Contacts of the strand formed by residues 236 - 242 (chain D) in PDB entry 4MXW
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 THR 236 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.4 7.6 - - - +
94D GLY* 2.6 43.7 + - - -
102D LEU* 6.0 0.9 - - - -
104D TRP* 4.0 4.5 - - - -
138D LEU 3.2 4.7 - - - -
139D VAL* 3.6 9.9 - - + -
140D GLY 3.3 15.3 - - - +
223D ILE* 5.9 0.4 - - - -
229D VAL* 3.5 19.5 - - + -
230D ASP 3.1 26.0 + - - +
231D PHE* 4.1 6.6 - - - -
233D ARG 3.6 2.5 + - - +
234D GLY* 5.8 0.4 - - - -
235D LYS* 1.3 84.7 - - - +
237D PHE* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU 4.5 5.8 - - - -
149A LEU* 4.0 16.4 - - + -
169A HIS* 5.0 4.7 - - + -
170A GLY 3.8 10.1 - - - -
171A ALA* 3.5 22.0 - - + -
91D HIS* 3.2 31.2 - + + +
92D LEU 3.0 18.2 - - - +
93D ILE* 4.3 3.6 - - + -
104D TRP* 3.6 8.1 - - - -
136D TYR* 3.6 12.1 - + - -
137D CYS* 3.5 2.3 - - - -
138D LEU* 2.9 72.1 + - + +
234D GLY* 4.2 21.5 - - - -
235D LYS 4.2 0.7 - - - -
236D THR* 1.3 84.1 - - - +
238D PHE* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D HIS* 5.0 0.2 - - - -
92D LEU* 2.9 62.4 + - + +
104D TRP* 3.6 49.4 - + + -
119D PHE* 4.2 15.3 - + - -
125D LEU* 4.3 15.9 - - + -
136D TYR* 3.1 20.6 - - - +
137D CYS* 3.8 17.0 - - + -
161D SER* 5.4 2.0 - - - -
219D VAL* 4.3 22.4 - - + -
220D TYR* 4.8 3.8 - - - -
221D VAL* 4.2 21.1 - - + -
237D PHE* 1.3 75.4 - - - +
239D GLY* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ALA* 3.1 15.7 - - - -
92D LEU* 4.5 2.7 - - - -
125D LEU* 5.1 1.3 - - - -
135D LEU* 3.5 4.0 - - - +
136D TYR* 2.9 52.8 + - - -
238D PHE* 1.3 82.3 - - - +
240D ALA* 1.3 61.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 3.0 4.6 - - - -
90D ALA* 2.7 35.1 + - - +
125D LEU* 4.2 13.9 - - + -
127D LEU* 4.0 23.8 - - + -
133D TYR* 4.7 1.1 - - + -
134D TYR 3.2 6.1 - - - -
135D LEU* 3.4 24.9 - - + -
136D TYR* 4.0 0.8 - - - -
239D GLY* 1.3 74.3 - - - -
241D VAL* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 4.9 0.7 - - + -
108A PHE* 5.6 2.5 - - + -
172A ALA* 3.3 34.1 - - + -
205A LEU* 2.8 34.8 - - + -
87D LEU* 4.1 11.0 - - + -
88D PRO 4.1 0.7 - - - -
89D ALA* 3.6 14.4 - - + -
90D ALA 5.1 0.2 - - - +
133D TYR* 3.2 6.3 - - - -
134D TYR* 2.8 37.8 + - + +
136D TYR* 4.9 2.9 - - + -
240D ALA* 1.3 82.7 - - - +
242D MET* 1.3 77.5 + - - +
243D VAL* 4.2 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 4.2 7.4 - - - +
87D LEU* 4.0 24.7 - - + +
88D PRO* 3.4 28.1 + - + +
129D GLN* 4.3 12.6 - - + +
130D ASP 4.3 14.4 - - - +
131D GLY* 4.7 4.7 - - - -
132D LEU 3.6 11.2 - - - +
133D TYR* 3.4 30.2 - - + -
241D VAL* 1.3 90.2 - - - +
243D VAL* 1.3 74.6 + - - +
----------------------------------------------------------
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