - - - +
357F GLY* 1.3 72.7 - - - +
359F ARG* 1.3 59.8 + - - +
361F LEU* 3.2 5.0 + - - +
362F ARG* 2.9 37.5 + - - +
367F ILE* 4.2 19.7 - - + +
371F ARG* 5.6 0.9 - - - +
389F LEU* 3.5 29.2 - - + -
400F VAL* 4.2 12.6 - - + -
401F LYS 3.2 27.1 - - - +
402F GLY* 3.4 25.1 - - - +
403F LEU* 3.4 24.9 - - + +
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Residues in contact with ARG 359 (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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355F GLY 3.1 14.4 + - - +
356F GLU* 3.0 45.6 + - - +
358F MET* 1.3 77.2 - - - +
360F ARG* 1.3 66.6 + - - +
362F ARG* 3.5 32.0 - - - +
363F GLU* 2.8 78.3 + - + +
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Residues in contact with ARG 360 (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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308F VAL* 3.2 34.8 + - + +
309F GLY* 3.9 15.8 + - - -
310F PRO* 3.5 26.2 - - + +
311F GLY 4.9 1.0 - - - +
356F GLU* 2.7 51.8 + - + +
357F GLY 4.0 1.3 - - - +
359F ARG* 1.3 88.1 - - - +
361F LEU* 1.3 62.4 + - - +
363F GLU* 4.2 7.4 - - - +
364F ASN* 2.7 30.6 + - - +
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Residues in contact with LEU 361 (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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306F ILE* 4.0 31.6 - - + -
308F VAL* 4.3 5.2 - - + -
309F GLY* 5.4 3.1 - - - +
348F ILE* 4.6 8.5 - - + -
357F GLY 3.2 12.4 + - - +
358F MET* 3.2 11.8 + - - +
359F ARG 3.1 0.4 - - - -
360F ARG* 1.3 78.8 - - - +
362F ARG* 1.3 61.8 + - - +
364F ASN 3.4 1.9 + - - -
365F ASP 3.2 3.3 + - - -
366F LEU* 2.9 44.2 + - + +
367F ILE* 4.1 12.6 - - + -
370F VAL* 5.3 5.6 - - + -
389F LEU* 3.9 22.4 - - + -
403F LEU* 3.8 32.5 - - + -
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Residues in contact with ARG 362 (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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355F GLY 5.5 0.6 + - - -
358F MET* 2.9 21.0 + - - +
359F ARG* 3.5 39.4 - - - +
361F LEU* 1.3 72.6 - - - +
363F GLU* 1.3 64.1 + - - +
364F ASN 3.0 4.9 - - - -
365F ASP* 2.7 25.6 + - - +
367F ILE* 3.6 24.8 - - + +
400F VAL* 5.8 4.6 - - - +
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Residues in contact with GLU 363 (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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359F ARG* 2.8 71.5 + - + +
360F ARG* 4.2 6.2 - - - +
362F ARG* 1.3 78.5 - - - +
364F ASN* 1.3 70.6 + - - +
365F ASP 3.4 0.6 + - - -
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Residues in contact with ASN 364 (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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308F VAL* 3.6 22.8 - - - +
336F GLU* 3.5 19.7 - - - +
337F SER* 4.1 2.1 - - - -
338F PRO* 3.7 8.8 - - - +
360F ARG* 2.7 29.7 + - - +
361F LEU 3.4 0.8 + - - -
362F ARG 3.0 1.2 - - - -
363F GLU* 1.3 85.1 + - - +
365F ASP* 1.3 73.0 + - - +
366F LEU* 3.2 15.7 + - + +
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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