Contacts of the helix formed by residues 237 - 239 (chain W) in PDB entry 6NE3
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 237 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J T 5.2 5.2 - - - +
236W VAL* 1.3 99.0 - - + +
238W LYS* 1.3 60.2 + - - +
239W SER* 4.3 6.3 - - - +
240W THR* 3.0 37.9 + - - +
287W TYR* 3.4 28.7 - - + +
308W ASP* 4.1 3.4 - - - +
309W GLU* 4.0 13.9 - - + -
312W ARG* 5.7 1.8 - - - +
564W LEU* 3.7 36.1 - - + -
565W GLY* 5.2 3.4 - - - +
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Residues in contact with LYS 238 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J T 3.5 58.5 + - - +
58J A 4.0 14.1 + - - +
237W PRO* 1.3 72.6 - - - +
239W SER* 1.3 58.6 + - - +
240W THR 3.1 5.0 + - - -
241W LEU* 3.8 16.4 + - - +
242W HIS* 5.1 2.4 + - - -
261W ILE* 4.8 8.3 - - + -
286W SER* 3.3 26.6 + - - +
287W TYR* 5.4 0.2 - - - -
531W GLY 5.0 1.1 - - - -
532W GLN 6.0 0.7 - - - -
533W THR 3.3 10.3 + - - -
534W PRO* 4.2 1.0 - - - +
535W HIS* 3.8 39.5 - - + +
538W ARG* 3.1 38.9 + - - +
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Residues in contact with SER 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J T 4.8 2.3 + - - -
237W PRO* 3.1 6.1 + - - +
238W LYS* 1.3 77.3 - - - +
240W THR* 1.3 61.6 + - - +
241W LEU 3.8 0.4 - - - -
242W HIS* 6.2 0.7 - - - -
243W ASN* 5.3 1.6 - - - +
529W LEU* 6.2 0.2 - - - -
538W ARG* 2.4 47.8 + - - +
539W GLN* 5.4 2.4 - - - +
542W ILE* 4.9 5.4 - - - +
561W ALA* 2.9 28.0 + - - +
562W GLY 5.5 0.2 - - - -
564W LEU* 6.2 0.9 - - - -
565W GLY 6.0 2.2 - - - -
566W ILE* 4.1 22.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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