Contacts of the strand formed by residues 258 - 265 (chain D) in PDB entry 4JF7
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 GLU 258 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ASN* 2.8 34.6 + - + +
281A LEU* 4.6 4.4 - - - +
373A ASN* 3.6 15.3 + - - +
241D PHE* 3.3 6.1 - - - +
242D VAL* 2.9 48.3 + - + +
257D PRO* 1.3 72.3 - - - +
259D GLN* 1.3 61.3 + - - +
260D ARG* 2.6 43.3 + - - +
274D ILE* 3.5 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TYR* 2.4 38.9 + - + +
240D CYS 3.7 1.3 - - - -
241D PHE* 3.8 14.3 - - - +
256D PRO* 5.4 1.3 - - + +
257D PRO* 3.2 26.9 + - - +
258D GLU* 1.3 73.6 - - - +
260D ARG* 1.3 62.4 + - - +
274D ILE* 3.3 9.3 - - - +
275D ILE* 3.0 53.9 + - + +
277D PRO* 5.0 6.1 - - + -
280D VAL* 5.9 3.8 - - + -
287D LEU* 3.0 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 3.2 29.5 + - - +
373A ASN* 3.1 24.2 + - - +
220D ASP* 5.1 1.2 + - - -
222D VAL* 4.1 19.2 - - - +
224D ARG* 3.7 13.0 - - - +
238D MET 3.8 0.3 - - - +
239D TYR* 3.4 7.6 - - - -
240D CYS* 2.8 47.3 + - + +
242D VAL* 3.6 16.5 - - + +
258D GLU* 2.6 30.0 + - + +
259D GLN* 1.3 78.9 - - - +
261D ILE* 1.3 63.3 + - - +
262D ILE* 4.1 7.1 - - + +
272D GLU* 3.1 41.0 + - + +
273D ARG 3.4 9.9 - - - +
274D ILE* 4.2 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D MET* 3.7 26.9 - - + -
238D MET 3.4 1.1 - - - +
239D TYR* 3.7 34.3 - - + -
260D ARG* 1.3 73.1 - - - +
262D ILE* 1.3 63.4 + - - +
263D ILE* 4.3 7.1 - - + +
271D VAL 3.8 2.1 - - - +
272D GLU* 3.5 1.6 - - - -
273D ARG* 3.0 31.9 + - + +
275D ILE* 3.6 36.5 - - + +
303D PHE* 4.0 9.9 - - + -
363D LEU* 4.4 0.7 - - + -
365D CYS* 3.9 21.8 - - - -
371D LEU* 3.8 17.5 - - + -
375D CYS* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D LEU* 4.8 9.6 - - + -
224D ARG* 4.1 7.2 - - - -
236D CYS 3.8 1.0 - - - +
237D MET* 3.3 2.3 - - - +
238D MET* 2.7 66.9 + - + +
240D CYS* 4.1 19.3 - - + -
260D ARG* 4.5 4.7 - - + +
261D ILE* 1.3 74.2 - - - +
263D ILE* 1.3 64.5 + - - +
264D MET* 3.9 22.1 - - + +
270D ILE* 3.8 26.7 - - + -
271D VAL 3.4 5.4 - - - +
272D GLU* 3.4 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 4.8 6.3 - - + -
236D CYS 3.4 10.3 - - - +
237D MET* 3.7 29.4 - - + -
261D ILE* 4.3 8.3 - - + +
262D ILE* 1.3 77.0 - - - +
264D MET* 1.3 64.1 + - - +
265D TYR* 3.5 42.2 - - + +
269D THR 3.7 1.0 - - - +
270D ILE* 3.2 6.2 - - - +
271D VAL* 2.8 45.5 + - + +
367D LEU* 4.6 4.0 - - + -
368D ARG 3.1 31.4 - - - +
369D GLN* 4.4 7.6 - - + -
371D LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D VAL* 3.9 36.6 - - + -
197D MET* 3.6 16.5 - - + +
216D LEU* 3.9 26.9 - - + -
218D LEU* 5.0 5.2 - - - -
229D ILE* 4.5 0.7 - - + -
235D GLY* 3.3 2.6 - - - -
236D CYS* 2.8 49.6 + - + +
238D MET* 3.9 32.5 - - + -
262D ILE* 3.9 27.1 - - + +
263D ILE* 1.3 78.2 - - - +
265D TYR* 1.3 64.0 + - - +
269D THR 3.6 4.0 - - - -
270D ILE* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D MET* 4.5 2.2 - - - +
214D LYS* 3.6 8.5 - - - +
232D VAL* 4.6 6.1 - - + -
233D PRO 3.9 15.7 - - - -
234D GLY* 3.3 19.3 - - - +
235D GLY* 4.4 1.8 - - - -
263D ILE* 3.5 32.4 - - + +
264D MET* 1.3 75.9 - - - +
266D TYR* 1.3 65.4 + - - +
267D ASN* 3.1 24.5 - - - +
268D ASP* 3.0 15.4 + - - -
269D THR* 3.0 31.3 + - + +
271D VAL* 5.3 1.1 - - + -
367D LEU* 4.4 13.3 - - + +
368D ARG* 5.4 0.5 - - - -
369D GLN* 3.7 42.2 + - + +
----------------------------------------------------------
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