Contacts of the helix formed by residues 366 - 379 (chain A) in PDB entry 5KL6
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 ARG 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.6 6.4 - - - -
364A PHE* 3.6 8.6 - - - +
365A SER* 1.3 91.2 + - - +
367A SER* 1.3 65.4 + - - +
368A ASP* 3.0 37.4 + - - +
369A ARG* 3.3 34.6 + - + +
370A LEU* 3.2 18.0 + - - +
9B G 4.0 4.4 + - - -
10B G 2.8 52.7 + - - -
11B T 3.9 7.4 + - - +
1C T 5.5 0.4 + - - -
2C A 3.9 5.9 - - - +
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.6 39.5 - - - -
366A ARG* 1.3 70.5 - - - +
368A ASP* 1.3 64.5 + - - +
370A LEU* 3.3 5.6 + - - +
371A LYS* 2.9 28.1 + - - +
1C T 4.7 10.0 - - - +
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Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ARG* 3.0 48.3 + - - +
367A SER* 1.3 78.3 + - - +
369A ARG* 1.3 69.8 + - - +
371A LYS* 3.4 10.8 + - + +
372A ARG* 2.9 28.2 + - - +
375A ARG* 5.8 0.2 + - - -
1C T 3.8 35.4 - - + +
2C A 3.9 10.9 + - - +
3C C 4.6 3.8 + - - -
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE* 3.8 22.0 - - + -
365A SER* 5.8 0.9 - - - +
366A ARG* 3.3 37.9 + - + +
367A SER 3.2 0.4 - - - -
368A ASP* 1.3 92.6 + - - +
370A LEU* 1.3 64.3 + - - +
372A ARG* 3.4 45.5 + - - +
373A HIS* 3.1 23.4 + - - +
7B G 5.0 0.5 + - - -
8B G 3.6 14.2 + - - +
9B G 2.5 54.5 + - - -
10B G 3.5 12.1 + - - -
3C C 3.9 9.5 - - - +
4C C 4.2 2.4 - - - +
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.9 24.7 - - + +
354A GLN 3.4 17.7 - - - +
355A CYS* 3.8 24.0 - - + +
364A PHE* 3.7 30.1 - - + -
366A ARG 3.2 12.9 + - - +
367A SER* 3.3 8.5 + - - +
369A ARG* 1.3 76.4 - - - +
371A LYS* 1.3 63.1 + - - +
373A HIS* 3.2 4.2 + - + +
374A GLN* 3.0 54.1 + - + +
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Residues in contact with LYS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A SER 2.9 16.1 + - - +
368A ASP* 3.7 8.7 - - + +
369A ARG 3.3 0.2 - - - -
370A LEU* 1.3 76.4 - - - +
372A ARG* 1.3 63.3 + - - +
374A GLN* 3.2 23.7 + - - +
375A ARG* 3.5 29.7 + - - +
1C T 4.2 27.2 + - - -
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Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A PHE* 6.2 1.4 - - - -
368A ASP 2.9 17.6 + - - +
369A ARG* 3.4 35.8 + - - +
371A LYS* 1.3 75.5 - - - +
373A HIS* 1.3 63.3 + - - +
375A ARG* 3.2 47.8 + - - +
376A ARG* 4.3 2.4 + - - +
394A ARG* 3.4 45.3 - - + +
396A ASP* 5.3 0.6 + - - -
7B G 3.4 27.9 + - - +
8B G 2.9 48.3 + - - -
4C C 5.7 0.2 - - - +
5C C 4.5 2.2 - - - +
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Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A CYS* 3.7 10.9 - - + +
360A CYS* 3.5 5.5 - - - -
362A ARG* 3.8 17.2 - - - +
364A PHE* 3.3 33.1 - + + -
369A ARG 3.1 5.7 + - - +
370A LEU* 3.2 8.0 + - + +
372A ARG* 1.3 79.8 - - - +
374A GLN* 1.3 62.7 + - + +
376A ARG* 2.9 48.7 + - - +
377A HIS* 3.1 7.8 + + - -
501A ZN 2.0 36.8 - - - -
7B G 2.7 34.7 + - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A GLN 4.9 0.2 + - - -
355A CYS* 3.9 10.2 - - - +
356A ASP* 4.6 3.0 - - - +
357A PHE* 3.6 35.6 - - + -
370A LEU* 3.0 43.8 + - + +
371A LYS* 3.2 16.2 + - - +
373A HIS* 1.3 88.7 - - + +
375A ARG* 1.3 62.9 + - - +
377A HIS* 3.0 19.8 + - - +
378A THR* 3.2 16.8 + - + +
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ASP 5.8 0.2 + - - -
371A LYS* 3.5 29.0 + - + +
372A ARG* 3.3 41.1 - - - +
373A HIS 3.1 0.8 - - - -
374A GLN* 1.3 77.9 - - - +
376A ARG* 1.3 55.9 + - - +
378A THR* 3.5 8.1 - - - +
379A GLY* 2.8 30.0 + - - -
380A VAL* 3.7 22.8 - - + +
382A PRO* 4.0 23.9 - - - +
383A PHE* 3.7 16.7 - - - -
393A SER* 2.7 46.4 + - - -
394A ARG* 4.3 3.2 - - - +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ARG* 4.5 8.1 - - - +
372A ARG 5.0 1.6 - - - +
373A HIS* 2.9 39.7 + - - +
375A ARG* 1.3 80.4 - - - +
377A HIS* 1.3 69.7 + - + +
379A GLY* 4.1 4.0 + - - -
7B G 3.3 29.3 + - - +
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A CYS* 3.6 1.3 - - - -
357A PHE* 3.4 49.4 - + + +
358A LYS 5.4 2.7 - - - -
360A CYS* 3.9 14.4 - - + -
373A HIS* 3.1 12.0 + + - -
374A GLN* 3.0 12.8 + - - +
376A ARG* 1.3 87.4 - - + +
378A THR* 1.3 60.5 + - - +
501A ZN 2.1 36.8 - - - -
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Residues in contact with THR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PHE* 3.8 25.1 - - + -
374A GLN* 3.4 17.4 + - + +
375A ARG* 3.5 6.1 - - - -
377A HIS* 1.3 77.9 - - - +
379A GLY* 1.3 62.5 + - - +
380A VAL* 3.3 30.0 + - + +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ARG 2.8 13.2 + - - -
376A ARG 4.1 3.2 + - - -
377A HIS 3.5 2.4 - - - -
378A THR* 1.3 77.4 - - - +
380A VAL* 1.3 64.8 + - - +
381A LYS* 3.5 25.2 + - - +
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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