Contacts of the helix formed by residues 489 - 498 (chain A) in PDB entry 1NA8
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 HIS 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A HIS* 1.3 91.3 + + - +
491A HIS* 3.0 8.1 - - - +
492A HIS* 3.2 26.0 + - - +
493A MET* 2.4 61.7 + - + +
566A LYS 4.6 8.3 + - - -
567A VAL* 4.9 7.8 - - + +
601A PRO* 5.4 8.1 - - + -
602A GLN* 5.8 8.0 + - + -
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Residues in contact with HIS 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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489A HIS* 1.3 109.8 + + + +
491A HIS* 1.3 97.9 + + - +
493A MET* 3.5 12.5 - - + +
494A GLU* 2.8 33.1 + - - +
566A LYS 5.2 1.3 - - - +
569A LYS* 4.0 27.7 - - - +
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Residues in contact with HIS 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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489A HIS 3.0 3.0 - - - +
490A HIS* 1.3 117.9 + + - +
492A HIS* 1.3 66.5 + - + +
494A GLU* 3.4 22.3 + - - +
495A LEU* 2.8 43.0 + - + +
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Residues in contact with HIS 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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489A HIS* 2.9 23.5 + - - +
491A HIS* 1.3 84.0 - - + +
493A MET* 1.3 63.8 + - - +
495A LEU* 4.2 12.0 - - + +
496A SER* 3.2 22.0 + - - -
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Residues in contact with MET 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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489A HIS* 2.4 55.9 + - + +
490A HIS* 3.5 14.1 - - - +
492A HIS* 1.3 68.4 - - - +
494A GLU* 1.3 53.6 + - - +
496A SER* 2.7 23.5 + - - -
497A LEU* 2.8 24.6 + - - +
539A ASP* 5.8 0.7 - - - +
566A LYS 4.2 3.8 - - - +
567A VAL 3.7 12.6 - - - +
568A MET* 3.7 16.2 - - - -
569A LYS* 3.8 24.0 - - + -
599A ALA* 3.8 13.0 - - + +
601A PRO* 3.3 39.0 - - + -
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Residues in contact with GLU 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 HIS* 2.8 23.8 + - - +
491A HIS* 3.4 29.7 + - - +
493A MET* 1.3 74.3 - - - +
495A LEU* 1.3 70.6 + - + +
497A LEU* 3.2 7.4 + - - +
498A ALA* 3.0 25.8 + - + +
569A LYS* 4.9 14.6 - - + +
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Residues in contact with LEU 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 HIS* 2.8 37.7 + - + +
492A HIS* 4.2 14.4 - - + +
494A GLU* 1.3 76.7 - - + +
496A SER* 1.3 61.0 + - - +
497A LEU 3.4 0.2 + - - -
498A ALA* 3.5 19.0 + - + +
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Residues in contact with SER 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 HIS 3.2 15.6 + - - -
493A MET* 2.7 22.2 + - - +
495A LEU* 1.3 77.3 - - - +
497A LEU* 1.3 65.9 + - - +
498A ALA 4.4 1.7 - - - +
500A ILE* 4.2 9.9 - - - +
537A ARG* 3.7 45.9 + - - +
540A VAL* 5.7 2.6 - - - +
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Residues in contact with LEU 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 MET 2.8 16.2 + - - +
494A GLU* 3.2 5.8 + - - +
496A SER* 1.3 83.7 - - - +
498A ALA* 1.3 56.6 + - - +
500A ILE* 3.2 9.0 - - + +
537A ARG* 6.5 0.7 - - - -
540A VAL* 5.2 8.5 - - + -
569A LYS* 3.8 36.1 - - + +
570A VAL 4.7 0.9 - - - +
571A LYS* 2.7 52.4 + - + +
597A LEU* 4.3 31.4 - - + +
599A ALA* 3.9 21.5 - - + +
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Residues in contact with ALA 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 GLU* 3.0 18.2 + - + +
495A LEU* 3.5 18.9 + - + +
496A SER 4.4 1.6 - - - +
497A LEU* 1.3 79.2 - - - +
499A SER* 1.3 64.7 + - - +
500A ILE* 2.6 18.2 + - - +
571A LYS* 4.3 1.3 - - - +
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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