Contacts of the strand formed by residues 131 - 143 (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 GLY 131 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D GLN 3.4 2.4 + - - -
130D ASP* 1.3 76.5 - - - +
132D LEU* 1.3 61.5 + - - -
133D TYR* 3.3 10.9 - - - -
212D GLN* 3.5 11.1 - - - +
213D LEU 2.9 34.7 + - - +
242D MET* 4.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.9 17.2 - - + +
89B ALA* 4.6 8.5 - - + -
112B PHE* 3.3 37.7 - - + -
114B THR* 5.7 0.7 - - + -
241B VAL* 4.3 7.0 - - + -
131D GLY* 1.3 73.1 - - - -
133D TYR* 1.3 62.1 + - - +
210D LEU* 3.5 35.2 - - + -
211D VAL 3.9 5.4 - - - +
212D GLN* 4.1 29.2 - - + +
242D MET* 3.6 8.2 - - - +
243D VAL* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PRO* 3.8 13.5 - - + +
127D LEU* 3.3 35.3 - - + +
129D GLN* 2.3 52.3 + - - +
131D GLY 3.3 24.7 - - - -
132D LEU* 1.3 75.0 - - - +
134D TYR* 1.3 60.9 + - - +
135D LEU* 3.8 7.8 + - + -
210D LEU* 3.3 8.4 - - - +
211D VAL* 2.9 36.9 + - - +
213D LEU* 3.8 28.9 - - + -
240D ALA 4.8 0.2 - - - -
241D VAL* 3.2 8.7 - - - +
242D MET* 3.4 39.4 - - + -
243D VAL* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.5 37.4 - + - -
168A TYR* 4.8 4.5 + - - -
134B TYR* 3.3 27.0 + + - -
136B TYR* 3.6 27.8 - + - +
133D TYR* 1.3 73.6 - - - +
135D LEU* 1.3 60.0 + - - +
136D TYR* 4.0 21.8 - + + +
208D GLY* 3.5 13.9 + - - -
209D GLY 3.6 20.4 - - - -
210D LEU* 3.8 24.2 - - + +
239D GLY 3.8 0.5 - - - +
240D ALA* 3.2 4.9 - - - -
241D VAL* 2.8 37.8 + - + +
243D VAL* 4.2 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU* 5.8 1.3 - - + -
127D LEU* 5.1 0.2 - - + -
133D TYR* 4.3 3.1 - - + +
134D TYR* 1.3 75.4 - - - +
136D TYR* 1.3 61.7 + - - +
161D SER* 4.5 9.2 - - - +
178D LEU* 3.9 19.3 - - + -
179D LEU* 3.7 10.6 - - + +
207D PHE* 6.1 0.2 - - - -
208D GLY* 3.1 2.6 - - - -
209D GLY 2.8 39.2 + - - +
211D VAL* 3.6 29.8 - - + -
213D LEU* 3.8 20.2 - - + -
219D VAL* 4.1 25.4 - - + -
239D GLY 3.5 2.7 - - - +
240D ALA* 3.4 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.1 15.5 - + - -
170A GLY 4.3 8.3 - - - +
171A ALA* 3.7 3.1 - - + -
172A ALA* 3.3 32.9 + - + +
90D ALA 3.5 4.0 + - - -
91D HIS* 2.5 42.9 + - - +
134D TYR* 4.0 19.3 - + + -
135D LEU* 1.3 77.7 - - - +
137D CYS* 1.3 64.2 + - - +
207D PHE* 3.4 11.7 - - - +
208D GLY* 4.1 1.8 - - - -
237D PHE* 3.6 25.6 - + - -
238D PHE* 3.1 6.1 - - - +
239D GLY* 2.9 67.6 + - - +
240D ALA* 4.0 4.5 - - - -
241D VAL* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TRP* 5.1 1.1 - - - -
136D TYR* 1.3 80.6 - - - +
138D LEU* 1.3 62.7 + - - +
139D VAL* 4.1 20.4 - - - -
159D LEU* 4.2 6.2 - - - +
160D ARG 5.7 0.4 - - - -
161D SER* 5.3 1.1 - - - -
205D VAL 4.2 0.5 - - - +
206D GLY* 3.2 2.6 - - - -
207D PHE* 2.9 62.4 + - + -
221D VAL* 3.8 29.2 - - + -
237D PHE* 3.5 13.2 - - - -
238D PHE* 3.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER 4.1 14.8 - - - +
151A SER* 5.3 2.2 - - - -
168A TYR 4.0 9.0 - - - +
169A HIS* 3.8 29.4 - - + -
170A GLY 6.0 0.2 - - - +
137D CYS* 1.3 74.3 - - - +
139D VAL* 1.3 68.2 + - - +
140D GLY 4.5 0.2 - - - +
204D SER* 4.6 13.2 - - - +
205D VAL 3.4 9.2 - - - +
206D GLY* 4.2 15.9 - - - +
235D LYS 3.1 29.4 - - - +
236D THR* 3.2 3.1 - - - -
237D PHE* 2.9 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TRP* 4.8 3.8 - - + -
137D CYS* 4.1 10.8 - - - -
138D LEU* 1.3 81.9 - - - +
140D GLY* 1.3 62.1 + - - +
141D TYR* 3.6 36.3 - - + +
159D LEU* 3.6 23.8 - - + +
204D SER* 3.5 0.7 - - - -
205D VAL* 2.9 35.0 + - - +
223D ILE* 3.4 25.6 - - + -
229D VAL* 3.8 9.9 - - + -
235D LYS 3.4 2.0 - - - -
236D THR* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL* 1.3 74.8 - - - +
141D TYR* 1.3 54.6 + - - -
203D THR 3.8 0.2 - - - -
204D SER* 3.5 18.4 - - - -
229D VAL* 3.4 7.6 - - - +
230D ASP* 2.5 42.6 + - - +
235D LYS* 2.7 22.3 + - - -
236D THR* 3.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL* 3.6 25.1 - - + -
140D GLY* 1.3 74.1 - - - -
142D ARG* 1.3 62.0 - - - +
157D VAL* 3.8 39.3 - - + -
158D THR 3.3 6.1 + - - -
159D LEU* 2.9 33.6 - - + +
201D TRP 3.4 3.7 - - - +
202D TYR* 3.6 6.2 - - - -
203D THR* 2.8 50.2 + - - +
205D VAL* 4.6 8.3 - - + -
223D ILE* 3.1 19.6 - - + +
224D SER* 4.3 1.5 + - - -
225D HIS 3.9 17.0 - - - -
228D MET* 3.2 26.5 - - + +
229D VAL* 3.7 8.5 - - + -
230D ASP* 4.0 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TYR* 1.3 75.8 - - - +
143D GLY* 1.3 64.9 + - - +
200D LEU* 4.1 20.2 - - + +
201D TRP 3.4 4.9 - - - -
202D TYR* 3.5 33.8 + - + -
228D MET* 3.0 29.6 + - - +
229D VAL 5.6 0.2 - - - -
230D ASP* 4.2 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ARG* 1.3 79.1 - - - +
144D ARG* 1.3 59.3 + - - -
200D LEU* 2.9 9.2 - - - +
201D TRP* 2.4 48.1 + - - -
228D MET* 4.8 9.4 - - - -
----------------------------------------------------------
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