Contacts of the strand formed by residues 150 - 160 (chain B) in PDB entry 4L9L
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 LYS 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 4.7 15.7 + - + +
169A SER* 4.8 3.6 + - - -
144B GLU* 3.3 26.9 + - - +
145B ILE* 3.6 8.3 + - - -
148B THR* 3.1 21.2 - - - +
149B GLN* 1.3 81.8 - - + +
151B ALA* 1.3 60.2 + - - +
205B ARG* 3.5 46.1 - - + +
206B VAL 3.8 8.7 - - - +
207B SER* 5.3 3.4 - - - -
208B ALA* 4.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PRO* 3.7 24.2 - - + -
144B GLU* 3.9 2.0 - - - -
145B ILE* 4.2 9.4 - - + -
150B LYS* 1.3 74.5 - - - +
152B THR* 1.3 62.8 + - - +
153B LEU* 5.7 1.0 - - - +
204B LEU 3.9 0.5 - - - +
205B ARG* 3.2 3.3 - - - +
206B VAL* 2.7 47.7 + - + +
207B SER 4.5 1.6 - - - +
208B ALA* 4.4 1.5 - - - +
211B TRP* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.5 8.0 - - - +
133A LEU* 3.6 25.4 - - + +
135A THR* 5.3 2.0 + - - -
138B PHE 4.3 1.0 - - - +
140B PRO* 3.3 24.5 - - - +
144B GLU* 2.7 29.1 + - - +
151B ALA* 1.3 72.2 - - - +
153B LEU* 1.3 72.6 + - - +
154B VAL* 4.1 1.4 + - + -
203B ARG* 4.2 19.7 - - + -
204B LEU 3.3 9.0 - - - +
205B ARG* 3.2 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 5.3 3.1 - - + -
138B PHE 3.7 10.5 - - - +
139B GLU* 4.3 1.6 - - - -
140B PRO* 3.9 15.7 - - + -
151B ALA 5.7 1.1 - - - +
152B THR* 1.3 73.8 - - - +
154B VAL* 1.3 62.5 + - - +
155B CYS 4.3 0.4 - - - -
169B TRP* 4.1 17.7 - - + -
202B SER 3.8 0.2 - - - +
203B ARG* 3.3 5.7 - - - -
204B LEU* 2.6 52.1 + - + +
206B VAL* 5.5 5.8 - - + -
211B TRP* 3.8 26.7 - - + -
218B PHE* 3.7 39.5 - - + -
249B ALA* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.6 27.1 - - + -
131A VAL* 4.7 6.1 - - + -
133A LEU* 4.5 8.5 - - + -
173A VAL* 3.8 27.6 - - + -
137B VAL* 3.4 0.4 - - - -
138B PHE* 2.8 48.2 + - + -
152B THR* 4.5 2.9 - - + -
153B LEU* 1.3 79.6 - - - +
155B CYS* 1.3 67.2 + - - +
156B LEU* 4.1 15.7 - - + -
169B TRP* 4.3 2.9 - - - -
202B SER 3.4 5.8 - - - +
203B ARG* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.5 18.4 - - - -
136B ALA 3.3 5.8 - - - +
137B VAL* 4.2 0.4 - - - -
154B VAL* 1.3 73.4 - - - +
156B LEU* 1.3 76.5 + - - +
157B ALA 4.2 0.2 - - - -
167B LEU* 4.0 11.9 - - - -
169B TRP* 3.4 17.8 - - + -
201B SER* 3.3 2.1 - - - -
202B SER* 2.9 33.4 + - - +
220B CYS* 2.0 48.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 4.1 11.9 - - + -
131A VAL* 3.6 17.7 - - + -
173A VAL* 4.2 1.3 - - + -
175A TRP* 3.7 46.0 - - + -
134B GLU 3.0 13.7 - - - +
135B VAL* 3.5 0.3 - - - -
136B ALA* 2.9 28.9 + - + +
138B PHE* 3.5 31.0 - - + -
154B VAL* 4.1 12.3 - - + -
155B CYS* 1.3 86.2 - - - +
157B ALA* 1.3 60.2 + - - +
158B THR* 3.9 12.1 - - + +
200B LEU 3.6 1.6 - - - +
201B SER* 3.9 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PRO* 4.3 13.2 - - + -
134B GLU 3.4 5.6 - - - -
135B VAL* 4.5 1.1 - - + +
155B CYS* 4.2 1.0 - - - -
156B LEU* 1.3 72.1 - - - +
158B THR* 1.3 58.3 + - - +
160B PHE* 3.3 12.6 - - + -
165B VAL* 5.8 0.2 - - + -
167B LEU* 4.7 3.1 - - + -
199B ALA* 3.3 2.9 - - - -
200B LEU* 2.8 47.8 + - + +
222B VAL* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 4.5 19.0 + - + +
175A TRP* 4.6 17.0 - - + +
133B PRO* 3.6 1.0 - - - +
134B GLU* 2.9 52.8 + - - +
156B LEU* 4.3 19.7 - - + +
157B ALA* 1.3 79.3 - - - +
159B GLY* 1.3 65.2 + - - +
160B PHE* 3.4 3.4 + - - -
189B GLU* 3.3 14.1 - - - +
198B TYR 3.8 2.9 - - - -
199B ALA* 4.2 10.5 - - + +
200B LEU 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.7 8.7 - - - +
132B PRO 3.7 9.7 - - - +
134B GLU* 5.6 4.9 - - - +
158B THR* 1.3 73.9 - - - +
160B PHE* 1.3 57.7 + - - +
189B GLU* 2.9 27.1 + - - -
197B ARG* 3.4 31.7 + - - -
198B TYR 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE 3.4 13.2 - - - +
132B PRO 4.2 0.2 - - - -
133B PRO* 3.6 34.5 - - + -
157B ALA* 3.3 31.9 - - + -
158B THR 4.0 1.8 - - - -
159B GLY* 1.3 77.6 - - - +
161B TYR* 1.3 61.0 + - - +
162B PRO 3.8 11.9 - - - -
163B ASP* 4.1 9.0 - - - -
165B VAL* 3.6 36.8 - - + -
186B PRO* 3.9 13.9 - - + -
197B ARG* 3.9 1.1 - - - +
198B TYR* 3.0 61.8 + - + -
199B ALA* 3.7 2.7 - - - -
200B LEU* 4.0 3.4 - - + -
224B PHE* 4.2 2.5 - + + -
----------------------------------------------------------
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