Contacts of the strand formed by residues 259 - 268 (chain F) in PDB entry 2JJD
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 259 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F ASN 5.9 0.2 - - - +
219F TRP* 4.4 28.7 - - + +
220F ARG* 4.8 9.6 - - + +
223F TRP* 3.8 34.8 - - + -
255F THR* 4.3 2.2 - - - -
256F TYR* 2.7 41.5 + - - +
257F GLY 3.3 2.4 + - - -
258F ASN* 1.3 89.5 - - + +
260F ARG* 1.3 58.6 + - - +
261F VAL* 3.7 11.5 + - + -
279F ILE* 4.2 27.1 - - + -
280F GLN 3.6 5.2 - - - +
281F PRO* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F CYS* 5.9 1.6 - - + -
254F TRP 3.5 9.0 - - - +
255F THR* 4.0 10.8 - - - +
258F ASN 4.2 0.8 - - - -
259F ILE* 1.3 70.9 - - - +
261F VAL* 1.3 62.6 + - - +
262F CYS* 4.8 7.3 - - - -
278F CYS 3.5 4.0 - - - +
279F ILE* 3.4 2.9 - - - -
280F GLN* 2.6 40.1 + - + +
281F PRO* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F TRP* 3.5 51.8 - - + -
249F PRO* 3.9 17.9 - - + +
253F CYS* 3.3 0.7 - - - -
254F TRP 2.9 33.5 + - - +
256F TYR* 3.7 17.9 - - + -
259F ILE* 4.3 6.7 - - + -
260F ARG* 1.3 75.0 - - - +
262F CYS* 1.3 67.1 + - - +
277F PHE* 3.9 19.1 - - + -
278F CYS 3.9 2.7 - - - -
279F ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F PRO* 4.5 0.4 - - - -
252F GLY 3.5 4.5 - - - +
253F CYS* 2.1 46.9 - - - -
260F ARG* 4.8 8.1 - - - -
261F VAL* 1.3 77.9 - - - +
263F VAL* 1.3 65.4 - - - +
264F GLU* 3.4 17.1 + - - +
277F PHE* 3.3 7.6 - - - -
278F CYS* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F TRP* 5.1 0.2 - - + -
249F PRO* 2.9 42.8 - - + +
250F ASP 3.8 14.6 - - - +
251F GLN* 5.3 0.2 - - - -
252F GLY* 3.1 19.5 + - - +
262F CYS* 1.3 72.1 - - - +
264F GLU* 1.3 67.6 + - - +
265F ASP* 4.1 22.0 - - - +
266F CYS* 4.9 7.0 - - + +
275F ARG* 5.4 3.6 - - + -
276F LYS 3.9 4.0 - - - +
277F PHE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU* 3.5 35.2 - - + +
572B THR* 6.1 0.5 - - - +
584B VAL* 5.0 14.3 - - + +
262F CYS* 3.9 13.8 - - - +
263F VAL* 1.3 80.1 - - - +
265F ASP* 1.3 61.6 + - - +
276F LYS* 2.8 22.4 + - + +
277F PHE 4.6 1.1 - - - -
278F CYS* 3.8 27.6 - - + +
292F LEU* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B GLN* 6.3 2.2 - - + +
584B VAL* 6.2 1.8 - - + -
263F VAL* 3.8 8.6 - - - +
264F GLU* 1.3 81.3 - - + +
266F CYS* 1.3 62.0 + - - +
267F VAL* 5.2 8.5 - - + -
274F ILE* 4.4 1.3 - - + -
275F ARG* 3.3 4.7 - - - +
276F LYS* 2.7 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F VAL* 4.9 6.2 - - + +
265F ASP* 1.3 74.6 - - - +
267F VAL* 1.3 64.1 + - - +
268F VAL* 4.1 8.8 + - + +
273F THR* 5.9 1.1 - - - +
274F ILE 3.3 5.4 - - - -
275F ARG* 3.8 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B GLY* 5.7 6.7 - - - +
265F ASP* 5.2 8.5 - - + -
266F CYS* 1.3 76.8 - - - +
268F VAL* 1.3 62.6 + - - +
269F LEU* 3.7 19.0 + - + +
273F THR* 3.2 3.3 - - - -
274F ILE* 2.8 58.1 + - + +
491F ARG* 4.0 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F CYS* 4.1 8.0 + - + +
267F VAL* 1.3 72.6 - - - +
269F LEU* 1.3 75.1 + - - +
273F THR* 3.7 28.7 - - + +
275F ARG* 6.1 1.8 - - - +
491F ARG* 3.4 26.3 + - - +
----------------------------------------------------------
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