Contacts of the helix formed by residues 151 - 162 (chain X) in PDB entry 5G04
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 GLN 151 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516H MET* 5.4 1.9 - - - +
520H ARG* 5.3 2.4 + - - -
548H LYS* 5.2 6.8 + - - -
94X ARG* 3.3 35.3 + - - +
146X TYR* 3.2 20.9 + - + +
147X THR* 5.5 0.2 - - - -
149X LEU* 3.4 35.1 + - - +
150X LYS* 1.3 74.2 - - - +
152X ASP* 1.3 64.4 + - - +
153X LYS 3.5 1.6 - - - -
154X ASP* 2.7 40.5 + - + +
155X ALA* 3.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147X THR* 5.3 6.1 - - - +
150X LYS* 3.3 18.2 + - - +
151X GLN* 1.3 70.6 - - - +
153X LYS* 1.3 67.4 + - + +
154X ASP 3.2 0.2 + - - -
155X ALA* 3.3 7.9 + - - +
156X ILE* 3.1 33.9 + - + +
178X LEU* 4.2 20.2 - - + +
181X LYS* 3.4 34.4 - - - +
182X ALA* 5.2 2.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516H MET* 5.0 19.3 - - + -
175L ILE* 5.3 3.2 - - - +
176L ASP* 4.0 29.2 - - - +
151X GLN 3.5 0.6 - - - -
152X ASP* 1.3 78.0 - - + +
154X ASP* 1.3 68.3 + - - +
156X ILE* 3.4 14.5 + - + +
157X ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516H MET* 3.1 30.8 - - - +
520H ARG* 4.7 7.8 + - - -
146X TYR* 3.1 38.1 - - + -
151X GLN* 2.7 39.4 - - - +
152X ASP 3.2 0.6 - - - -
153X LYS* 1.3 76.1 - - - +
155X ALA* 1.3 64.3 + - - +
157X ALA* 3.4 6.1 + - - +
158X ILE* 3.2 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143X ALA* 3.9 26.9 - - + +
146X TYR* 3.9 16.0 - - + +
147X THR* 4.2 4.0 - - - +
151X GLN 3.8 4.1 + - - +
152X ASP* 3.3 10.9 + - - +
154X ASP* 1.3 77.9 - - - +
156X ILE* 1.3 64.5 + - - +
158X ILE* 3.3 4.3 + - - +
159X LEU* 3.3 28.9 + - - +
178X LEU* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701H LYS* 6.4 0.4 - - - +
152X ASP* 3.1 24.5 + - + +
153X LYS* 3.6 13.9 - - + +
154X ASP 3.3 0.2 - - - -
155X ALA* 1.3 76.7 - - - +
157X ALA* 1.3 54.7 + - - +
159X LEU* 3.3 2.6 + - - +
160X ASP* 2.8 36.6 + - + +
175X LEU* 4.7 9.7 - - + +
178X LEU* 4.1 34.3 - - + +
179X TYR* 4.0 35.0 - - + +
182X ALA* 4.4 14.1 - - + -
184X GLN* 5.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517H GLN* 5.8 7.0 - - + +
701H LYS* 5.6 5.6 - - - +
153X LYS 3.1 14.2 + - - +
154X ASP* 3.5 11.9 - - - +
156X ILE* 1.3 77.9 - - - +
158X ILE* 1.3 68.6 + - + +
160X ASP* 3.8 5.8 - - - +
161X GLY* 3.2 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517H GLN* 5.8 4.9 - - - +
520H ARG* 6.6 0.2 - - + -
104X LEU* 5.2 1.6 - - + -
139X LYS* 3.8 50.5 + - + +
142X MET* 4.6 20.4 - - + -
143X ALA* 5.2 2.0 - - + +
146X TYR* 4.1 28.0 - - + +
154X ASP* 3.2 19.4 + - - +
155X ALA* 3.3 6.2 + - - +
157X ALA* 1.3 80.9 - - + +
159X LEU* 1.3 63.2 + - + +
161X GLY* 3.5 7.8 + - - -
162X ILE* 3.6 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139X LYS 4.5 3.1 - - - +
140X TYR* 4.5 13.2 - - - -
143X ALA* 3.9 17.9 - - + -
155X ALA 3.3 17.2 + - - +
156X ILE 3.3 3.2 + - - +
157X ALA 3.2 0.2 - - - -
158X ILE* 1.3 75.4 - - - +
160X ASP* 1.3 65.5 + - - +
161X GLY 3.0 2.0 - - - -
162X ILE* 3.0 33.2 + - + +
167X ARG* 3.8 9.3 - - - -
171X ILE* 3.7 24.0 - - + +
174X MET* 3.9 24.2 - - + -
175X LEU* 4.0 38.1 - - + +
178X LEU* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701H LYS* 2.9 31.3 + - - +
156X ILE* 2.8 22.5 + - + +
157X ALA* 3.8 6.5 - - - +
159X LEU* 1.3 76.6 - - - +
161X GLY* 1.3 62.2 + - - +
162X ILE 3.2 8.4 + - - +
167X ARG* 4.8 12.7 + - - +
175X LEU* 5.0 2.6 - - + +
179X TYR* 4.3 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139X LYS* 4.5 10.2 + - - -
157X ALA 3.2 12.6 + - - -
158X ILE* 3.5 5.8 + - - -
159X LEU 3.0 1.6 - - - -
160X ASP* 1.3 78.3 - - - +
162X ILE* 1.3 60.9 + - - +
163X PRO* 3.5 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136X ILE* 4.0 26.2 - - + +
139X LYS* 3.6 38.8 - - + +
158X ILE 3.6 9.0 - - - +
159X LEU* 3.0 33.5 + - + +
160X ASP 3.3 10.6 - - - +
161X GLY* 1.3 77.1 - - - +
163X PRO* 1.3 84.3 - - + +
164X SER 3.6 0.3 + - - -
166X GLN* 4.0 13.5 - - + +
167X ARG* 3.1 25.8 + - + +
171X ILE* 4.4 11.2 - - + -
----------------------------------------------------------
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