Contacts of the helix formed by residues 475 - 489 (chain A) in PDB entry 3M6L
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 ASP 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A PHE 5.6 1.0 - - - +
336A LYS 5.4 1.8 - - - +
338A LEU* 4.7 3.4 - - + -
340A THR* 4.0 11.4 - - - +
473A PRO* 3.3 3.5 + - - +
474A ALA* 1.3 84.4 - - - +
476A GLY* 1.3 66.1 + - - +
477A VAL* 3.2 14.0 + - - +
478A GLU* 2.8 28.6 + - - +
479A ASN* 3.0 21.5 + - - +
502A LEU* 5.3 1.8 - - + +
503A LYS 4.0 13.9 - - - +
504A ALA* 3.9 9.3 - - + +
505A LEU* 3.0 38.7 + - + +
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Residues in contact with GLY 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PHE* 3.4 36.9 + - - +
336A LYS 5.2 2.0 + - - -
338A LEU* 3.6 10.0 - - - +
343A SER* 3.7 19.7 - - - -
475A ASP* 1.3 77.9 - - - +
477A VAL* 1.3 56.9 + - - +
479A ASN* 3.3 2.0 + - - +
480A VAL* 2.9 24.1 + - - +
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ASP* 4.9 1.6 - - - +
333A PHE* 3.8 8.6 - - + +
334A LYS* 3.6 39.9 - - + +
475A ASP* 3.2 14.1 + - - +
476A GLY* 1.3 70.8 - - - +
478A GLU* 1.3 68.9 + - + +
480A VAL* 3.2 8.5 + - - +
481A LYS* 3.0 53.2 + - - +
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Residues in contact with GLU 478 (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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472A ARG 4.3 0.9 - - - +
473A PRO* 3.5 14.2 - - + +
474A ALA* 2.7 34.4 + - - +
475A ASP* 2.8 24.0 + - - +
477A VAL* 1.3 80.2 - - + +
479A ASN* 1.3 55.2 + - - +
481A LYS* 3.3 2.7 + - + +
482A ALA* 2.8 31.2 + - - +
505A LEU* 3.8 3.1 - - - +
513A VAL* 3.8 20.7 - - + +
518A TYR* 2.6 32.3 + - - +
534A GLY 5.2 0.3 + - - -
558A SER* 2.6 21.6 + - - -
560A PRO* 3.5 19.0 - - + +
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Residues in contact with ASN 479 (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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340A THR* 3.4 4.4 + - + -
343A SER* 2.7 26.6 + - - +
344A ASN* 3.1 44.0 + - - +
347A ILE* 3.5 9.3 - - + +
473A PRO* 3.5 19.4 - - + +
475A ASP 3.0 14.8 + - - +
476A GLY 3.4 8.5 - - - +
477A VAL 3.2 0.2 - - - -
478A GLU* 1.3 75.6 - - - +
480A VAL* 1.4 62.0 + - - +
482A ALA* 3.4 3.6 + - - +
483A TRP* 3.2 25.1 + - - -
495A PHE* 4.2 7.8 - - - -
497A LEU* 4.2 3.6 - - - +
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Residues in contact with VAL 480 (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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330A TYR* 3.5 31.1 - - + -
331A PRO 3.7 21.1 - - - +
333A PHE* 3.8 7.9 - - + -
347A ILE* 3.5 24.0 - - + -
476A GLY 2.9 17.3 + - - +
477A VAL* 3.6 10.1 - - - +
479A ASN* 1.4 74.5 - - - +
481A LYS* 1.3 65.9 + - + +
483A TRP* 3.0 6.2 + - - +
484A GLN* 3.0 34.6 + - - +
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Residues in contact with LYS 481 (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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477A VAL* 3.0 42.1 + - + +
478A GLU* 3.8 2.2 - - - +
480A VAL* 1.3 76.0 - - + +
482A ALA* 1.3 61.4 + - - +
484A GLN* 3.3 18.7 + - - +
485A ILE* 3.1 31.1 + - + +
508A PRO* 4.1 16.0 - - - +
512A ASP* 2.9 40.1 + - - +
513A VAL* 3.6 25.5 - - + +
518A TYR* 5.7 1.6 + - - -
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Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 3.5 44.9 - - + -
473A PRO* 5.4 3.4 - - + -
478A GLU 2.8 17.0 + - - +
479A ASN* 3.5 9.0 - - - +
480A VAL 3.2 0.2 - - - -
481A LYS* 1.3 77.1 - - - +
483A TRP* 1.3 56.9 + - - +
485A ILE* 3.2 4.0 + - - +
486A ALA* 2.9 28.4 + - - +
495A PHE* 3.7 13.5 - - + -
513A VAL* 4.1 3.8 - - + +
560A PRO* 6.2 0.7 - - + -
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Residues in contact with TRP 483 (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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330A TYR* 4.1 17.3 - - + +
344A ASN* 2.9 21.2 - - - +
347A ILE* 3.5 20.2 - - + +
348A LEU* 3.7 20.4 - - + +
351A LEU* 3.6 21.8 - - + -
358A PHE* 4.0 15.5 - + - -
410A PHE* 5.2 0.2 - - + -
436A PHE* 3.6 50.9 - + + -
438A ILE* 3.9 9.9 - - + -
479A ASN* 3.2 28.2 + - - +
480A VAL 3.0 9.0 + - - +
482A ALA* 1.3 77.9 - - - +
484A GLN* 1.3 65.2 + - - +
486A ALA* 4.2 2.2 - - + -
487A LEU* 2.9 38.3 + - + +
495A PHE* 3.6 26.0 - + - -
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Residues in contact with GLN 484 (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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328A ILE 5.1 1.8 + - - -
330A TYR* 3.4 42.1 - - + -
480A VAL* 3.0 19.3 + - - +
481A LYS* 3.3 27.4 + - - +
483A TRP* 1.3 75.4 - - - +
485A ILE* 1.3 64.1 + - + +
487A LEU* 3.7 2.9 + - - +
488A ASN* 3.2 28.9 + - - +
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Residues in contact with ILE 485 (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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469A LEU* 4.1 10.1 - - + -
471A PHE* 3.9 17.9 - - + -
481A LYS* 3.1 18.3 + - + +
482A ALA 3.6 4.3 - - - +
483A TRP 3.1 0.2 - - - -
484A GLN* 1.3 78.6 - - + +
486A ALA* 1.3 58.2 + - - +
488A ASN* 3.1 6.7 + - - +
489A ALA* 2.9 28.4 + - + +
513A VAL* 3.7 18.2 - - + +
514A LYS* 3.5 41.1 - - + +
564A LEU* 4.1 18.8 - - + -
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Residues in contact with ALA 486 (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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434A LYS* 2.9 25.8 + - - -
436A PHE* 3.9 11.4 - - + -
471A PHE* 4.3 1.8 - - + -
482A ALA 2.9 17.2 + - - +
483A TRP* 3.2 4.9 + - + +
485A ILE* 1.3 77.6 - - - +
487A LEU* 1.4 57.3 + - - +
489A ALA* 3.2 9.0 + - - +
491A ILE 4.7 0.5 - - - +
493A SER* 3.4 28.9 + - - +
495A PHE* 3.6 22.2 - - + -
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Residues in contact with LEU 487 (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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325A PHE* 3.4 61.6 - - + -
328A ILE* 4.7 0.9 - - + -
330A TYR* 3.3 26.9 - - - +
351A LEU* 3.8 17.7 - - + -
355A LEU* 4.7 7.4 - - + -
358A PHE* 5.1 3.6 - - + -
408A LEU* 5.1 3.1 - - + -
434A LYS* 3.1 14.8 + - - +
436A PHE* 3.7 25.8 - - + -
483A TRP* 2.9 28.8 + - + +
484A GLN* 4.2 3.8 - - - +
486A ALA* 1.4 76.0 - - - +
488A ASN* 1.3 59.6 + - - +
489A ALA 4.3 0.2 - - - +
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Residues in contact with ASN 488 (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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325A PHE* 3.9 24.6 - - - +
326A ASN* 4.5 13.1 + - - +
484A GLN* 3.2 19.2 + - - +
485A ILE* 3.1 6.3 + - - +
487A LEU* 1.3 78.0 - - - +
489A ALA* 1.3 67.0 + - - +
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Residues in contact with ALA 489 (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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434A LYS* 2.8 24.6 + - - +
469A LEU* 4.1 22.0 - - + -
485A ILE* 2.9 17.6 + - + +
486A ALA* 3.2 10.5 + - - +
488A ASN* 1.3 83.1 - - - +
490A ASP* 1.3 61.1 + - - +
491A ILE* 3.4 17.5 - - + +
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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