Contacts of the strand formed by residues 316 - 320 (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 MET 316 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 4.5 5.2 - - - -
309B LEU 3.2 13.5 - - - +
310B ILE* 4.8 0.9 - - + -
314B GLY 4.0 0.8 + - - -
315B LEU* 1.3 76.8 - - - +
317B TYR* 1.3 70.9 + - - +
318B THR* 4.3 1.6 - - + -
328B GLY 5.5 0.4 - - - +
342B LEU* 3.8 6.0 - - - +
343B CYS* 2.9 52.6 + - + +
346B PHE* 4.0 26.5 - - + +
351B VAL* 3.9 28.3 - - + +
354B VAL* 3.8 29.4 - - - -
361B MET* 4.0 20.0 - - + -
363B VAL* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TYR* 5.5 0.7 + - - -
342A LEU* 3.3 19.1 - - - +
292B ILE* 4.4 12.8 - - + -
295B GLN* 2.6 45.3 + - - -
297B ILE* 5.2 3.1 - - + -
307B THR 4.0 0.2 - - - +
308B ALA* 3.3 2.9 - - - -
309B LEU* 2.7 49.9 + - + +
311B THR* 3.9 19.3 - - + -
315B LEU* 4.4 2.5 - - + -
316B MET* 1.3 76.5 - - - +
318B THR* 1.3 62.3 + - - +
319B PHE* 4.6 1.3 - - - -
340B PRO* 3.7 30.5 - - + -
341B THR 3.3 7.0 - - - -
342B LEU* 3.5 44.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B HIS* 5.2 0.2 - - - -
307B THR 3.3 12.1 - - - +
308B ALA* 3.9 14.1 - - + -
316B MET* 4.3 3.6 - - + -
317B TYR* 1.3 79.1 - - - +
319B PHE* 1.3 65.3 + - - +
327B LEU* 2.8 42.9 + - + +
329B LEU* 3.6 16.1 - - - +
337B HIS* 4.7 1.0 - - - +
341B THR* 2.9 33.4 + - - -
343B CYS* 3.6 10.4 - - - -
361B MET* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 4.8 1.8 - - + -
272B GLY 3.5 3.6 - - - +
273B GLN* 3.2 24.5 - - - -
274B LEU 3.6 5.2 - - - -
275B GLY* 3.4 29.2 - - - -
289B ILE* 3.7 20.0 - - + -
306B HIS* 3.3 4.2 - - - +
307B THR* 2.9 55.1 + - + -
309B LEU* 3.7 30.3 - - + -
317B TYR 4.6 0.9 - - - -
318B THR* 1.3 83.0 - - - +
320B GLY* 1.3 59.7 + - - +
327B LEU* 3.6 7.4 - - - +
337B HIS* 3.5 16.4 - - - +
339B ILE 3.5 13.5 - - - +
340B PRO* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE 3.0 18.0 - - - +
272B GLY 3.5 13.2 + - - -
273B GLN 3.5 4.0 - - - -
305B ASN 3.7 5.6 - - - -
319B PHE* 1.3 74.7 - - - +
321B ASP* 1.3 66.6 - - - -
322B GLY 3.3 1.7 + - - -
327B LEU* 3.4 5.2 - - - +
336B ASN* 3.4 0.3 - - - -
337B HIS 2.8 32.4 + - - +
----------------------------------------------------------
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