Contacts of the helix formed by residues 504 - 519 (chain A) in PDB entry 4N78
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 LYS 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLN 4.6 0.4 - - - +
499A ALA* 2.5 33.5 + - + +
502A LYS* 3.8 31.9 - - + +
503A LYS* 1.3 69.9 - - - +
505A ASN* 1.3 63.8 + - - +
506A VAL* 3.1 8.7 - - + -
507A ILE* 2.9 26.5 + - + -
508A GLN* 3.0 11.0 + - - +
583A SER* 3.3 46.1 + - - +
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Residues in contact with ASN 505 (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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503A LYS* 3.0 42.7 + - - +
504A LYS* 1.3 73.2 - - - +
506A VAL* 1.3 62.3 + - - +
508A GLN* 3.6 19.5 - - - +
509A SER* 3.1 24.9 + - - -
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Residues in contact with VAL 506 (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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504A LYS* 4.3 8.1 - - + +
505A ASN* 1.3 79.1 - - - +
507A ILE* 1.3 70.9 + - + +
509A SER* 2.6 23.5 + - - +
510A VAL* 3.4 13.1 - - + +
580A LEU* 3.6 38.4 - - + -
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Residues in contact with ILE 507 (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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495A PRO 5.2 0.2 - - - +
499A ALA* 3.9 9.6 - - + -
504A LYS* 2.9 17.9 + - + +
506A VAL* 1.3 84.2 - - + +
508A GLN* 1.3 66.7 + - - +
510A VAL* 3.1 7.5 + - - +
511A LEU* 2.9 44.5 + - + +
569A LEU* 4.4 12.6 - - + -
580A LEU* 3.7 32.1 - - + +
583A SER* 3.8 20.6 - - - +
584A LEU* 3.7 32.3 - - + -
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Residues in contact with GLN 508 (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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496A LEU* 3.9 14.6 - - + -
499A ALA* 3.8 14.6 - - + +
500A ILE* 3.4 33.1 - - + +
503A LYS* 6.0 0.3 - - - -
504A LYS 3.0 11.2 + - - +
505A ASN* 3.6 24.5 - - - +
507A ILE* 1.3 77.0 - - - +
509A SER* 1.3 53.9 + - - +
511A LEU* 3.2 2.4 + - - +
512A GLN* 2.8 71.9 + - - +
533A LEU* 6.2 0.4 - - - +
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Residues in contact with SER 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ASN 3.1 14.4 + - - -
506A VAL* 2.6 26.7 + - - +
508A GLN* 1.3 76.4 - - - +
510A VAL* 1.3 59.0 + - - +
512A GLN* 3.7 10.2 - - - +
513A ALA* 2.8 31.3 + - - +
516A LYS* 5.1 2.1 + - - -
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Residues in contact with VAL 510 (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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59A TYR* 4.7 13.9 - - + +
506A VAL* 3.4 17.7 - - + +
507A ILE 3.1 6.8 + - - +
509A SER* 1.3 76.3 + - - +
511A LEU* 1.3 66.1 + - - +
513A ALA* 3.1 7.7 + - - +
514A ILE* 2.9 30.3 + - + +
565A MET* 3.9 32.8 - - + +
568A SER* 4.5 3.1 - - - +
569A LEU* 3.7 33.0 - - + -
580A LEU* 5.0 7.0 - - + -
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Residues in contact with LEU 511 (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 LEU* 3.9 32.6 - - + +
495A PRO* 3.6 13.7 - - + +
496A LEU* 3.4 46.7 - - + +
499A ALA* 4.5 0.9 - - + -
507A ILE* 2.9 38.5 + - + +
508A GLN 3.7 3.6 - - - +
510A VAL* 1.3 75.3 - - - +
512A GLN* 1.3 57.3 + - - +
514A ILE* 3.4 8.0 + - + +
515A ARG* 3.0 37.7 + - - +
569A LEU* 3.8 23.3 - - + -
584A LEU* 5.8 0.9 - - + -
592A ILE* 5.2 2.0 - - + -
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Residues in contact with GLN 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 3.8 21.5 - - + +
500A ILE* 4.4 4.5 - - - +
508A GLN* 2.8 56.2 + - - +
509A SER* 3.9 8.4 - - - +
511A LEU* 1.3 71.2 - - - +
513A ALA* 1.3 61.2 + - - +
515A ARG* 4.0 5.8 - - - +
516A LYS* 2.8 44.5 + - - +
533A LEU* 5.3 6.8 - - - +
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Residues in contact with ALA 513 (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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56A ILE* 4.2 21.0 - - + +
509A SER 2.8 19.5 + - - +
510A VAL* 3.1 7.4 + - - +
512A GLN* 1.3 77.3 - - - +
514A ILE* 1.3 55.5 + - - +
516A LYS* 3.1 21.9 - - - +
517A THR* 2.5 30.1 + - - -
565A MET* 3.8 19.9 - - - +
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Residues in contact with ILE 514 (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 LEU* 6.3 0.2 - - + -
487A PHE* 5.4 1.3 - - + -
488A SER* 4.9 3.4 - - - -
492A LEU* 4.0 18.4 - - + -
510A VAL* 2.9 25.8 + - + +
511A LEU* 3.5 11.0 - - + +
512A GLN 3.2 0.2 - - - -
513A ALA* 1.3 76.0 - - - +
515A ARG* 1.3 66.7 + - - +
517A THR* 3.1 13.3 + - - -
518A VAL* 3.3 19.6 + - + +
562A VAL* 4.1 25.6 - - + +
565A MET* 3.6 35.4 - - + -
566A LEU* 3.6 35.2 - - + +
569A LEU* 4.7 1.8 - - + -
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Residues in contact with ARG 515 (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 SER* 2.9 21.7 + - - +
489A GLN 3.1 26.1 + - - -
492A LEU* 4.3 21.8 + - + +
493A ARG* 3.8 12.3 - - - +
496A LEU* 3.9 30.4 - - - +
511A LEU* 3.0 19.4 + - - +
512A GLN* 4.0 4.9 - - - +
514A ILE* 1.3 76.6 - - - +
516A LYS* 1.3 63.5 + - - +
519A CYS* 2.9 44.5 + - - +
521A TRP* 3.2 33.1 + - + -
526A GLU* 5.3 5.3 + - - -
527A PRO* 5.8 1.8 - - - +
530A ASP* 6.3 1.2 - - - -
533A LEU* 6.2 1.6 - - - +
545A ILE* 5.3 0.6 - - - +
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Residues in contact with LYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.0 22.2 - - + +
509A SER 5.1 1.2 + - - -
512A GLN* 2.8 29.5 + - - +
513A ALA* 3.1 32.7 - - - +
515A ARG* 1.3 77.0 - - - +
517A THR* 1.3 64.6 + - - +
519A CYS 4.8 3.1 + - - +
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Residues in contact with THR 517 (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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56A ILE* 5.0 6.4 - - - +
513A ALA 2.5 23.1 + - - -
514A ILE* 3.1 7.9 + - - -
516A LYS* 1.3 84.8 - - - +
518A VAL* 1.3 70.6 + - + +
558A GLN* 3.2 33.5 + - + +
561A MET* 5.0 13.0 - - + +
562A VAL* 5.2 1.8 - - + -
565A MET* 4.5 6.6 - - - +
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU* 4.2 26.7 - - + -
485A GLN* 3.0 16.4 + - - +
488A SER* 3.9 24.0 - - - +
514A ILE* 3.3 13.2 + - + +
517A THR* 1.3 89.2 - - + +
519A CYS* 1.3 75.1 + - - +
520A ASP* 4.2 1.9 - - - +
558A GLN* 3.8 28.9 + - + +
562A VAL* 3.4 31.4 - - + -
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Residues in contact with CYS 519 (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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485A GLN* 3.5 6.1 - - - +
488A SER* 3.5 25.8 - - - -
489A GLN* 3.8 9.2 - - + -
515A ARG* 2.9 45.5 + - - +
516A LYS 4.7 2.5 - - - +
517A THR 3.9 0.2 - - - -
518A VAL* 1.3 82.4 - - - +
520A ASP* 1.3 58.8 + - - +
521A TRP* 3.7 40.5 + - + +
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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