Contacts of the strand formed by residues 164 - 171 (chain B) in PDB entry 3E88
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 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B G96 3.4 10.1 - - - -
160B LYS* 3.9 2.4 - - - +
161B GLY 2.8 34.6 + - - +
162B THR 3.6 1.2 - - - -
163B PHE* 1.3 82.3 - - - +
165B LYS* 1.3 61.2 + - - +
182B ILE 3.4 12.8 - - - -
183B LEU* 4.4 0.7 - - - -
184B ARG* 4.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B G96 3.5 6.4 - - - -
157B LEU* 3.7 20.9 - - + -
159B GLY 3.7 5.2 - - - +
160B LYS* 4.0 9.9 - - + +
164B GLY* 1.3 75.5 - - - +
166B VAL* 1.3 61.2 + - - +
167B ILE* 4.3 24.4 - - + +
180B MET 3.8 0.3 - - - +
181B LYS* 3.5 1.4 - - - -
182B ILE* 2.7 56.7 + - + +
224B ARG* 6.1 1.3 - - - +
448B ILE* 5.8 1.8 - - - +
449B THR* 3.5 20.6 + - - +
451B TPO 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B G96 3.5 83.5 - - + +
157B LEU* 3.4 5.2 - - - +
158B LEU* 3.0 27.2 + - + -
159B GLY 2.8 14.4 + - - +
165B LYS* 1.3 73.7 - - - +
167B ILE* 1.3 65.3 + - - +
179B ALA* 4.4 5.4 - - + -
180B MET 3.2 18.4 - - - +
181B LYS* 3.9 17.7 - - + +
229B MET* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 4.2 18.6 - - + -
155B LEU 4.1 8.5 - - - +
156B LYS 3.2 15.3 - - - +
157B LEU* 4.1 13.2 - - + -
158B LEU* 4.2 5.6 - - - +
165B LYS* 4.3 26.5 - - + +
166B VAL* 1.3 82.7 - - - +
168B LEU* 1.3 79.1 + - - +
169B VAL* 3.4 13.5 + - + +
179B ALA* 3.5 0.5 - - - -
180B MET* 2.8 42.3 + - + +
182B ILE* 4.4 9.0 - - + -
448B ILE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.0 39.9 + - + +
156B LYS* 2.8 22.6 + - + +
158B LEU* 3.8 15.8 - - + +
167B ILE* 1.3 73.1 - - - +
169B VAL* 1.3 61.6 + - - +
177B TYR* 4.6 9.9 - - + -
178B TYR 3.7 15.3 - - - +
231B TYR* 3.8 37.0 - - + +
433B GLU 4.6 0.4 - - - +
434B VAL* 3.9 32.3 - - + -
436B THR* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PHE* 4.0 22.2 - - + -
153B ASP 3.1 17.0 - - - +
154B TYR* 3.7 29.8 - - + -
155B LEU* 4.5 5.6 - - - -
167B ILE* 3.4 10.5 + - + +
168B LEU* 1.3 78.5 - - - +
170B ARG* 1.3 60.3 + - - +
177B TYR* 3.4 6.1 - - - +
178B TYR* 2.8 58.2 + - + +
180B MET* 4.0 22.0 - - + -
228B VAL* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PHE* 3.3 5.5 - - - -
153B ASP* 2.9 58.0 + - + +
155B LEU* 3.8 21.1 - - + +
169B VAL* 1.3 72.8 - - - +
171B GLU* 1.3 70.0 + - - +
172B LYS* 3.3 2.7 + - - +
175B GLY* 3.5 35.6 - - - +
176B ARG 3.5 3.6 - - - +
177B TYR* 3.6 35.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A HIS* 5.4 0.9 + - - -
151B ASP* 4.6 3.1 - - + +
152B PHE* 3.8 24.4 - - + -
169B VAL 4.1 0.8 - - - -
170B ARG* 1.3 68.7 - - - +
172B LYS* 1.3 58.2 + - - +
173B ALA* 4.1 13.0 - - + +
174B THR* 2.9 35.6 + - - +
175B GLY* 2.7 36.0 + - - -
176B ARG* 2.8 15.0 + - - +
178B TYR* 3.6 23.3 + - + -
216B LYS* 4.5 3.5 - - - -
217B TYR* 2.6 40.3 + - - -
----------------------------------------------------------
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