Contacts of the strand formed by residues 233 - 237 (chain D) in PDB entry 5FHK
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 233 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D LEU* 4.1 24.5 - - + -
165D VAL 3.3 11.2 - - - +
166D ALA* 4.1 8.5 - - + -
170D TYR* 3.9 13.7 - - + -
177D PRO* 4.3 7.2 - - + -
183D LEU* 4.1 16.8 - - + -
186D HIS* 3.8 34.8 - - + +
187D PHE 2.9 9.2 + - - +
188D LEU* 3.4 10.1 - - + -
189D LEU 2.8 26.8 + - - +
197D TRP* 3.6 6.8 - - + -
232D GLY* 1.3 75.5 - - - -
234D THR* 1.3 69.1 + - - +
253D ILE* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ILE 3.6 1.0 - - - +
164D LEU* 3.2 9.3 - - - +
165D VAL* 3.0 46.9 + - + +
189D LEU* 2.7 25.6 + - - -
190D LYS* 4.7 0.9 - - - -
191D GLY 4.9 1.0 + - - -
197D TRP* 4.1 1.3 - - - -
220D LEU* 6.0 0.3 - - - +
223D VAL* 3.1 20.5 - - + +
227D CYS* 3.8 17.5 - - + -
232D GLY 4.2 0.4 + - - -
233D ILE* 1.3 75.2 - - - +
235D LEU* 1.3 69.6 + - - +
236D MET* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASP* 3.7 15.0 - - + +
163D ILE* 3.4 35.2 - - - +
164D LEU* 3.7 14.4 - - + +
191D GLY 5.5 1.4 + - - +
194D LEU* 3.6 28.7 - - + +
196D LYS 5.3 0.2 - - - +
197D TRP* 3.4 57.5 - - + +
199D LEU* 4.4 9.2 - - + -
220D LEU* 4.7 4.5 - - - +
234D THR* 1.3 81.6 + - - +
236D MET* 1.3 64.5 + - - +
259D ALA* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASP* 3.9 3.1 - - - -
163D ILE* 2.8 33.2 + - - +
165D VAL* 4.8 2.0 - - + -
194D LEU* 4.3 0.4 - - - -
220D LEU* 4.2 32.5 - - - +
223D VAL* 4.8 1.8 - - + -
224D ARG* 3.8 37.2 - - + +
227D CYS* 5.7 0.4 - - + -
234D THR* 3.5 29.2 - - + +
235D LEU* 1.3 75.9 - - - +
237D PRO* 1.3 83.8 - - + +
238D ASP 3.3 0.3 + - - -
240D MET* 4.4 10.1 - - + +
241D ILE* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASN* 5.5 1.1 - - + +
101D LEU* 3.8 24.7 - - + -
160D VAL* 4.0 4.7 - - + -
161D LYS 3.7 1.8 - - - +
162D ASP* 3.3 23.5 - - - +
194D LEU* 3.9 13.0 - - + -
220D LEU* 4.2 10.5 - - + -
236D MET* 1.3 90.7 - - + +
238D ASP* 1.3 68.5 + - - +
239D VAL 3.2 0.4 - - - +
240D MET* 3.0 37.4 + - + +
241D ILE* 3.8 4.5 + - - +
262D ARG* 3.6 13.5 - - - +
----------------------------------------------------------
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