Contacts of the helix formed by residues 505 - 518 (chain B) in PDB entry 5N7I
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 ALA 505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504B GLU* 1.4 75.8 - - - +
506B ILE* 1.3 57.7 + - - +
508B ARG* 3.2 11.3 + - - +
509B ILE* 3.0 40.1 + - + +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B MET* 5.7 9.2 - - + +
493B LEU 4.6 7.6 - - - +
494B PRO* 3.4 37.5 - - + +
504B GLU 3.9 15.5 - - - +
505B ALA* 1.3 76.2 - - - +
507B SER* 1.3 71.0 + - - +
509B ILE* 3.3 19.3 + - + +
510B HIS* 3.1 21.1 + - - +
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B GLU* 3.4 20.7 + - - -
506B ILE* 1.3 83.2 - - - +
508B ARG* 1.4 64.5 + - - +
510B HIS* 3.2 18.6 + - - +
511B GLU* 3.2 12.5 + - - +
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Residues in contact with ARG 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B GLU* 3.1 17.8 + - + +
505B ALA* 3.2 12.1 + - - +
507B SER* 1.4 76.7 - - - +
509B ILE* 1.3 61.0 + - + +
511B GLU* 3.3 34.1 + - - +
512B GLU* 3.3 12.1 + - - +
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B MET* 6.0 4.7 - - + -
505B ALA* 3.0 29.7 + - + +
506B ILE* 3.6 20.4 - - + +
507B SER 3.3 0.2 - - - -
508B ARG* 1.3 72.2 - - + +
510B HIS* 1.3 65.7 + - - +
512B GLU* 3.3 17.1 + - + +
513B PHE* 3.3 12.5 + - + +
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Residues in contact with HIS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B MET* 4.1 38.2 - - + +
506B ILE 3.1 12.0 + - - +
507B SER* 3.2 12.7 + - - +
509B ILE* 1.3 76.1 - - - +
511B GLU* 1.3 61.9 + - - +
513B PHE* 3.2 8.5 + + - +
514B LYS* 3.0 49.2 + - + -
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Residues in contact with GLU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B SER 3.2 8.0 + - - +
508B ARG* 3.4 31.2 + - - +
509B ILE 3.2 0.6 - - - -
510B HIS* 1.3 82.1 + - - +
512B GLU* 1.3 59.7 + - - +
514B LYS* 3.2 13.6 + - + +
515B LYS* 2.9 29.6 + - + +
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Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ARG 3.3 7.3 + - - +
509B ILE* 3.3 13.7 + - + +
511B GLU* 1.3 77.4 - - - +
513B PHE* 1.3 62.5 + - - +
515B LYS* 3.2 38.1 + - - +
516B LYS* 2.7 61.6 + - - +
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Residues in contact with PHE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B PHE* 4.4 12.1 - + + -
486B LEU* 3.8 37.0 - - + -
487B ASP* 3.0 30.1 - - - -
490B MET* 4.0 31.2 - - + -
509B ILE* 3.3 8.7 + - + +
510B HIS* 3.2 15.1 + - - +
512B GLU* 1.3 77.1 - - - +
514B LYS* 1.3 63.8 + - + +
516B LYS* 3.1 11.7 + - + +
517B LYS* 2.9 64.7 + - + +
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B HIS* 3.0 34.5 + - + +
511B GLU* 3.5 16.2 - - + +
513B PHE* 1.3 83.1 - - + +
515B LYS* 1.3 61.1 + - - +
517B LYS* 3.3 9.2 + - - +
518B ASN* 3.2 36.2 + - - +
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Residues in contact with LYS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B GLU* 2.9 14.1 + - - +
512B GLU* 3.3 43.9 + - - +
514B LYS* 1.3 77.7 - - - +
516B LYS* 1.3 67.6 + - + +
518B ASN* 3.8 3.6 + - - -
519B ASP* 3.6 16.6 + - - +
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Residues in contact with LYS 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B PHE* 3.8 21.0 - - + -
486B LEU* 6.2 3.6 - - + -
512B GLU* 2.7 56.6 + - - +
513B PHE* 3.6 11.9 - - + +
515B LYS* 1.3 78.6 - - + +
517B LYS* 1.3 65.6 + - - +
519B ASP* 3.2 21.3 + - - +
522B PHE* 5.6 0.9 - - - +
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B PHE* 3.9 36.5 - - + -
487B ASP* 5.0 4.3 - - - +
513B PHE* 2.9 49.1 + - + +
514B LYS* 3.3 9.8 + - - +
516B LYS* 1.3 77.7 - - - +
518B ASN* 1.3 89.7 + - - +
519B ASP 3.4 2.0 + - - +
522B PHE* 4.5 8.8 - - - -
523B LEU* 5.9 2.1 - - - +
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Residues in contact with ASN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B LYS* 3.2 26.0 + - - +
515B LYS* 3.8 5.6 - - - +
516B LYS 3.3 0.2 - - - -
517B LYS* 1.3 104.5 + - - +
519B ASP* 1.4 63.8 + - - -
520B PRO* 3.2 10.0 - - - +
523B LEU* 4.6 24.9 - - + +
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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