Contacts of the helix formed by residues 165 - 179 (chain A) in PDB entry 3QK2
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 165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR 3.9 0.2 + - - -
164A THR* 1.3 75.4 - - - +
166A GLU* 1.3 73.3 + - - +
168A ALA* 3.3 1.7 + - - +
169A ALA* 3.1 24.3 + - - +
186A ARG* 4.1 2.6 + - - +
188A ASN* 3.8 12.4 + - - -
190A TYR 3.7 13.7 + - - -
191A ASN* 3.1 37.2 + - - +
192A HIS* 4.0 1.9 - - - +
193A ASN* 3.5 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.6 18.9 + - - +
165A LYS* 1.3 83.4 + - - +
167A LYS* 1.3 63.7 + - + +
169A ALA* 3.5 6.9 + - - +
170A LEU* 3.4 23.8 + - - +
218A PHE* 5.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 3.5 23.8 - - + +
164A THR* 3.2 17.4 + - - +
166A GLU* 1.3 77.6 - - + +
168A ALA* 1.3 60.3 + - - +
170A LEU* 3.2 3.3 + - - +
171A LEU* 2.8 31.8 + - - +
213A GLN* 5.3 2.2 + - - +
216A CME 3.5 52.7 + - - +
218A PHE* 2.7 46.3 + - + +
219A SER* 3.0 24.9 + - - -
220A PHE 3.1 12.3 + - - -
221A LEU* 3.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 3.6 14.1 - - + +
164A THR 2.9 12.4 + - - +
167A LYS* 1.3 78.2 - - - +
169A ALA* 1.3 58.5 + - - +
171A LEU* 4.2 4.7 - - - -
172A TYR* 2.9 31.5 + - - +
186A ARG* 3.6 8.7 - - - -
193A ASN* 3.3 39.9 - - + +
195A LEU* 3.8 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS 3.1 13.4 + - - +
166A GLU* 3.6 11.4 - - - +
167A LYS 3.2 0.2 - - - -
168A ALA* 1.3 78.8 - - - +
170A LEU* 1.3 62.7 + - + +
172A TYR* 3.6 12.0 - - - +
173A LYS* 4.0 14.4 + - - +
186A ARG* 3.8 28.2 - - - +
245A GLU* 4.8 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU 3.4 11.6 + - - +
167A LYS* 3.2 7.2 + - - +
169A ALA* 1.3 77.7 - - + +
171A LEU* 1.3 67.0 + - - +
172A TYR 3.2 0.7 + - - -
173A LYS* 3.3 13.3 + - + +
174A LYS* 3.2 27.3 + - + +
216A CME 3.5 33.0 - - + -
218A PHE* 5.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 4.0 21.1 - - + -
163A THR* 4.5 4.5 - - + -
167A LYS 2.8 13.5 + - - +
168A ALA* 3.9 0.7 - - - +
170A LEU* 1.3 75.8 - - - +
172A TYR* 1.3 61.4 + - - +
174A LYS* 4.3 4.0 - - + +
175A ILE* 2.8 59.0 + - + +
195A LEU* 3.6 14.8 - - + -
212A ALA* 4.4 7.0 - - + -
215A LEU* 3.7 28.3 - - + -
216A CME 3.5 19.1 - - + -
221A LEU* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA 2.9 17.8 + - - +
169A ALA 3.6 8.1 - - - +
171A LEU* 1.3 79.2 - - - +
173A LYS* 1.3 73.7 + - + +
176A MET* 3.3 43.3 + - + +
184A ILE* 3.7 42.2 - - + +
186A ARG* 3.9 18.2 - - + -
195A LEU* 4.0 9.6 - - + +
245A GLU* 3.6 44.6 + - + +
246A GLU* 3.1 30.3 + - - -
247A SER* 3.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA 4.2 14.4 - - - +
170A LEU* 3.3 11.6 + - + +
171A LEU 3.2 0.4 - - - -
172A TYR* 1.3 88.4 - - + +
174A LYS* 1.3 61.8 + - + +
176A MET* 3.4 9.3 + - - +
177A GLU* 3.0 30.4 + - - +
245A GLU* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.2 22.6 + - + +
171A LEU* 3.1 5.2 + - + +
173A LYS* 1.3 75.8 - - + +
175A ILE* 1.3 61.6 + - - +
177A GLU* 3.4 29.7 + - - +
178A LYS* 2.8 32.2 + - - +
211A TYR* 3.5 22.1 + - - +
215A LEU* 3.9 28.5 - - + -
216A CME 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 4.2 22.0 - - + -
171A LEU* 2.8 41.6 + - + +
174A LYS* 1.3 69.4 - - - +
176A MET* 1.3 68.4 + - - +
178A LYS* 4.5 2.2 - - - +
179A TYR* 3.0 39.7 + - + +
181A VAL* 3.8 5.2 - - + +
184A ILE* 3.9 11.2 - - + -
195A LEU* 4.5 4.3 - - + -
197A PHE* 3.6 41.5 - - + -
208A ILE* 4.7 3.1 - - + -
211A TYR* 4.0 22.7 - - + -
212A ALA* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.3 41.8 + - + +
173A LYS* 3.5 8.3 - - - +
174A LYS 3.3 0.2 - - - -
175A ILE* 1.3 80.0 - - - +
177A GLU* 1.3 56.7 + - - +
180A SER* 3.1 28.2 + - - -
181A VAL* 3.5 24.9 + - + +
184A ILE* 3.4 24.9 - - + -
247A SER* 4.0 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 3.0 15.9 + - - +
174A LYS* 3.7 36.1 + - - +
176A MET* 1.3 76.8 - - - +
178A LYS* 1.3 69.0 + - - +
179A TYR 3.4 0.3 + - - -
180A SER* 3.6 10.8 + - - +
211A TYR* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS 2.8 22.4 + - - +
177A GLU* 1.3 78.3 - - - +
179A TYR* 1.3 97.7 + - + +
180A SER* 3.9 1.9 + - - -
211A TYR* 3.6 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 3.0 36.4 + - + +
176A MET 4.0 0.2 - - - -
178A LYS* 1.3 108.0 - - + +
180A SER* 1.3 73.3 + - - +
181A VAL* 3.0 6.3 + - + -
197A PHE* 4.9 1.8 - + - -
199A THR* 4.0 16.9 - - + +
200A PRO* 3.4 15.8 - - - +
201A HIS* 5.8 1.3 - - - -
203A HIS* 3.5 31.8 + + - +
207A ALA* 3.7 5.6 + - + +
208A ILE* 3.3 39.4 - - + +
211A TYR* 3.3 36.6 - + - +
----------------------------------------------------------
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