Contacts of the helix formed by residues 482 - 498 (chain A) in PDB entry 3NG8
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A GLN* 3.2 13.7 + - - -
480A PRO 3.5 2.5 + - - -
481A LEU* 1.3 79.2 - - - +
483A LEU* 1.3 58.7 + - - +
484A ALA* 3.7 6.8 + - - +
485A ALA* 3.0 26.7 + - - +
486A GLY* 2.9 24.4 + - - -
509A VAL* 3.9 1.2 - - - +
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Residues in contact with LEU 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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481A LEU 3.7 1.8 + - - -
482A SER* 1.3 74.1 - - - +
484A ALA* 1.3 64.4 + - - +
486A GLY* 3.2 1.6 + - - -
487A VAL* 2.9 32.6 + - + +
507A ILE* 4.4 22.2 - - + +
508A ALA* 5.0 1.8 - - - -
509A VAL* 3.8 32.7 - - + +
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Residues in contact with ALA 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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482A SER* 3.3 6.8 + - - +
483A LEU* 1.3 80.8 - - - +
485A ALA* 1.3 61.6 + - - +
487A VAL* 3.4 11.5 + - - +
488A LYS* 3.0 23.1 + - - +
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Residues in contact with ALA 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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478A GLN* 4.3 5.6 - - - +
481A LEU* 4.0 16.2 - - + -
482A SER* 3.0 23.0 + - - +
484A ALA* 1.3 74.4 - - - +
486A GLY* 1.3 66.5 + - - +
488A LYS* 3.1 10.6 + - - +
489A LEU* 3.0 26.4 + - - +
545A THR* 4.9 3.3 - - - +
547A LEU* 4.2 12.9 - - + +
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Residues in contact with GLY 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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481A LEU* 4.3 12.2 - - - +
482A SER 2.9 14.9 + - - -
483A LEU 3.5 3.6 - - - -
485A ALA* 1.3 77.5 - - - +
487A VAL* 1.3 64.2 + - - +
489A LEU* 3.2 10.5 + - - +
490A LEU* 3.2 16.1 + - - +
509A VAL* 4.4 1.8 - - - -
514A LEU* 3.4 30.4 - - - +
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Residues in contact with VAL 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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483A LEU* 2.9 28.5 + - + +
484A ALA* 3.6 13.5 - - - +
486A GLY* 1.3 75.3 - - - +
488A LYS* 1.3 62.3 + - - +
490A LEU* 3.2 14.4 + - + +
491A GLU* 2.9 28.6 + - - +
501A SER* 5.8 0.2 - - - -
507A ILE* 4.2 30.3 - - + -
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Residues in contact with LYS 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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484A ALA 3.0 14.6 + - - +
485A ALA* 3.4 13.0 - - - +
487A VAL* 1.3 74.6 - - - +
489A LEU* 1.3 65.1 + - - +
491A GLU* 3.1 9.2 + - + +
492A ILE* 3.1 34.4 + - + +
544A GLN* 4.7 12.6 + - - +
545A THR* 3.9 22.7 - - + -
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Residues in contact with LEU 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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474A ILE* 4.2 20.0 - - + -
476A THR* 4.1 16.6 - - + -
481A LEU* 4.8 2.9 - - + -
485A ALA 3.0 16.9 + - - +
486A GLY* 3.3 10.1 - - - +
488A LYS* 1.3 77.1 - - - +
490A LEU* 1.3 58.7 + - - +
492A ILE* 3.3 1.1 + - - -
493A LEU* 2.9 31.0 + - - +
514A LEU* 4.3 15.7 - - + -
541A LEU* 3.5 38.2 - - + +
545A THR* 3.9 23.3 - - + +
547A LEU* 4.0 19.1 - - + -
549A ILE* 4.1 11.0 - - + -
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Residues in contact with LEU 490 (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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474A ILE* 5.1 1.3 - - + -
486A GLY 3.2 11.5 + - - +
487A VAL* 3.2 14.3 + - + +
489A LEU* 1.3 77.1 - - - +
491A GLU* 1.3 59.1 + - - +
493A LEU* 3.6 9.1 - - + +
494A ALA* 2.8 31.4 + - - +
501A SER* 4.6 5.2 - - - -
504A PHE* 3.6 40.6 - - + -
507A ILE* 3.8 34.3 - - + -
514A LEU* 3.8 28.9 - - + -
516A PHE* 4.0 20.0 - - + -
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Residues in contact with GLU 491 (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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487A VAL 2.9 13.8 + - - +
488A LYS* 3.1 14.5 + - + +
490A LEU* 1.3 76.6 - - - +
492A ILE* 1.3 58.5 + - + +
494A ALA* 3.3 3.5 + - - +
495A GLU* 2.9 52.0 + - - +
501A SER* 2.7 35.3 + - - -
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Residues in contact with ILE 492 (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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488A LYS* 3.1 28.1 + - + +
489A LEU 3.8 0.4 - - - +
491A GLU* 1.3 76.2 - - + +
493A LEU* 1.3 63.0 + - - +
495A GLU* 3.3 15.6 + - - +
496A HIS* 3.1 22.0 + - - +
537A VAL* 5.4 3.1 - - + -
540A GLU* 3.9 34.1 - - + +
541A LEU* 3.6 26.0 - - + +
544A GLN* 3.3 38.1 - - + +
545A THR* 3.9 18.6 - - + -
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Residues in contact with LEU 493 (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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474A ILE* 4.6 7.6 - - + -
489A LEU 2.9 17.9 + - - +
490A LEU* 3.6 13.9 - - + +
492A ILE* 1.3 78.9 - - - +
494A ALA* 1.3 62.4 + - - +
496A HIS* 3.1 7.6 + - + +
497A VAL* 2.9 38.8 + - + +
504A PHE* 3.9 25.4 - - + -
516A PHE* 5.0 4.3 - - + -
530A VAL* 3.8 19.5 - - + +
533A GLN* 4.1 4.7 - - + -
534A ALA* 3.7 40.2 - - + +
537A VAL* 4.5 8.7 - - + -
541A LEU* 4.2 6.2 - - + +
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Residues in contact with ALA 494 (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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490A LEU 2.8 21.7 + - - +
491A GLU* 3.6 6.5 - - - +
493A LEU* 1.3 71.7 - - - +
495A GLU* 1.3 64.0 + - + +
497A VAL* 3.3 7.7 + - - -
498A HIS* 2.9 20.4 + - - -
499A MET* 3.1 29.3 + - + +
500A SER 4.1 0.7 - - - -
501A SER* 3.6 26.7 - - - +
504A PHE* 4.0 8.7 - - + -
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Residues in contact with GLU 495 (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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491A GLU* 2.9 39.6 + - - +
492A ILE* 3.6 18.7 - - - +
494A ALA* 1.3 77.7 - - + +
496A HIS* 1.3 62.9 + - - +
498A HIS* 3.4 22.2 + - - -
499A MET 5.0 0.4 - - - -
540A GLU* 5.5 2.3 - - - +
544A GLN* 5.1 2.9 - - - +
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Residues in contact with HIS 496 (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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492A ILE* 3.1 14.2 + - + +
493A LEU* 3.4 10.8 - - + +
495A GLU* 1.3 78.2 - - - +
497A VAL* 1.3 71.6 + - + +
498A HIS* 3.3 14.1 + - - -
533A GLN* 2.9 36.7 + - + -
536A LEU* 5.8 0.4 - - + -
537A VAL* 3.3 39.8 - - + +
540A GLU* 5.3 7.3 + - - +
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Residues in contact with VAL 497 (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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493A LEU* 2.9 30.1 + - + +
494A ALA* 3.8 9.2 - - - +
496A HIS* 1.3 92.1 - - + +
498A HIS* 1.3 71.1 + - - +
499A MET* 4.0 15.7 - - + -
504A PHE* 5.4 0.7 - - + -
523A GLN* 4.6 2.4 - - - +
525A LEU* 3.8 36.0 - - + +
530A VAL* 5.0 10.8 - - + -
533A GLN* 3.8 25.8 - - + -
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Residues in contact with HIS 498 (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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494A ALA 2.9 6.5 + - - -
495A GLU* 3.4 13.1 + - - +
496A HIS* 3.3 16.7 + - - -
497A VAL* 1.3 79.7 - - - +
499A MET* 1.3 59.1 + - - +
523A GLN* 3.2 27.1 + - + +
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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
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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