Contacts of the helix formed by residues 354 - 366 (chain B) in PDB entry 4K9N
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 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B VAL* 4.0 15.1 - - + +
347B ASP 3.4 24.9 + - - -
348B GLN* 3.0 35.9 + - - +
349B ASP* 5.2 5.3 + - - -
352B ARG 4.7 1.1 + - - -
353B LEU* 1.3 75.0 - - - +
355B PRO* 1.3 71.8 - - - +
356B GLU* 3.6 15.2 + - - +
357B THR* 3.0 19.7 + - - +
358B VAL* 3.2 10.8 + - - +
524B VAL* 3.6 26.9 - - + +
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Residues in contact with PRO 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B LEU 4.1 3.6 - - - +
354B HIS* 1.3 84.4 - - + +
356B GLU* 1.3 74.0 + - - +
358B VAL* 3.0 4.3 + - + +
359B PHE* 3.0 32.5 + - + -
379B THR* 3.6 37.0 - - + -
382B GLN* 4.4 7.9 - - - +
453B MET* 3.9 22.4 - - + -
523B THR* 5.1 6.3 - - - -
524B VAL* 4.2 15.0 - - + +
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Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B VAL* 3.7 36.1 - - + +
354B HIS* 3.6 9.5 + - + +
355B PRO* 1.3 89.6 - - - +
357B THR* 1.3 57.7 + - - +
359B PHE* 3.4 1.9 + - - -
360B ASP* 2.9 35.9 + - - +
382B GLN* 3.8 29.7 + - + +
386B ARG* 3.4 35.0 - - - +
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B VAL* 4.7 7.8 + - - +
348B GLN* 2.7 41.8 + - + +
353B LEU* 3.8 10.3 - - + -
354B HIS* 3.0 15.6 + - - +
356B GLU* 1.3 75.7 - - - +
358B VAL* 1.3 64.9 + - - +
360B ASP* 3.4 5.8 + - - +
361B THR* 2.9 30.7 + - - +
500B LEU* 3.7 30.7 - - + -
503B LEU* 4.9 0.2 - - + -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.9 18.8 - - + -
354B HIS 3.7 12.1 - - - +
355B PRO* 3.0 7.4 + - + +
357B THR* 1.3 77.6 - - - +
359B PHE* 1.3 63.3 + - + +
361B THR* 3.3 1.9 + - - -
362B LEU* 2.9 46.3 + - + +
425B VAL* 5.4 0.4 - - + -
451B VAL* 4.6 10.3 - - + -
453B MET* 3.9 33.0 - - + -
503B LEU* 4.0 21.0 - - + +
521B VAL* 4.1 13.2 - - + -
523B THR* 4.5 1.1 - - + -
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PRO* 3.0 31.2 + - + +
356B GLU* 3.9 2.2 - - - +
358B VAL* 1.3 75.3 - - + +
360B ASP* 1.3 66.7 + - - +
362B LEU* 3.3 15.3 + - + -
363B ASN* 2.9 24.9 + - - +
376B SER* 5.3 0.2 - - - -
379B THR* 3.5 43.3 - - - -
382B GLN* 4.2 7.2 - - + -
383B MET* 3.6 46.0 - - + -
386B ARG* 3.8 20.0 - - + -
387B LEU* 3.6 13.0 - - + +
425B VAL* 3.8 29.6 - - + -
453B MET* 4.4 6.1 - - + -
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B PRO* 5.1 1.9 - - - +
345B LYS* 4.5 18.2 - - - +
346B VAL 5.1 1.4 + - - -
356B GLU 2.9 19.4 + - - +
357B THR* 3.8 7.3 - - + +
359B PHE* 1.3 74.4 - - - +
361B THR* 1.3 58.8 + - - +
363B ASN* 3.3 7.3 + - - +
364B ASP* 3.0 37.4 + - - +
386B ARG* 3.0 43.6 + - - +
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Residues in contact with THR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B THR* 2.9 19.1 + - - +
358B VAL 3.7 3.8 - - - -
360B ASP* 1.3 75.8 - - - +
362B LEU* 1.3 65.1 + - - +
364B ASP* 3.1 8.1 + - + +
365B MET* 3.0 39.7 + - + +
500B LEU* 3.7 18.2 - - - +
503B LEU* 4.0 12.1 - - + -
504B LYS* 4.3 18.6 + - + +
507B LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B VAL* 2.9 35.2 + - + +
359B PHE* 3.6 15.9 - - + +
361B THR* 1.3 76.2 - - - +
363B ASN* 1.3 58.6 + - - +
365B MET* 4.9 0.7 - - - -
366B ALA* 2.8 36.7 + - + +
372B TYR* 4.2 14.1 - - + -
387B LEU* 4.2 7.6 - - + -
423B ILE* 4.2 27.8 - - + -
425B VAL* 3.9 27.4 - - + -
451B VAL* 4.8 4.5 - - + -
507B LEU* 3.8 33.4 - - + -
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ARG* 5.3 4.2 - - - +
342B GLU* 5.7 2.0 + - - -
359B PHE 2.9 13.5 + - - +
360B ASP* 3.6 6.1 - - - +
362B LEU* 1.3 76.9 - - - +
364B ASP* 1.3 68.7 + - - +
366B ALA 4.4 8.1 + - - +
372B TYR* 4.5 4.6 + - - -
386B ARG 3.4 25.4 + - - +
387B LEU* 3.8 7.4 - - + +
388B ASN* 2.9 40.0 + - - +
390B ARG* 5.7 0.3 + - - -
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ASP* 3.0 26.2 + - - +
361B THR* 3.1 8.9 + - + +
363B ASN* 1.3 87.4 + - - +
365B MET* 1.3 63.2 + - + +
366B ALA 4.9 1.1 - - - +
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Residues in contact with MET 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B THR* 3.0 36.8 + - + +
362B LEU* 4.3 2.2 - - - +
364B ASP* 1.3 85.5 - - + +
366B ALA* 1.3 64.4 + - - +
367B PRO* 3.9 1.2 - - - +
504B LYS* 3.5 34.8 - - + +
507B LEU* 3.9 11.0 - - + -
508B GLN* 3.6 27.1 - - + +
511B LEU* 3.6 20.8 - - + +
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 2.8 25.1 + - + +
363B ASN 4.4 7.5 - - - +
364B ASP 4.9 1.0 - - - +
365B MET* 1.3 76.0 - - - +
367B PRO* 1.3 78.0 - - + +
368B GLU* 3.7 2.8 + - - +
370B ALA* 4.1 1.6 - - + -
372B TYR* 3.3 20.0 - - + +
423B ILE* 3.8 20.4 - - + -
511B LEU* 4.5 5.1 - - + +
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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