Contacts of the helix formed by residues 164 - 179 (chain B) in PDB entry 3KEU
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 SER 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.6 2.8 - - - +
163B HIS* 1.3 82.7 - - - +
165B GLN* 1.3 69.0 + - - +
166B GLU* 3.8 9.1 + - - +
167B GLU* 3.1 26.8 + - - +
168B ALA* 3.0 21.5 + - - +
190B LEU* 3.5 11.5 - - - +
191B PRO* 5.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 1.3 73.2 - - - +
166B GLU* 1.3 65.3 + - + +
168B ALA* 3.1 4.6 + - - +
169B LEU* 2.9 38.4 + - + +
190B LEU* 3.9 13.0 - - + +
191B PRO* 5.6 1.0 - - - +
202B LEU* 4.5 13.5 - - + -
220B ARG* 2.6 49.5 - - - +
312B LEU* 3.6 27.7 - - + +
518B MPD 4.4 8.6 - - - +
522B MPD 3.7 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.2 9.4 + - - +
165B GLN* 1.3 81.7 - - + +
167B GLU* 1.3 63.5 + - + +
169B LEU* 3.4 11.2 + - + +
170B ARG* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS 3.5 13.1 - - - +
162B ILE* 4.1 7.4 - - - -
163B HIS* 2.9 53.1 + - - +
164B SER* 3.1 19.7 + - - +
166B GLU* 1.3 77.9 - - + +
168B ALA* 1.3 63.4 + - - +
170B ARG* 3.3 19.4 + - - +
171B VAL* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.8 16.0 - - + +
164B SER 3.0 13.4 + - - +
165B GLN 3.3 8.7 - - - +
167B GLU* 1.3 75.9 - - - +
169B LEU* 1.3 50.9 + - - +
171B VAL* 2.8 14.2 - - - +
172B MET* 2.7 39.3 + - + +
185B ILE* 4.2 6.3 - - + -
190B LEU* 4.3 2.9 - - + -
202B LEU* 3.3 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 2.9 33.9 + - + +
166B GLU* 3.8 9.9 - - + +
167B GLU 3.3 0.2 - - - -
168B ALA* 1.3 76.3 - - - +
170B ARG* 1.3 57.7 + - - +
172B MET* 3.2 26.1 + - + +
173B ASP* 2.9 33.7 + - - +
202B LEU* 5.0 3.1 - - + -
203B GLY 5.8 0.2 - - - +
218B ARG* 3.8 54.5 + - + +
219B ILE 5.9 0.2 - - - +
312B LEU* 4.3 21.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
160B ARG* 3.5 27.0 - - - +
166B GLU* 3.2 15.7 + - - +
167B GLU* 3.6 23.0 + - - +
169B LEU* 1.3 74.0 - - - +
171B VAL* 1.3 67.1 + - - +
173B ASP* 3.2 11.0 + - + +
174B MET* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA* 4.4 8.3 - - + +
158B SER* 3.5 27.4 - - - +
160B ARG* 4.0 10.1 - - + -
161B LYS 5.0 0.7 - - - +
162B ILE* 3.2 37.9 - - + -
167B GLU* 3.0 17.8 + - + +
168B ALA* 2.8 22.7 - - - +
170B ARG* 1.3 76.0 - - + +
172B MET* 1.3 59.6 + - + +
174B MET* 3.0 21.9 + - + +
175B LEU* 2.7 33.9 + - + +
185B ILE* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA 2.7 33.4 + - - +
169B LEU* 3.5 31.2 - - + +
170B ARG 3.1 0.2 - - - -
171B VAL* 1.3 78.4 - - + +
173B ASP* 1.3 57.3 + - - +
175B LEU* 3.2 9.8 + - + +
176B HIS* 2.9 33.6 + - - -
183B VAL* 3.8 22.2 - - + +
185B ILE* 3.7 18.2 - - + -
202B LEU* 3.5 42.2 - - + +
203B GLY 4.5 0.9 - - - -
204B SER* 4.1 27.4 - - - +
218B ARG* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU 2.9 19.3 + - - +
170B ARG* 3.6 10.4 - - + +
172B MET* 1.3 72.8 - - - +
174B MET* 1.3 67.0 + - - +
176B HIS* 3.2 7.5 + - - +
177B SER 2.9 19.1 + - - -
204B SER* 4.9 0.5 + - - -
216B MET* 3.5 21.3 - - - +
218B ARG* 3.5 23.4 + - - -
520B MPD 3.3 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 4.2 18.8 - - - +
160B ARG* 3.4 58.1 - - + +
170B ARG* 2.9 23.0 + - + +
171B VAL* 3.0 40.6 + - + +
173B ASP* 1.3 77.4 - - - +
175B LEU* 1.3 61.8 + - - +
177B SER* 2.5 26.2 + - - +
178B MET* 3.1 15.4 + - + +
520B MPD 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 4.6 2.0 - - + +
147B ILE* 4.2 18.6 - - + -
149B PRO* 4.4 3.4 - - + -
154B ALA* 4.0 30.7 - - + +
157B LEU* 3.9 23.1 - - + -
158B SER* 4.6 7.0 - - - +
171B VAL* 2.7 24.8 + - + +
172B MET* 3.4 9.2 - - + +
174B MET* 1.3 72.7 - - + +
176B HIS* 1.3 62.0 + - - +
178B MET* 3.0 35.8 + - + +
179B GLY 3.3 7.8 + - - -
180B PRO* 3.6 8.3 - - - +
183B VAL* 3.8 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B MET 2.9 27.5 + - - -
173B ASP* 3.2 8.5 + - - +
175B LEU* 1.3 73.6 - - - +
177B SER* 1.3 57.6 + - - +
179B GLY* 2.9 26.3 + - - +
180B PRO 2.8 23.1 + - - +
181B ASP* 3.0 29.1 + - - +
183B VAL* 3.7 12.2 - - + +
204B SER* 2.7 38.0 + - - -
206B ARG* 3.5 17.0 + - + -
216B MET* 3.5 22.2 - - + +
520B MPD 3.7 17.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP 2.9 6.5 + - - -
174B MET* 2.5 26.7 + - - -
176B HIS* 1.3 77.1 - - - +
178B MET* 1.3 61.6 + - - +
179B GLY* 3.4 0.7 + - - -
520B MPD 3.0 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS* 3.6 38.8 - - + +
141B VAL* 3.9 20.2 - - + -
142B PRO* 3.3 26.6 - - + +
157B LEU* 3.9 22.7 - - + +
158B SER* 5.2 2.7 - - - -
174B MET* 3.1 13.4 + - - +
175B LEU* 3.0 35.0 + - + +
177B SER* 1.3 78.9 - - - +
179B GLY* 1.3 58.5 + - - +
180B PRO* 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL 4.0 4.0 - - - -
142B PRO* 4.3 8.5 - - - -
144B ALA 3.8 4.7 - - - +
176B HIS 2.9 12.9 + - - +
177B SER 3.1 1.3 - - - -
178B MET* 1.3 82.4 - - - +
180B PRO* 1.3 71.8 - - - +
181B ASP* 3.5 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