Contacts of the helix formed by residues 468 - 485 (chain A) in PDB entry 3IAD
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 ASN 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU 3.6 1.0 + - - -
467A ASP* 1.3 80.2 + - + +
469A TYR* 1.3 64.9 + - - +
470A SER* 3.1 31.4 + - - +
471A ASP* 3.1 33.1 + - - +
472A ARG* 3.1 26.7 + - - +
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Residues in contact with TYR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU* 5.9 2.2 - - - -
425A SER* 6.0 0.9 - - - -
428A LYS* 3.8 23.6 - - + +
429A MET* 3.7 30.8 - - + +
432A ASP* 2.9 27.2 + - - -
468A ASN* 1.3 72.9 - - - +
470A SER* 1.3 60.2 + - - +
472A ARG* 3.6 12.9 - - + +
473A ILE* 2.8 60.3 + - + +
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ASN* 3.1 18.0 + - - +
469A TYR* 1.3 82.5 - - - +
471A ASP* 1.3 62.1 + - - +
473A ILE* 3.2 9.7 - - - +
474A GLN* 2.9 46.5 + - - +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A MET* 3.2 38.6 - - - +
465A LEU 5.6 0.9 - - - +
466A LEU* 4.1 18.9 - - + +
467A ASP* 4.9 4.2 + - - +
468A ASN* 3.1 28.4 + - - +
470A SER* 1.3 77.9 - - - +
472A ARG* 1.3 62.2 + - - +
474A GLN* 3.6 5.9 + - - +
475A VAL* 3.3 29.3 + - - +
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Residues in contact with ARG 472 (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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350A VAL* 2.9 33.0 + - - +
351A PHE* 3.7 14.5 - - + +
352A THR* 4.2 8.9 - - - +
355A GLU* 2.9 41.8 + - - +
466A LEU* 2.9 48.5 + - + +
467A ASP 5.2 0.4 - - - -
468A ASN* 3.1 20.9 + - - +
469A TYR* 3.6 13.5 - - + +
471A ASP* 1.3 77.8 - - - +
473A ILE* 1.3 60.5 + - - +
475A VAL* 3.6 1.2 + - - +
476A LEU* 3.4 27.6 + - + +
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Residues in contact with ILE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A MET* 3.9 35.4 - - + +
432A ASP* 4.0 17.3 - - + +
433A ILE* 4.4 8.7 - - + -
469A TYR* 2.8 55.1 + - + +
470A SER* 3.2 17.7 - - - +
472A ARG* 1.3 71.8 - - - +
474A GLN* 1.3 61.7 + - + +
476A LEU* 3.2 12.4 + - + -
477A GLN* 2.8 49.7 + - + +
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Residues in contact with GLN 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 6.3 0.4 - - + -
448A ASP* 2.7 42.7 + - + +
449A LEU* 5.7 0.7 - - - -
452A MET* 3.8 27.9 - - - +
470A SER* 2.9 31.8 + - - +
471A ASP* 3.9 8.8 - - - +
472A ARG 3.4 0.2 - - - -
473A ILE* 1.3 77.9 - - + +
475A VAL* 1.3 60.4 + - - +
477A GLN* 3.5 19.6 - - - +
478A ASN* 2.9 40.5 + - - +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 4.9 6.5 - - + -
351A PHE* 4.0 22.2 - - + -
449A LEU* 5.2 3.6 - - + -
452A MET* 4.5 10.5 - - + -
464A LEU* 4.8 1.8 - - + -
466A LEU* 3.9 23.6 - - + -
471A ASP 3.3 17.8 + - - +
472A ARG 3.9 5.2 - - - +
473A ILE 3.3 0.6 - - - -
474A GLN* 1.3 76.7 - - - +
476A LEU* 1.3 57.9 + - - +
478A ASN* 3.4 3.7 + - - -
479A MET* 2.8 29.8 + - + +
550A TRP* 3.8 25.4 - - + -
553A LEU* 4.4 17.3 - - + -
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.5 2.9 - - + -
351A PHE* 3.4 40.4 - - + -
355A GLU* 4.2 32.3 - - + +
358A ALA* 5.6 0.2 - - + -
359A ALA* 4.4 14.8 - - + -
429A MET* 4.9 4.0 - - - -
433A ILE* 4.1 20.3 - - + +
472A ARG* 3.4 16.1 + - + +
473A ILE* 3.2 20.9 + - + +
475A VAL* 1.3 73.0 - - - +
477A GLN* 1.3 65.1 - - - +
479A MET* 3.5 14.3 - - - +
480A VAL* 3.2 30.1 + - - +
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Residues in contact with GLN 477 (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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432A ASP* 3.0 36.1 - - - +
433A ILE* 4.1 14.6 - - + +
436A ALA* 3.7 21.4 - - + +
437A THR* 5.7 1.0 - - - +
445A LEU* 4.2 19.2 - - + +
448A ASP* 5.7 0.2 + - - -
473A ILE* 2.8 29.6 + - + +
474A GLN* 3.5 33.2 - - - +
476A LEU* 1.3 74.7 - - - +
478A ASN* 1.3 58.0 + - - +
480A VAL* 4.1 1.9 - - - +
481A HIS* 3.1 27.9 + - - +
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Residues in contact with ASN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 3.2 47.2 + - - +
448A ASP* 5.0 1.4 - - - +
449A LEU* 3.7 39.1 - - + +
474A GLN* 2.9 33.7 + - - +
475A VAL 3.9 2.7 - - - +
477A GLN* 1.3 74.1 - - - +
479A MET* 1.3 60.3 + - - +
481A HIS* 3.6 4.9 - - - +
482A CYS* 2.8 36.7 + - - -
546A LEU* 4.1 14.2 - - - +
550A TRP* 4.3 5.2 - - + -
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Residues in contact with MET 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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338A THR* 4.2 13.5 - - + +
341A LEU* 3.4 26.3 - - + +
342A LEU* 3.5 43.1 - - + -
347A LEU* 3.4 33.2 - - + -
351A PHE* 4.4 9.4 - - + -
359A ALA* 5.2 2.0 - - - -
475A VAL* 2.8 17.7 + - + +
476A LEU* 3.5 14.8 - - + +
477A GLN 3.3 0.4 - - - -
478A ASN* 1.3 77.4 - - - +
480A VAL* 1.3 57.7 + - - +
482A CYS* 3.4 6.1 + - - +
483A ALA* 3.0 22.5 + - - +
550A TRP* 3.8 21.0 - - + -
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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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334A VAL* 4.1 10.6 - - + +
338A THR* 3.8 15.9 - - + +
359A ALA* 4.0 15.5 - - + +
362A ALA 5.4 0.4 - - - -
363A SER* 3.6 31.0 - - - +
366A HIS* 5.5 3.6 - - + -
433A ILE* 3.7 28.5 - - + -
437A THR* 4.2 16.2 - - + -
476A LEU 3.2 15.5 + - - +
477A GLN 4.2 1.8 - - - +
479A MET* 1.3 73.9 - - + +
481A HIS* 1.3 60.5 + - - +
483A ALA* 3.2 2.4 + - - +
484A ASP* 2.8 26.2 + - + +
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Residues in contact with HIS 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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436A ALA 4.3 11.2 + - - +
437A THR* 4.8 12.3 + - + +
438A ASP 5.5 0.4 - - - -
439A MET* 3.7 23.3 - - + +
442A HIS* 3.0 34.0 + - + +
445A LEU* 3.9 24.0 - - + -
477A GLN 3.1 18.9 + - - +
478A ASN* 3.6 6.5 - - - +
479A MET 3.3 0.2 - - - -
480A VAL* 1.3 74.4 - - - +
482A CYS* 1.3 59.0 + - - +
484A ASP* 3.0 11.1 + - - +
485A LEU* 2.9 50.3 + - + +
546A LEU* 3.5 28.9 - - + -
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Residues in contact with CYS 482 (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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341A LEU* 4.1 4.5 - - + -
449A LEU* 5.5 0.2 - - - -
478A ASN* 2.8 28.8 + - - +
479A MET* 3.4 6.1 - - - +
481A HIS* 1.3 72.4 - - - +
483A ALA* 1.3 62.5 + - - +
485A LEU 3.1 5.4 - - - -
486A SER 3.1 18.0 + - - -
546A LEU* 3.9 32.3 - - - -
547A TRP* 3.3 34.3 - - + -
550A TRP* 4.1 33.2 - - - -
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Residues in contact with ALA 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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268A TRP* 5.4 0.2 - - - -
330A HIS* 5.5 0.2 - - - -
333A ASP* 4.5 1.6 - - - +
334A VAL* 3.6 27.6 - - + +
337A SER* 3.9 13.7 - - - -
338A THR* 3.4 26.7 - - - +
341A LEU* 4.2 3.7 - - + +
479A MET 3.0 10.6 + - - +
480A VAL 3.2 9.2 + - - +
482A CYS* 1.3 74.4 - - - +
484A ASP* 1.3 61.1 + - - +
486A SER* 2.8 26.6 + - - -
487A ASN* 5.7 0.3 - - - +
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Residues in contact with ASP 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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325A TYR* 4.2 13.3 + - - -
330A HIS* 3.1 12.1 + - - -
334A VAL* 3.9 7.1 - - + +
366A HIS* 3.3 13.6 + - - -
437A THR* 4.0 21.0 - - + +
439A MET* 4.5 10.6 - - - +
480A VAL 2.8 16.8 + - - +
481A HIS* 3.0 16.0 + - - +
483A ALA* 1.3 73.6 - - - +
485A LEU* 1.3 66.9 + - + +
486A SER 3.4 2.3 + - - -
487A ASN* 4.7 2.9 + - - -
620A ZN 2.2 35.6 - - - -
621A MG 4.3 4.5 - - - -
901A 15X 5.0 3.7 - - - +
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Residues in contact with LEU 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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439A MET* 3.6 25.1 - - + -
442A HIS* 4.2 6.3 - - - +
481A HIS* 2.9 48.4 + - + +
482A CYS 3.1 5.1 + - - +
484A ASP* 1.3 80.1 - - + +
486A SER* 1.3 57.4 + - - +
487A ASN* 3.7 2.5 - - - +
488A PRO* 3.9 5.5 - - - +
538A PHE* 4.2 16.8 - - + -
542A ILE* 4.3 13.9 - - + -
543A VAL* 3.8 17.1 - - + +
546A LEU* 3.7 17.7 - - + -
547A TRP* 3.2 14.9 + - - -
604A PHE* 4.7 0.2 - - + -
901A 15X 3.7 25.4 - - + -
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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
------------------------------------------------------------
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