Contacts of the strand formed by residues 337 - 342 (chain C) in PDB entry 4JHN
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 337 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLY* 3.2 8.0 - - - +
318C THR 4.6 0.7 - - - +
319C PHE* 3.4 8.7 - - - +
320C GLY 2.8 33.9 + - - -
327C LEU* 3.5 20.0 - - + -
329C LEU* 3.5 17.4 - - + +
333C ASN* 3.3 26.7 + - - -
335C THR* 3.1 34.4 + - - -
336C ASN* 1.3 74.4 - - - +
338C PHE* 1.3 61.5 + - - +
339C ILE* 3.4 5.9 - - + +
341C THR* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLY 3.8 3.8 - - - -
270C GLN 3.4 20.0 - - - -
271C PHE* 3.8 1.3 - - - -
272C GLY* 3.4 28.0 - - - -
275C GLY* 3.1 15.4 + - - -
276C LEU 3.3 0.2 + - - -
277C GLY* 2.9 53.1 + - - +
278C THR* 3.9 25.1 - - + -
280C LEU 5.6 0.7 - - - -
281C PHE* 3.8 31.9 - + - -
336C ASN* 3.9 28.9 + - + -
337C HIS* 1.3 76.5 - - - +
339C ILE* 1.3 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLY 4.8 1.1 - - - +
276C LEU 5.1 0.2 - - - -
277C GLY* 3.9 17.7 - - - +
278C THR* 5.4 0.9 - - + +
291C ASN* 4.2 22.4 - - + +
319C PHE* 3.6 10.2 - - - +
337C HIS* 4.0 3.4 - - + +
338C PHE* 1.3 87.0 - - + +
340C PRO* 1.4 79.4 - - + +
341C THR* 2.8 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLY* 3.4 19.1 - - - +
289C ILE* 3.6 23.6 - - + -
291C ASN* 3.5 21.8 + - + +
292C ILE* 3.8 25.4 - - + -
309C LEU* 4.6 1.6 - - + -
317C TYR* 4.0 16.7 - - + -
319C PHE* 3.5 34.3 - - + -
339C ILE* 1.4 90.6 - - + +
341C THR* 1.3 59.7 + - - +
342C LEU 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TYR* 3.3 4.2 - - - -
318C THR 2.9 35.3 + - - +
329C LEU* 3.6 22.8 - - + +
337C HIS* 3.0 32.7 + - + +
339C ILE* 2.8 21.0 + - - +
340C PRO* 1.3 71.2 + - - +
342C LEU* 1.3 72.5 + - - +
343C CYS 3.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 4.1 28.7 - - + -
316C MET 3.7 16.4 - - - +
317C TYR* 3.5 36.3 - - + +
329C LEU* 3.4 8.8 - - - +
340C PRO 4.3 0.2 + - - -
341C THR* 1.3 77.5 - - - +
343C CYS* 1.3 63.2 - - - +
344C SER* 3.0 20.9 + - - +
347C LEU* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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