Contacts of the helix formed by residues 369 - 384 (chain H) in PDB entry 6IY6
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 SER 369 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H MET* 4.9 0.2 - - - +
367H ASP 3.1 8.6 + - - -
368H LEU* 1.3 72.3 - - - +
370H THR* 1.3 60.2 + - - +
371H PRO* 3.6 10.9 - - - +
372H ASN* 2.9 49.4 + - - +
373H GLU* 3.0 11.6 + - - +
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Residues in contact with THR 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368H LEU 3.8 0.8 + - - -
369H SER* 1.3 69.1 - - - +
371H PRO* 1.4 69.2 - - - +
373H GLU* 3.4 21.5 + - - +
374H LYS* 3.2 20.1 + - - +
423H GLU* 6.2 4.5 - - + -
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Residues in contact with PRO 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H SER* 3.3 15.5 - - - +
370H THR* 1.4 94.8 - - - +
372H ASN* 1.3 58.6 + - - +
374H LYS* 3.2 10.6 + - + +
375H LEU* 3.0 27.2 + - - +
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Residues in contact with ASN 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H LEU* 4.1 9.0 - - + +
360H VAL* 3.5 33.5 - - - +
362H MET* 3.7 22.2 - - - +
368H LEU* 3.9 16.8 - - + +
369H SER* 2.9 26.8 + - - +
371H PRO* 1.3 75.4 - - - +
373H GLU* 1.3 55.9 - - - +
375H LEU* 3.2 9.1 + - - +
376H LEU* 2.7 38.3 + - - +
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Residues in contact with GLU 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H ASP* 5.7 0.2 - - - +
368H LEU* 3.9 29.3 - - + +
369H SER 3.0 14.1 + - - +
370H THR* 3.4 24.4 + - - +
372H ASN* 1.3 75.8 - - - +
374H LYS* 1.3 61.6 + - - +
376H LEU* 3.9 5.5 - - - +
377H GLY 3.2 17.8 + - - -
389H TYR* 4.1 4.2 + - - -
394H TYR* 4.3 3.5 + - - -
417H ASP* 4.2 2.4 - - - +
419H PHE* 3.6 32.8 - - + -
422H GLY* 3.0 16.0 - - - +
423H GLU* 5.7 0.2 - - - -
424H GLU* 3.3 31.1 + - - +
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Residues in contact with LYS 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H THR 3.2 9.0 + - - +
371H PRO* 3.2 14.3 + - + +
373H GLU* 1.3 76.8 - - - +
375H LEU* 1.3 64.2 + - - +
377H GLY* 3.6 1.6 + - - -
378H HIS* 3.4 17.2 + - - +
421H ARG 5.3 10.7 + - - +
422H GLY* 3.4 17.3 + - - +
423H GLU* 4.3 21.2 + - + +
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Residues in contact with LEU 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F LYS* 5.5 10.5 - - + +
355H LEU* 3.6 22.4 - - + -
358H ALA* 4.8 7.4 - - + +
360H VAL* 3.8 22.4 - - + -
371H PRO 3.0 13.2 + - - +
372H ASN* 3.2 11.6 + - - +
374H LYS* 1.3 73.0 - - - +
376H LEU* 1.3 58.4 + - - +
378H HIS* 2.8 36.1 + - + +
379H LEU* 2.9 35.2 + - + -
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Residues in contact with LEU 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346H LEU* 4.9 1.3 - - + -
351H ALA* 3.8 34.5 - - + +
354H MET* 4.3 27.4 - - + -
355H LEU* 4.2 11.4 - - + -
368H LEU* 3.7 29.2 - - + -
372H ASN 2.7 21.2 + - - +
373H GLU* 3.9 3.4 - - - +
375H LEU* 1.3 71.4 - - - +
377H GLY* 1.3 51.7 + - - +
379H LEU* 3.2 10.1 + - + +
380H VAL* 2.9 41.5 + - + +
389H TYR* 3.4 24.5 - - + +
391H LEU* 4.2 7.6 - - + -
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Residues in contact with GLY 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H GLU 3.2 9.9 + - - -
374H LYS 3.9 0.2 - - - -
375H LEU 3.2 1.0 - - - -
376H LEU* 1.3 75.9 - - - +
378H HIS* 1.3 50.4 + - - +
380H VAL* 3.3 3.8 + - - +
381H LYS* 2.9 33.5 + - - +
386H THR 4.7 2.1 - - - +
387H ASP* 6.1 0.3 - - - -
389H TYR* 3.7 17.7 + - - -
421H ARG 5.8 0.4 - - - -
422H GLY* 3.8 27.8 - - - -
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Residues in contact with HIS 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374H LYS 3.4 11.1 + - - +
375H LEU* 2.8 23.6 + - + +
377H GLY* 1.3 67.7 - - - +
379H LEU* 1.3 61.2 + - + +
381H LYS* 3.2 14.2 + - + +
382H GLU* 2.8 66.3 + - + +
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Residues in contact with LEU 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F LYS* 6.2 0.4 - - - +
354H MET* 3.7 48.9 - - + +
355H LEU* 4.2 9.4 - - + -
358H ALA* 3.9 13.2 - - + -
375H LEU* 2.9 42.4 + - + +
376H LEU* 3.4 9.0 - - - +
378H HIS* 1.3 84.8 - - + +
380H VAL* 1.3 61.4 + - - +
382H GLU* 3.3 12.1 + - - +
383H LYS* 3.1 23.9 + - - +
201J ILE* 5.3 0.3 - - - +
202J GLN* 4.2 21.3 - - - +
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Residues in contact with VAL 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H LEU* 3.5 27.8 - - + -
346H LEU* 3.6 28.3 - - + -
354H MET* 4.3 8.1 - - + -
376H LEU* 2.9 20.1 + - + +
377H GLY 3.5 7.6 - - - +
379H LEU* 1.3 73.3 - - - +
381H LYS* 1.3 59.5 + - - +
383H LYS 3.3 0.3 + - - -
384H TYR* 2.9 32.9 + - + +
385H ASP 3.4 2.9 + - - -
386H THR* 3.8 18.4 - - + +
389H TYR* 3.9 29.2 - - + -
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Residues in contact with LYS 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335H GLU* 4.0 8.8 + - - -
338H LYS* 3.5 26.9 - - - +
377H GLY 2.9 14.7 + - - +
378H HIS* 3.2 18.4 + - + +
380H VAL* 1.3 73.8 - - - +
382H GLU* 1.3 65.8 + - + +
385H ASP* 2.9 57.4 + - - +
386H THR 3.9 11.9 + - - +
387H ASP* 3.9 22.2 + - - +
198J LYS* 5.0 0.7 + - - -
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Residues in contact with GLU 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378H HIS* 2.8 49.9 + - + +
379H LEU* 3.4 14.6 - - - +
380H VAL 3.3 0.2 - - - -
381H LYS* 1.3 75.4 - - + +
383H LYS* 1.3 56.6 + - - +
198J LYS* 2.9 32.0 + - - +
201J ILE* 3.7 25.3 - - + +
202J GLN* 4.0 18.5 + - - -
104L HIS* 5.3 8.1 + - - -
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Residues in contact with LYS 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354H MET* 5.4 5.4 - - + -
379H LEU 3.1 13.4 + - - +
380H VAL* 3.3 0.8 + - - -
382H GLU* 1.3 77.6 - - - +
384H TYR* 1.3 87.3 + - + +
385H ASP* 3.5 0.6 - - - +
119J LEU* 3.2 49.2 - - + +
121J ASP* 2.6 38.2 + - - +
123J VAL* 3.5 21.8 - - + +
125J ASN* 4.6 1.7 + - - -
198J LYS* 3.2 46.6 + - - +
200J SER 4.7 0.4 - - - +
201J ILE* 3.3 15.5 - - + -
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Residues in contact with TYR 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H LEU* 4.4 3.7 - - + +
344H LEU* 3.4 38.8 - - + +
346H LEU* 4.4 20.0 - - + +
354H MET* 5.4 4.3 - - + -
380H VAL* 2.9 17.5 + - + +
383H LYS* 1.3 99.0 - - + +
385H ASP* 1.3 71.1 + - - +
386H THR* 3.8 15.7 - - + -
602H PO4 5.1 1.5 + - - -
121J ASP* 2.8 30.4 + - - +
123J VAL* 3.5 21.5 - - + -
125J ASN* 4.2 6.0 - - - +
155J HIS* 4.4 4.2 - - - -
186J THR* 3.9 19.7 - - + -
188J ILE* 3.6 27.4 - - + +
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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