Contacts of the helix formed by residues 353 - 370 (chain A) in PDB entry 3I5Y
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 ALA 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LYS* 3.5 3.0 - - + +
352A PHE* 1.3 84.7 - - - +
354A ASN* 1.3 64.1 + - - +
356A ILE* 2.9 33.3 + - + +
357A PHE* 3.7 8.7 - - + -
554A GLU* 4.5 0.6 + - - -
558A THR* 4.0 24.1 + - + -
561A VAL* 3.9 34.8 - - + -
562A LEU* 5.3 3.4 - - + -
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Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.4 17.2 - - - +
350A GLU* 4.2 4.9 - - - +
351A LYS* 3.4 38.7 + - - +
352A PHE 3.1 0.6 - - - -
353A ALA* 1.3 78.8 - - - +
355A SER* 1.3 56.8 + - - +
357A PHE* 3.0 15.6 + - - -
358A ALA 2.9 23.2 + - - -
505A TYR* 3.5 8.3 + - + -
506A GLU* 3.4 14.6 + - - -
507A PRO* 3.3 37.0 - - + +
512A LYS* 5.3 2.6 + - - -
561A VAL* 5.1 3.8 - - - +
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL 5.1 0.2 + - - -
349A SER* 3.8 6.3 + - - -
351A LYS 4.2 0.2 + - - -
352A PHE* 3.0 17.6 + - - -
354A ASN* 1.3 74.5 - - - +
356A ILE* 1.3 63.6 + - - +
358A ALA* 3.8 9.5 - - - +
359A ALA* 3.1 24.9 + - - +
451A ILE* 3.9 16.6 - - - +
479A PHE* 3.6 25.0 + - - +
480A ILE* 3.6 29.1 + - - -
481A CYS 4.1 0.5 + - - -
484A GLU* 4.9 0.9 + - - -
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 5.2 1.6 - - + +
353A ALA* 2.9 23.5 + - - +
355A SER* 1.3 78.9 - - - +
357A PHE* 1.3 62.3 + - + +
359A ALA* 3.8 2.3 - - - +
360A VAL* 3.1 30.2 + - + +
385A PHE* 3.9 36.8 - - + -
388A PHE* 4.1 17.9 - - + -
389A LEU* 4.7 6.4 - - + +
392A ILE* 3.5 26.5 - - + -
451A ILE* 4.1 12.3 - - + +
515A VAL* 4.5 12.1 - - + -
558A THR* 5.3 2.0 - - + -
562A LEU* 4.4 16.2 - - + -
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Residues in contact with PHE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 3.7 19.3 - - + -
354A ASN* 3.0 21.2 + - - +
356A ILE* 1.3 77.7 - - + +
358A ALA* 1.3 67.2 + - - +
360A VAL* 3.2 6.0 + - - +
361A GLU* 3.0 24.1 + - - +
505A TYR* 3.4 19.1 + - - +
507A PRO* 4.0 17.5 - - + -
511A ILE* 4.2 13.0 - - + -
512A LYS* 4.0 28.9 - - + -
515A VAL* 3.7 43.1 - - + -
516A LEU* 4.2 23.1 - - + -
561A VAL* 4.5 11.0 - - + -
562A LEU* 5.2 4.9 - - + -
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 4.4 4.3 - - + -
349A SER* 4.5 1.1 - - - +
354A ASN 2.9 10.7 + - - +
355A SER* 3.8 5.6 - - - +
357A PHE* 1.3 77.1 - - - +
359A ALA* 1.3 57.5 + - - +
361A GLU* 3.3 2.3 + - - +
362A HIS* 3.0 29.1 + - - +
479A PHE* 3.6 26.7 - - + -
505A TYR* 3.4 40.4 - - + -
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A SER 3.1 19.2 + - - +
356A ILE 3.8 2.2 - - - +
358A ALA* 1.3 75.8 - - - +
360A VAL* 1.3 63.5 + - + +
362A HIS* 3.3 1.7 + - - +
363A ILE* 3.0 33.2 + - + +
378A ILE* 4.3 11.4 - - + -
389A LEU* 5.9 0.4 - - + -
393A LEU* 5.7 1.6 - - + -
449A LEU* 5.1 0.4 - - + +
451A ILE* 3.7 26.0 - - + -
479A PHE* 4.0 23.5 - - + -
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.1 18.1 + - + +
357A PHE* 3.2 8.0 + - - +
359A ALA* 1.3 76.7 - - - +
361A GLU* 1.3 64.2 + - - +
363A ILE* 4.8 0.9 - - - -
364A LYS* 2.9 23.8 + - - +
389A LEU* 6.2 1.1 - - + -
392A ILE* 3.8 28.0 - - + -
393A LEU* 4.5 10.5 - - + -
396A GLU* 3.9 28.9 - - + +
397A PHE* 3.3 19.2 - - + -
511A ILE* 4.1 14.6 - - + -
515A VAL* 4.3 10.1 - - + -
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Residues in contact with GLU 361 (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 3.0 18.4 + - - +
358A ALA* 3.8 4.0 - - - +
360A VAL* 1.3 77.5 - - - +
362A HIS* 1.3 58.1 + - - +
364A LYS* 3.5 11.7 - - + +
365A LYS* 3.0 27.7 + - - +
505A TYR* 2.8 33.1 + - + +
506A GLU 5.2 0.2 - - - +
507A PRO* 5.1 1.0 - - - +
508A SER* 4.8 6.4 + - - -
511A ILE* 3.8 31.0 - - + +
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Residues in contact with HIS 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 6.1 1.0 - - - +
358A ALA 3.0 16.4 + - - +
359A ALA 3.5 5.2 - - - +
360A VAL 3.2 0.2 - - - -
361A GLU* 1.3 73.8 - - - +
363A ILE* 1.3 66.7 + - - +
365A LYS* 3.0 12.8 + - + +
366A GLN* 2.9 45.4 + - + +
374A TYR* 4.1 2.7 - - - -
447A GLU* 2.9 33.4 + - - -
449A LEU* 3.9 18.7 - - + +
477A VAL* 3.9 20.6 - - + +
479A PHE* 3.9 17.1 - + + -
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Residues in contact with ILE 363 (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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359A ALA 3.0 21.5 + - - +
362A HIS* 1.3 74.9 - - - +
364A LYS* 1.3 62.2 + - - +
366A GLN* 3.2 7.5 + - - +
367A ILE* 3.0 34.8 + - + +
374A TYR* 4.5 9.6 - - + -
378A ILE* 4.6 6.3 - - + -
393A LEU* 3.6 31.9 - - + -
397A PHE* 3.4 28.5 - - + -
429A ILE* 3.7 27.8 - - + -
449A LEU* 3.7 28.9 - - + -
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Residues in contact with LYS 364 (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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360A VAL* 2.9 27.5 + - - +
361A GLU* 3.5 11.2 - - + +
363A ILE* 1.3 77.8 - - - +
365A LYS* 1.3 60.8 + - - +
367A ILE* 3.6 4.9 + - - +
368A LYS* 3.3 22.2 + - - +
396A GLU* 3.6 11.7 + - - -
397A PHE* 3.4 17.2 - - + -
511A ILE* 4.7 7.2 - - + +
514A GLU* 2.7 36.6 + - - -
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Residues in contact with LYS 365 (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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361A GLU 3.0 13.3 + - - +
362A HIS* 3.0 15.1 + - + +
364A LYS* 1.3 74.9 - - - +
366A GLN* 1.3 65.6 + - + +
368A LYS* 3.7 4.9 + - - +
369A GLU* 3.1 55.6 + - + +
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Residues in contact with GLN 366 (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 HIS* 2.9 40.9 + - + +
363A ILE 3.2 5.1 + - - +
365A LYS* 1.3 80.8 - - - +
367A ILE* 1.3 60.6 + - - +
369A GLU* 4.6 13.8 + - - +
370A ARG* 2.6 74.7 + - - +
374A TYR* 3.7 37.9 - - + +
447A GLU* 4.0 12.5 + - - -
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Residues in contact with ILE 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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363A ILE* 3.0 27.6 + - + +
364A LYS* 3.8 4.9 - - - +
366A GLN* 1.3 76.4 - - - +
368A LYS* 1.3 63.0 + - - +
371A ASP* 3.1 4.2 + - - -
372A SER* 2.8 41.9 + - - +
374A TYR* 4.6 6.1 - - + -
397A PHE* 3.3 36.3 - - + -
400A ASP* 3.7 39.0 - - + +
401A LEU* 4.2 24.0 - - + -
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Residues in contact with LYS 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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364A LYS 3.3 14.8 + - - +
365A LYS* 4.0 5.8 - - - +
367A ILE* 1.3 80.7 - - - +
369A GLU* 1.3 66.4 + - + +
371A ASP* 3.4 11.3 + - - +
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Residues in contact with GLU 369 (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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365A LYS* 3.1 48.6 + - + +
366A GLN* 4.1 15.0 + - - +
368A LYS* 1.3 84.5 - - + +
370A ARG* 1.3 63.9 + - + +
371A ASP* 3.3 1.1 + - - +
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Residues in contact with ARG 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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366A GLN* 2.6 44.8 + - - +
369A GLU* 1.3 78.8 - - + +
371A ASP* 1.3 68.0 + - - +
372A SER 3.2 0.4 - - - -
373A ASN* 2.9 44.5 + - + +
374A TYR* 3.4 30.6 - - + -
446A HIS* 3.8 32.5 + - - +
447A GLU* 4.4 13.1 + - - +
475A SER* 5.4 3.8 + - - -
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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
------------------------------------------------------------
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