Contacts of the helix formed by residues 506 - 515 (chain B) in PDB entry 3N57
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 PRO 506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301B LEU* 6.6 0.2 - - + -
503B GLU* 6.0 1.6 - - - +
504B ALA* 3.4 8.4 - - + +
505B ILE* 1.4 92.1 - - + +
507B ASP* 1.3 57.3 + - - +
508B GLU* 3.2 16.8 - - + +
509B VAL* 2.8 48.7 + - + +
510B ILE 3.3 4.3 + - - -
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Residues in contact with ASP 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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299B LYS* 4.2 18.1 + - - -
505B ILE 3.4 5.2 + - - +
506B PRO* 1.3 71.0 - - - +
508B GLU* 1.3 56.8 + - - +
510B ILE* 3.4 11.7 + - - +
511B LYS* 2.9 30.2 + - - +
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Residues in contact with GLU 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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506B PRO* 4.1 15.2 - - + +
507B ASP* 1.3 76.9 - - - +
509B VAL* 1.3 72.4 + - - +
511B LYS* 3.7 13.9 - - + +
512B LYS* 3.1 29.6 + - - +
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Residues in contact with VAL 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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388B GLU* 4.0 26.7 - - + +
505B ILE* 4.0 9.9 - - + -
506B PRO* 2.8 34.3 + - + +
508B GLU* 1.3 85.1 - - - +
510B ILE* 1.3 65.0 + - - +
512B LYS* 3.3 7.8 + - - +
513B TRP* 3.1 55.9 + - + -
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Residues in contact with ILE 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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299B LYS* 3.4 34.1 - - + +
473B PRO* 3.6 11.4 - - + +
474B GLU* 3.8 16.8 - - + +
505B ILE* 3.8 28.5 - - + +
506B PRO 3.3 10.4 + - - +
507B ASP* 3.6 15.3 - - - +
509B VAL* 1.3 75.9 - - - +
511B LYS* 1.3 59.3 + - - +
513B TRP* 3.0 20.7 + - + +
514B GLN* 2.9 50.7 + - - +
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Residues in contact with LYS 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 ASP 2.9 17.6 + - - +
508B GLU* 3.7 12.6 - - + +
510B ILE* 1.3 76.6 - - - +
512B LYS* 1.3 63.7 + - - +
514B GLN* 3.1 18.5 + - - +
515B ASN* 3.0 41.6 + - - +
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Residues in contact with LYS 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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388B GLU* 4.9 11.2 - - - +
392B LEU* 3.8 24.5 - - + +
508B GLU 3.1 16.2 + - - +
509B VAL* 3.3 12.1 + - - +
511B LYS* 1.3 77.0 - - - +
513B TRP* 1.3 65.9 + - + +
515B ASN* 3.3 28.0 + - - +
516B ALA* 3.7 4.0 + - - +
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Residues in contact with TRP 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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387B VAL* 6.0 0.2 - - + -
388B GLU* 3.1 36.0 + - + +
391B ILE* 3.5 44.2 - - + -
392B LEU* 3.6 32.0 - - + +
395B PHE* 3.8 19.0 - + + +
473B PRO* 3.6 20.0 - - + +
476B VAL* 5.4 4.5 - - + -
478B VAL* 4.7 7.0 - - + -
505B ILE* 4.1 18.2 - - + -
509B VAL* 3.1 32.3 + - + -
510B ILE* 3.0 32.5 + - + +
512B LYS* 1.3 75.7 - - + +
514B GLN* 1.3 64.6 + - - +
516B ALA* 3.2 20.4 - - - +
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Residues in contact with GLN 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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399B GLN* 6.0 0.9 - - - +
473B PRO* 3.6 20.4 - - + -
474B GLU* 2.7 32.6 + - - +
510B ILE* 2.9 28.5 + - - +
511B LYS* 3.1 22.6 + - - +
513B TRP* 1.3 76.9 - - - +
515B ASN* 1.3 63.2 + - - +
516B ALA* 3.2 4.4 + - - +
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Residues in contact with ASN 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 LYS* 3.0 45.5 + - - +
512B LYS* 3.3 25.1 + - - +
513B TRP 3.2 0.8 - - - -
514B GLN* 1.3 79.8 - - - +
516B ALA* 1.3 63.3 + - - +
517B ASP* 3.1 7.8 + - - +
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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