Contacts of the helix formed by residues 169 - 183 (chain A) in PDB entry 3KDO
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 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 1.3 74.6 - - - +
170A PRO* 1.3 64.8 - - - +
171A GLU* 3.3 7.6 + - - +
172A GLU* 2.9 36.5 + - - +
173A PHE* 2.8 34.7 + - - +
199A TYR 3.5 4.9 - - - -
200A ASN* 3.5 2.9 - - - -
134E ARG* 3.3 22.7 + - - -
357E TYR* 5.7 0.2 - - - -
66H ARG* 3.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 1.3 90.7 - - - +
171A GLU* 1.3 66.7 + - - +
173A PHE* 3.4 8.5 - - + +
174A GLU* 2.7 30.5 + - - +
199A TYR 3.3 15.0 - - - +
200A ASN* 3.6 17.7 - - - +
204A GLU* 3.5 34.3 - - + +
205A ARG* 5.2 0.7 - - - +
208A ILE* 3.3 30.1 - - + +
134E ARG* 4.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.3 6.7 + - - +
170A PRO* 1.3 85.7 - - - +
172A GLU* 1.3 63.7 + - + +
174A GLU* 3.3 22.0 + - - +
175A LYS* 3.4 12.5 + - - +
208A ILE* 5.0 0.9 - - + -
134E ARG* 2.9 38.0 + - - -
357E TYR* 5.1 2.0 - - - +
358E SER* 3.3 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.2 9.0 - - - +
169A SER* 2.9 34.4 + - - +
171A GLU* 1.3 76.6 - - + +
173A PHE* 1.3 63.6 + - - +
175A LYS* 3.2 9.2 + - - +
176A LEU* 3.1 20.4 + - - +
355E LYS* 5.8 0.3 + - - -
61H TRP* 3.8 30.0 - - + +
62H TYR* 3.5 13.1 - - - +
63H GLU* 3.0 21.3 + - - +
66H ARG* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.8 25.1 - - + -
168A TYR* 3.9 26.0 - + + -
169A SER 2.8 21.0 + - - +
170A PRO* 3.4 9.4 - - + +
172A GLU* 1.3 72.7 - - - +
174A GLU* 1.3 59.3 + - - +
176A LEU* 3.1 5.1 + - + +
177A ALA* 2.8 30.6 + - + +
188A MET* 3.9 20.6 - - + -
189A KCX 5.9 0.2 - - - -
190A ASP* 5.2 2.5 - - - -
200A ASN* 4.5 0.4 - - - +
205A ARG* 3.6 31.0 - - + -
208A ILE* 4.6 9.2 - - + -
209A MET* 3.4 44.4 - - + -
226A TRP* 4.4 6.1 - - - -
61H TRP* 4.1 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO 2.7 19.8 + - - +
171A GLU* 3.5 13.3 - - - +
172A GLU 3.2 0.2 - - - -
173A PHE* 1.3 73.0 - - - +
175A LYS* 1.3 63.7 + - - +
178A TYR* 3.2 11.7 + - + +
208A ILE* 3.5 25.3 - - + +
211A LYS* 2.6 34.3 + - - +
212A ILE* 3.0 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU 3.4 7.9 + - - +
172A GLU* 3.2 11.0 + - - +
174A GLU* 1.3 81.2 - - - +
176A LEU* 1.3 62.6 + - - +
178A TYR* 3.5 7.6 + - + +
179A ASP* 2.8 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 6.0 0.2 - - + -
162A PRO* 4.1 22.9 - - + -
163A LYS 5.3 0.2 - - - +
172A GLU 3.1 9.2 + - - +
173A PHE* 3.1 10.4 + - + +
175A LYS* 1.3 77.7 - - - +
177A ALA* 1.3 66.2 + - - +
179A ASP* 3.1 9.7 + - + +
180A LEU* 2.9 45.3 + - + +
188A MET* 4.7 2.0 - - + -
395A LEU* 5.9 5.2 - - + -
401A PRO* 3.6 37.9 - - + -
61H TRP* 3.6 46.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 2.8 22.8 + - + +
174A GLU* 3.8 4.0 - - - +
176A LEU* 1.3 71.6 - - - +
178A TYR* 1.3 63.9 + - - +
181A LEU* 3.0 31.6 + - + +
188A MET* 3.9 22.8 - - + +
209A MET* 3.8 31.4 - - + -
212A ILE* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.2 15.4 + - + +
175A LYS* 3.8 8.3 - - + +
177A ALA* 1.3 77.6 - - - +
179A ASP* 1.3 73.7 + - - +
182A SER* 2.8 45.2 + - - -
212A ILE* 4.1 16.9 - - + +
215A LYS* 3.3 39.5 - - + -
216A VAL* 3.8 17.5 - - + -
219A GLU* 2.3 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 2.8 55.7 + - - +
176A LEU* 3.1 14.4 + - + +
178A TYR* 1.3 88.1 - - - +
180A LEU* 1.3 65.2 + - + +
182A SER* 4.7 1.6 - - - -
183A ASN* 2.9 30.7 + - - +
401A PRO* 5.2 2.4 - - + +
402A ALA* 4.6 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 3.8 25.8 - - + -
176A LEU* 2.9 39.2 + - + +
177A ALA 3.9 1.3 - - - +
179A ASP* 1.3 68.1 - - - +
181A LEU* 1.3 58.1 + - - +
182A SER 2.9 0.9 - - - -
183A ASN* 2.3 39.2 + - - -
184A GLY 3.4 0.7 + - - -
185A ALA* 3.5 16.7 + - + -
188A MET* 3.7 26.0 - - + -
394A THR* 3.9 15.3 - - + -
395A LEU* 6.5 0.4 - - + -
401A PRO* 3.5 40.8 - - + +
405A ALA* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA 3.0 20.0 + - - +
180A LEU* 1.3 76.6 - - - +
182A SER* 1.3 59.9 + - - +
183A ASN 3.3 0.7 + - - -
184A GLY 3.8 2.9 + - - -
185A ALA* 3.4 25.1 - - + +
186A ASP 3.8 2.7 - - - +
187A TYR* 3.5 34.3 - - - +
188A MET* 4.1 8.1 - - + -
209A MET* 3.9 28.7 - - + -
212A ILE* 4.3 12.6 - - + -
213A ILE* 4.9 2.9 - - + -
216A VAL* 4.1 12.6 - - + +
220A THR* 5.3 0.9 - - - +
224A LYS* 3.2 49.1 + - + -
225A THR 4.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 2.8 41.5 + - - -
179A ASP* 3.6 1.1 - - - -
180A LEU 2.7 2.6 + - - -
181A LEU* 1.3 74.7 - - - +
183A ASN* 1.3 72.0 + - - +
184A GLY 3.6 1.6 + - - -
216A VAL* 3.6 24.9 - - - +
219A GLU* 4.7 2.4 + - - -
220A THR* 4.7 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 2.9 19.3 + - - +
180A LEU 2.3 26.1 + - - +
182A SER* 1.3 83.9 + - - +
184A GLY* 1.3 54.9 + - - +
402A ALA* 3.5 25.2 - - - +
405A ALA* 2.8 19.0 - - + +
406A ARG* 2.7 52.1 + - + -
----------------------------------------------------------
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