Contacts of the helix formed by residues 195 - 204 (chain A) in PDB entry 5I94
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 ASP 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 3.8 7.0 - - - -
151A GLU 5.0 0.7 - - - +
152A LYS* 3.4 24.5 - - + +
193A MET 3.4 4.6 + - - -
194A LEU* 1.3 75.7 - - - +
196A LYS* 1.3 65.1 + - + +
197A ASP* 2.9 20.2 + - - +
198A LEU* 2.6 38.8 + - - +
199A PHE* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 3.0 45.2 + - + +
143A PHE* 3.7 30.4 - - + -
144A TYR* 4.3 16.4 - - + +
195A ASP* 1.3 74.1 - - - +
197A ASP* 1.3 61.0 + - + +
199A PHE* 4.2 2.5 - - - +
200A LYS* 3.5 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASP* 3.0 16.9 - - - +
196A LYS* 1.3 81.4 - - + +
198A LEU* 1.3 59.9 + - - +
199A PHE 3.4 0.2 - - - -
200A LYS* 3.5 14.2 + - - +
201A LYS* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 3.6 38.8 - - + +
192A VAL* 4.6 6.7 - - + -
193A MET 4.2 8.7 - - - +
194A LEU* 3.6 27.6 - - + +
195A ASP* 2.6 24.7 + - - +
197A ASP* 1.3 69.8 - - - +
199A PHE* 1.3 65.6 + - - +
201A LYS* 3.2 20.3 + - + +
202A CYS* 3.1 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU 3.4 24.5 - - - -
142A LEU* 3.9 15.9 - - + -
143A PHE* 3.6 37.7 - + + -
146A ILE* 3.6 32.5 - - + -
153A ILE* 4.5 8.1 - - + -
158A PHE* 3.9 17.7 - + - -
194A LEU* 3.7 31.4 - - + +
195A ASP 3.0 17.9 + - - +
196A LYS 4.2 1.8 - - - +
198A LEU* 1.3 76.6 - - - +
200A LYS* 1.3 65.3 + - - +
202A CYS* 3.0 4.4 + - - -
203A VAL* 3.0 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 4.5 7.5 + - - -
139A GLU* 3.1 46.8 + - + +
140A ASP* 5.1 4.9 - - + +
196A LYS 3.5 18.2 + - - +
197A ASP* 3.8 13.5 - - - +
198A LEU 3.3 0.6 - - - -
199A PHE* 1.3 81.6 - - + +
201A LYS* 1.3 57.5 + - - +
203A VAL* 3.8 9.4 - - - -
204A GLN* 2.8 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 3.3 35.1 - - + +
184A THR* 5.1 7.3 + - - +
197A ASP 3.0 14.6 + - - +
198A LEU* 3.4 25.4 - - + +
199A PHE 3.2 0.2 - - - -
200A LYS* 1.3 78.7 - - - +
202A CYS* 1.3 61.1 + - - +
204A GLN* 4.1 23.7 + - - +
205A SER* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A CYS* 3.3 32.1 - - - -
180A MET* 3.8 21.2 - - + +
181A LEU* 3.9 33.2 - - + -
184A THR* 3.6 23.1 - - - -
194A LEU* 4.2 8.7 - - + -
198A LEU* 3.1 21.6 + - - +
199A PHE* 3.0 7.0 + - - +
201A LYS* 1.3 79.0 - - - +
203A VAL* 1.3 63.8 + - + +
204A GLN 3.7 0.4 - - - -
205A SER* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 4.6 4.3 - - + -
142A LEU* 5.4 0.2 - - + -
158A PHE* 4.5 7.4 - - + -
177A CYS* 4.4 5.4 - - - -
181A LEU* 6.3 0.2 - - + -
194A LEU* 6.2 0.4 - - + -
199A PHE* 3.0 56.2 + - + +
200A LYS* 3.8 10.8 - - - -
202A CYS* 1.3 87.9 - - + +
204A GLN* 1.3 66.6 + - - +
205A SER* 3.3 2.7 - - - +
206A ASN 3.5 2.4 + - - +
207A ILE* 3.0 37.5 + - + +
210A LEU* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.3 21.7 - - - +
180A MET* 6.3 0.4 - - - +
200A LYS* 2.8 39.9 + - + +
201A LYS* 4.1 23.7 + - - +
202A CYS 3.7 0.6 - - - -
203A VAL* 1.3 79.0 - - - +
205A SER* 1.3 65.0 + - - +
206A ASN 3.1 1.6 + - - -
207A ILE* 3.3 18.5 + - - +
----------------------------------------------------------
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