Contacts of the strand formed by residues 297 - 302 (chain B) 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 ILE 297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.6 32.4 - - + +
263B VAL* 3.6 22.9 - - + -
292B ILE* 3.7 22.4 - - + -
295B GLN* 3.8 12.0 + - + +
296B THR* 1.3 74.6 - - - +
298B SER* 1.3 61.4 + - - +
299B TYR 3.5 22.4 - - - +
300B ILE* 4.0 5.6 - - + -
309B LEU* 4.1 18.4 - - + -
310B ILE 3.6 4.3 - - - +
311B THR* 3.8 25.4 - - + -
317B TYR* 5.2 3.1 - - + -
227D GLN* 3.5 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLN* 3.1 8.1 - - - +
258B LEU* 3.7 3.0 - - - +
296B THR 3.7 1.2 + - - -
297B ILE* 1.3 74.5 - - - +
299B TYR* 1.3 57.8 + - - +
310B ILE* 2.7 29.1 + - - +
311B THR 3.2 19.7 + - - -
312B ASP* 4.1 1.6 - - - -
227D GLN* 2.9 29.8 + - - -
228D LEU* 3.9 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU 5.7 0.7 + - - -
194B TRP* 4.1 22.3 - + - -
247B GLN* 3.6 14.6 - - - +
297B ILE* 3.5 5.3 - - - +
298B SER* 1.3 84.1 + - - +
300B ILE* 1.3 88.7 + - - +
301B SER* 4.0 3.9 + - - -
309B LEU* 3.5 4.0 - - - -
310B ILE* 3.0 55.0 + - + -
353B LEU* 6.0 0.2 - - - -
354B VAL* 3.6 32.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TRP* 5.7 1.0 - - + +
247B GLN* 3.2 19.7 + - + +
248B VAL* 3.9 6.5 - - - -
249B ALA* 3.6 20.5 - - + +
256B VAL* 3.3 46.4 - - + +
258B LEU* 3.8 28.0 - - + +
263B VAL* 4.6 3.1 - - + -
297B ILE* 4.0 10.3 - - + -
299B TYR* 1.3 100.9 + - - +
301B SER* 1.3 61.5 + - - +
308B ALA 3.7 3.6 - - - -
309B LEU* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 4.2 4.3 - - - -
299B TYR* 4.0 7.3 + - - -
300B ILE* 1.3 77.4 - - - +
302B CYS* 1.3 64.6 + - - +
307B THR* 3.4 8.7 - - - +
308B ALA 2.9 32.7 + - - +
354B VAL* 3.8 25.3 + - - -
355B ALA* 3.8 5.7 - - - -
356B CYS* 3.5 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 3.3 27.4 - - + +
250B CYS 3.9 23.6 - - - +
251B GLY* 3.9 7.2 - - - +
254B HIS* 3.6 16.2 - - - -
256B VAL* 3.2 37.2 - - - -
301B SER* 1.3 76.9 + - - +
303B GLY* 1.3 60.6 + - - +
306B HIS 3.7 2.7 - - - -
307B THR* 4.4 0.2 - - - -
356B CYS* 3.3 17.0 + - - +
----------------------------------------------------------
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