Contacts of the strand formed by residues 229 - 235 (chain A) in PDB entry 2MJN
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 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 4.2 14.6 - - + +
223A PHE* 3.5 31.9 - - + -
224A SER* 3.6 24.5 - - - +
227A GLY 3.7 5.6 - - - +
228A GLN* 1.3 84.2 + - - +
230A MET* 1.3 65.5 + - - +
231A GLU 3.7 10.3 - - - +
232A ILE* 3.6 31.4 - - + -
243A VAL* 3.8 8.1 - - + -
244A ARG 3.6 2.0 - - - +
245A PHE* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 5.3 2.2 - - - +
229A ILE* 1.3 79.4 - - - +
231A GLU* 1.3 60.5 + - + +
244A ARG* 2.7 23.9 + - + +
245A PHE 3.5 6.3 - - - +
246A ASN* 3.5 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.8 0.6 - - - -
230A MET* 1.3 81.0 - - - +
232A ILE* 1.3 79.3 + - - +
233A ARG* 2.6 46.3 + - + +
242A PHE 4.4 1.8 - - - +
244A ARG* 2.7 73.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU* 3.4 42.0 - - + +
219A MET* 3.9 11.2 - - + -
220A ARG* 3.7 39.3 - - + +
229A ILE* 3.6 23.1 - - + -
231A GLU* 1.3 87.0 - - - +
233A ARG* 1.3 62.2 + - - +
234A VAL* 3.7 15.1 + - + +
241A SER* 5.6 0.2 - - - -
242A PHE 3.7 2.5 - - - +
243A VAL* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 2.6 48.4 + - - +
232A ILE* 1.3 74.4 - - - +
234A VAL* 1.3 61.4 + - - +
235A PHE* 3.9 23.1 - - + -
241A SER* 3.1 4.9 - - - -
242A PHE* 2.7 61.0 + - + +
244A ARG* 3.6 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.0 15.0 - - + +
215A THR* 3.6 24.0 - - - +
216A GLU* 4.1 19.3 - - + +
219A MET* 4.0 3.4 - - + -
232A ILE* 3.7 17.9 - - + +
233A ARG* 1.3 77.6 - - - +
235A PHE* 1.3 74.8 + - - +
236A PRO* 3.9 6.2 - - + +
240A TYR 4.0 0.2 - - - -
241A SER* 3.2 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.7 1.5 - - - +
233A ARG* 3.9 34.5 - - + -
234A VAL* 1.3 80.4 - - - +
236A PRO* 1.4 63.3 - - - +
237A ASP* 3.2 11.0 - - - +
238A LYS* 3.3 24.2 + - + -
239A GLY 2.9 22.0 + - - -
240A TYR* 2.9 61.6 + + + +
242A PHE* 4.1 15.3 - + - -
----------------------------------------------------------
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