Contacts of the helix formed by residues 463 - 480 (chain A) in PDB entry 3GVU
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 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ILE* 3.8 21.3 - - - +
455A GLU* 4.8 3.1 + - - +
461A THR* 5.5 4.7 - - - -
462A PHE* 1.3 76.5 - - - +
464A ILE* 1.3 67.3 + - - +
465A LYS* 2.8 23.1 + - - +
466A SER* 2.9 27.3 + - - -
467A ASP 3.1 5.4 + - - -
526A PRO* 5.1 1.2 - - - +
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A MET* 4.4 5.4 - - + -
400A LEU* 5.0 0.7 - - + -
401A GLU* 3.7 51.4 - - + +
405A PHE 3.7 22.4 - - - +
406A ILE* 3.7 7.9 - - + +
463A SER* 1.3 75.5 - - - +
465A LYS* 1.3 74.9 + - + +
467A ASP* 3.1 21.5 + - - +
468A VAL* 3.0 25.5 + - - +
532A PHE* 3.8 18.8 - - + -
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU* 5.2 1.0 + - - -
463A SER* 2.8 12.4 + - - +
464A ILE* 1.3 90.5 - - + +
466A SER* 1.3 59.0 + - - +
468A VAL* 3.2 8.0 + - + +
469A TRP 3.2 13.3 + - - -
526A PRO* 3.3 43.5 - - + +
527A ALA* 4.6 8.1 - - - +
529A ARG* 2.7 46.6 + - + +
530A PRO 3.0 23.2 + - - +
531A SER* 3.3 12.7 - - - +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ILE* 5.2 0.3 - - - +
451A TRP 4.9 1.0 - - - +
453A ALA* 3.7 13.2 + - - +
455A GLU* 3.7 6.5 + - - -
456A SER* 3.4 23.5 + - - -
461A THR 4.5 0.2 - - - -
462A PHE* 3.4 15.3 - - - +
463A SER* 2.9 36.3 + - - -
465A LYS* 1.3 72.3 - - - +
467A ASP* 1.3 67.3 + - - +
469A TRP* 3.3 4.7 + - - +
470A ALA* 3.1 20.8 + - - +
529A ARG* 3.8 8.0 - - - +
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Residues in contact with ASP 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A MET* 3.6 10.4 - - + +
406A ILE* 3.4 16.2 - - - +
407A HIS* 2.6 34.5 + - - +
408A ARG* 2.8 30.2 + - - -
409A ASP 4.4 0.7 + - - -
410A LEU* 3.9 5.5 + - + +
463A SER 3.1 6.6 + - - +
464A ILE* 3.1 15.4 + - - +
466A SER* 1.3 78.7 + - - +
468A VAL* 1.3 56.2 + - - +
470A ALA* 3.1 8.5 + - - +
471A PHE* 2.8 28.4 + - - +
532A PHE* 3.8 15.3 - - + -
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU* 4.9 1.3 - - - +
464A ILE 3.0 20.2 + - - +
465A LYS* 3.2 16.5 + - + +
467A ASP* 1.3 75.9 - - - +
469A TRP* 1.3 62.6 + - - +
471A PHE* 3.1 4.0 + - - +
472A GLY 3.0 17.7 + - - -
521A CYS* 3.4 33.3 - - + +
529A ARG* 4.0 9.9 - - + -
530A PRO* 3.4 30.3 - - + +
531A SER* 4.6 1.1 - - - -
532A PHE* 3.6 33.0 - - + +
535A THR* 5.0 2.2 - - - +
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Residues in contact with TRP 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LYS 4.8 1.4 + - - -
451A TRP 3.6 17.5 + - - -
452A THR 3.8 7.9 + - - -
453A ALA* 3.7 20.6 - - + -
454A PRO* 3.6 26.2 - - + -
465A LYS 3.2 6.3 + - - -
466A SER 3.4 8.7 - - - +
468A VAL* 1.3 76.9 - - - +
470A ALA* 1.3 64.4 + - - +
472A GLY 2.9 11.4 + - - -
473A VAL* 3.3 22.2 + - + +
486A TYR* 4.3 6.2 + - - -
498A LEU* 3.8 32.9 - - + +
503A ARG* 3.8 15.9 - - - -
521A CYS 3.4 11.8 + - - +
522A TRP* 3.2 54.4 + + + -
523A LYS 3.6 7.0 - - - -
529A ARG* 3.6 25.1 - - - +
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Residues in contact with ALA 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ARG 6.5 0.2 - - - -
410A LEU* 3.5 32.7 - - + +
451A TRP* 3.4 27.4 - - + +
466A SER 3.1 9.3 + - - +
467A ASP* 3.1 10.1 + - - +
469A TRP* 1.3 79.2 - - - +
471A PHE* 1.3 52.4 + - - +
473A VAL* 3.0 7.2 + - - +
474A LEU* 2.8 34.1 + - - +
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Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA* 3.8 11.7 - - + -
393A ILE* 3.5 37.2 - - + -
394A SER* 4.0 7.4 - - - -
397A MET* 5.1 0.2 - - + -
410A LEU* 3.8 13.1 - - + +
467A ASP 2.8 13.5 + - - +
468A VAL 3.1 8.0 + - - +
470A ALA* 1.3 75.4 - - - +
472A GLY* 1.3 59.5 + - - +
474A LEU* 3.2 13.7 + - + +
475A LEU* 2.8 37.0 + - + +
517A LEU* 5.1 0.2 - - + -
521A CYS* 4.2 11.9 - - - -
532A PHE* 3.7 20.9 - + + -
535A THR* 3.7 16.6 - - + -
539A PHE* 3.5 40.4 - + - -
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Residues in contact with GLY 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A VAL 3.0 6.9 + - - -
469A TRP 2.9 9.9 + - - -
471A PHE* 1.3 77.5 - - - +
473A VAL* 1.3 60.0 + - - +
475A LEU* 3.3 8.5 + - - +
476A TRP 3.1 17.3 + - - -
518A MET* 3.7 7.3 - - - +
521A CYS* 3.8 17.9 - - - -
522A TRP* 3.4 24.1 - - - -
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LYS 3.6 24.5 - - - +
451A TRP* 3.5 28.5 - - + +
469A TRP* 3.7 20.6 - - + +
470A ALA 3.0 7.2 + - - +
472A GLY* 1.3 74.8 - - - +
474A LEU* 1.3 63.8 + - - +
476A TRP* 3.0 6.0 + - - +
477A GLU* 2.9 21.1 + - - +
485A PRO* 3.8 24.5 - - + -
486A TYR* 4.9 2.2 - - - +
504A MET* 4.2 7.6 - - + -
522A TRP* 3.5 25.1 - - + +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.6 3.8 - - + -
393A ILE* 3.7 18.6 - - + -
410A LEU* 3.8 20.0 - - + -
411A ALA* 3.5 33.2 - - - +
412A ALA* 3.7 12.6 - - - +
415A CYS* 4.0 11.4 - - - -
451A TRP* 4.5 0.4 - - - -
470A ALA 2.8 13.4 + - - +
471A PHE* 3.3 17.9 - - + +
473A VAL* 1.3 76.9 - - - +
475A LEU* 1.3 57.2 + - - +
477A GLU* 3.0 16.6 + - - +
478A ILE* 2.9 50.3 + - + +
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Residues in contact with LEU 475 (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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390A ALA* 4.1 26.2 - - + -
471A PHE* 2.8 29.0 + - + +
472A GLY* 3.5 6.1 - - - +
473A VAL 3.2 0.2 - - - -
474A LEU* 1.3 75.3 - - - +
476A TRP* 1.3 57.4 + - - +
478A ILE* 3.3 9.6 + - + +
479A ALA* 2.8 28.2 + - - +
514A VAL* 3.9 35.4 - - + +
517A LEU* 4.3 7.9 - - + -
518A MET* 3.9 26.5 - - + +
521A CYS* 5.7 0.7 - - - -
539A PHE* 4.1 20.6 - - + -
1002A STI 4.7 5.4 - - + -
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Residues in contact with TRP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLY 3.1 11.7 + - - +
473A VAL* 3.0 13.6 + - - +
475A LEU* 1.3 73.2 - - - +
477A GLU* 1.3 68.0 + - - +
479A ALA* 3.3 0.9 + - - -
480A THR* 2.9 47.9 + - + +
483A MET* 3.4 47.6 - - + -
484A SER 3.6 14.1 - - - -
485A PRO* 3.6 21.1 - - + -
487A PRO* 3.9 11.0 - - + -
504A MET* 3.4 36.5 - - + +
505A GLU 3.5 20.1 + - - -
507A PRO* 3.7 18.3 - - + +
518A MET* 3.6 23.5 - - - +
522A TRP* 4.1 3.8 - + + -
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Residues in contact with GLU 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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370A LEU* 3.6 17.8 - - - +
373A LEU* 4.0 2.2 - - - +
412A ALA* 3.0 41.8 + - + +
413A ARG* 4.8 0.9 + - - -
451A TRP* 2.9 43.2 + - + +
473A VAL 2.9 15.7 + - - +
474A LEU* 3.2 13.3 - - - +
476A TRP* 1.3 78.1 - - + +
478A ILE* 1.3 62.4 + - - +
480A THR* 3.2 7.2 + - - -
481A TYR 3.1 4.0 + - - -
482A GLY* 2.8 32.7 + - - +
483A MET 4.2 12.8 - - - +
485A PRO* 4.6 6.0 - - + +
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.3 6.1 - - + -
373A LEU* 4.0 18.6 - - + +
386A LEU* 3.8 53.2 - - + +
389A MET* 4.5 6.3 - - + -
390A ALA* 4.0 30.7 - - + +
393A ILE* 4.1 9.6 - - + -
471A PHE* 5.8 0.4 - - + -
474A LEU* 2.9 37.4 + - + +
475A LEU* 3.5 17.0 - - + +
476A TRP 3.3 0.2 - - - -
477A GLU* 1.3 75.2 - - + +
479A ALA* 1.3 63.1 + - - +
481A TYR* 3.1 13.0 + - - -
1002A STI 5.0 3.1 - - + -
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 5.2 0.2 - - - -
475A LEU 2.8 20.6 + - - +
476A TRP 3.3 4.9 + - - +
478A ILE* 1.3 72.7 - - - +
480A THR* 1.3 59.1 + - - +
481A TYR* 3.5 3.3 + - - -
507A PRO* 3.8 25.3 - - + +
508A GLU 4.4 2.9 - - - +
510A CYS* 4.3 3.8 - - + +
518A MET* 3.9 10.3 - - + -
1002A STI 3.7 51.7 - - + -
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Residues in contact with THR 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 4.8 2.8 + - - -
476A TRP* 2.9 47.6 + - + +
477A GLU* 3.2 3.5 + - - -
478A ILE 3.2 0.2 - - - -
479A ALA* 1.3 74.4 - - - +
481A TYR* 1.3 72.6 + - - +
482A GLY 3.3 0.2 + - - -
483A MET* 3.2 46.4 + - + +
507A PRO* 3.6 30.1 - - + -
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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
------------------------------------------------------------
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