Contacts of the helix formed by residues 182 - 194 (chain G) in PDB entry 4KYI
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 182 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G ASN 3.3 10.5 + - - -
179G LEU 3.1 10.7 + - - +
180G THR 4.9 0.9 - - - -
181G LYS* 1.3 78.0 - - - +
183G VAL* 1.3 58.1 + - - +
184G LYS* 3.4 19.5 - - - +
185G ASP* 3.4 28.0 + - - +
186G LEU* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 4.6 9.0 - - - +
180G THR 5.9 1.1 - - - +
181G LYS 3.8 6.7 + - - +
182G SER* 1.3 71.0 - - - +
184G LYS* 1.3 73.4 + - - +
186G LEU* 3.5 9.8 - - + +
187G GLU* 2.9 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G SER* 3.1 16.1 - - - +
183G VAL* 1.3 97.0 - - - +
185G ASP* 1.3 62.0 + - - +
187G GLU* 3.5 8.4 + - - +
188G LYS* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G GLY 5.0 7.3 - - - +
168G ILE* 3.4 31.6 - - + +
179G LEU* 3.5 20.7 - - + +
182G SER* 3.3 21.0 + - - +
184G LYS* 1.3 77.7 - - - +
186G LEU* 1.3 61.9 + - - +
187G GLU 3.4 0.2 - - - -
188G LYS* 3.4 24.2 + - - +
189G LEU* 3.4 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LYS 3.7 23.1 - - - +
103G LEU* 4.8 3.4 - - + -
117G ARG* 3.4 35.0 - - - +
121G ILE* 3.8 26.9 - - + -
179G LEU* 3.4 29.2 - - + +
180G THR* 3.9 17.3 - - - +
182G SER 2.9 13.3 + - - +
183G VAL* 3.5 11.9 - - + +
184G LYS 3.2 0.4 - - - -
185G ASP* 1.3 78.3 - - - +
187G GLU* 1.3 62.4 + - - +
189G LEU* 3.3 20.0 - - + +
190G ASP* 3.5 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 3.4 23.4 + - - +
183G VAL* 2.9 36.5 + - + +
184G LYS* 4.0 7.6 - - - +
186G LEU* 1.3 73.4 - - - +
188G LYS* 1.3 65.0 + - - +
189G LEU 3.2 0.6 + - - -
190G ASP* 3.7 5.7 + - - +
191G LYS* 3.7 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G ALA* 3.2 41.1 - - + +
168G ILE* 4.2 0.2 - - + -
184G LYS* 3.0 35.3 + - - +
185G ASP* 3.4 30.2 + - - +
186G LEU 3.3 0.4 - - - -
187G GLU* 1.3 77.6 - - - +
189G LEU* 1.3 63.9 + - - +
191G LYS* 3.5 7.9 + - - +
192G ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 4.5 1.8 - - + +
120G ASN* 3.7 22.9 - - + -
121G ILE* 3.6 31.9 - - + -
124G VAL* 3.6 17.9 - - + -
163G LEU* 3.8 13.9 - - + -
168G ILE* 4.0 12.5 - - + +
179G LEU* 4.5 9.2 - - + -
185G ASP 3.4 9.7 + - - +
186G LEU* 3.3 17.4 + - + +
187G GLU 3.2 0.2 - - - -
188G LYS* 1.3 79.1 - - - +
190G ASP* 1.3 58.1 + - - +
192G ALA* 3.2 4.2 + - - +
193G LEU* 2.7 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ASP* 4.5 3.3 - - - +
116G ASP* 4.4 8.5 - - - +
117G ARG* 3.5 52.7 + - - +
120G ASN* 3.8 15.5 + - - +
186G LEU 3.5 7.6 + - - +
187G GLU 3.7 7.1 + - - +
188G LYS 3.4 0.4 - - - -
189G LEU* 1.3 77.1 - - - +
191G LYS* 1.3 56.1 + - - +
193G LEU 3.0 0.9 + - - -
194G ASN* 2.6 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G GLU 3.7 9.6 + - - +
188G LYS* 3.5 10.6 + - - +
190G ASP* 1.3 78.0 - - - +
192G ALA* 1.3 61.5 + - - +
194G ASN* 4.6 4.5 - - - +
195G SER* 4.1 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G LYS* 3.2 39.9 - - - +
163G LEU* 4.5 7.2 - - + -
165G ARG* 6.0 0.4 - - + -
166G ALA* 4.1 12.3 - - + +
188G LYS 3.0 18.0 + - - +
189G LEU 3.5 3.8 - - - +
191G LYS* 1.3 77.7 - - - +
193G LEU* 1.3 58.5 + - - +
195G SER* 2.4 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ASN* 3.5 49.4 - - + +
123G ASP* 4.6 9.4 - - + +
124G VAL* 4.1 7.2 - - + -
159G TYR* 4.6 11.4 - - + +
162G LYS* 4.5 5.4 - - + -
163G LEU* 3.7 26.0 - - + -
189G LEU* 2.7 38.5 + - + +
192G ALA* 1.3 72.9 - - - +
194G ASN* 1.3 55.0 + - - +
195G SER 3.1 5.5 + - - -
196G ILE* 3.4 26.1 + - + +
212G ARG* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ASP* 3.8 21.9 + - - +
119G ARG* 3.9 24.2 - - - +
120G ASN* 4.1 3.4 + - - +
190G ASP* 2.6 45.4 + - - +
191G LYS* 4.6 4.4 - - - +
193G LEU* 1.3 68.5 - - - +
195G SER* 1.3 59.0 + - - +
196G ILE* 3.1 13.1 + - - +
197G PRO* 5.3 0.9 - - - +
212G ARG* 4.6 2.0 - - - +
----------------------------------------------------------
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