Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 3H4B
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 ASN 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.3 9.2 - - - +
30A ILE* 3.8 11.1 - - - +
200A ALA* 3.4 1.8 + - - +
201A SER* 1.3 81.3 + - - +
203A LYS* 1.3 60.9 + - - +
204A LEU* 2.9 15.2 - - - +
205A LEU* 2.8 37.0 - - - +
206A ALA* 3.2 22.2 + - - +
287A GLY 2.9 22.3 + - - +
288A GLU* 4.4 0.5 - - - -
289A ASP* 3.1 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 4.6 2.7 - - - +
30A ILE* 4.2 11.2 - - + +
121A GLU* 2.8 35.8 + - - +
129A PHE* 3.3 51.8 - - + -
202A ASN* 1.3 75.5 - - - +
204A LEU* 1.3 56.4 + - - +
206A ALA* 4.5 0.2 - - - -
207A LYS* 3.0 26.7 + - - +
289A ASP* 3.3 7.8 + - - +
291A SER* 3.2 29.4 + - - +
292A PRO 3.4 14.7 + - - +
293A VAL* 4.1 13.9 - - + -
294A ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASN* 2.9 7.7 - - - +
203A LYS* 1.3 75.0 - - - +
205A LEU* 1.3 65.1 + - + +
207A LYS* 3.9 4.3 - - - +
208A LEU* 3.0 46.2 + - + +
230A ILE* 4.7 1.3 - - + -
239A ILE* 4.4 6.7 - - + -
240A PRO* 3.8 25.8 - - + +
284A LEU* 3.4 36.6 - - + +
287A GLY* 3.7 36.3 - - - -
289A ASP* 3.0 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.4 17.0 - - + -
201A SER* 4.1 15.0 - - - +
202A ASN* 2.8 37.5 - - - +
204A LEU* 1.3 78.2 - - + +
206A ALA* 1.3 57.1 + - - +
208A LEU* 3.0 12.8 + - + +
209A VAL* 2.7 37.8 + - - +
221A LEU* 3.7 20.4 - - + -
226A CYS* 4.3 16.4 - - + +
229A LEU* 4.2 7.5 - - + +
230A ILE* 5.2 2.2 - - + -
287A GLY* 3.2 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.1 15.5 - - + +
31A VAL 4.3 0.7 - - - -
32A HIS* 3.4 22.4 - - + +
129A PHE* 4.7 0.2 - - + -
198A GLY* 3.7 18.1 - - - +
200A ALA* 3.4 13.8 - - + +
202A ASN 3.2 16.2 + - - +
203A LYS 3.9 3.1 - - - +
205A LEU* 1.3 78.1 - - - +
207A LYS* 1.3 63.1 + - - +
209A VAL* 3.7 6.3 - - - +
210A SER* 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 3.5 19.7 + - + +
34A ASP* 5.6 0.6 + - - -
123A LEU* 4.0 9.2 - - + +
127A GLU* 2.5 32.5 + - - +
129A PHE* 3.9 21.1 - - + -
203A LYS 3.0 18.9 + - - +
204A LEU* 3.9 4.5 - - - +
206A ALA* 1.3 79.3 - - - +
208A LEU* 1.3 59.4 + - - +
210A SER* 3.0 17.5 + - - -
211A GLY 4.2 1.4 + - - -
240A PRO* 3.9 33.0 - - + -
872P C 4.2 4.9 - - - -
873P DOC 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.0 41.4 + - + +
205A LEU* 3.0 4.7 + - + +
207A LYS* 1.3 77.6 - - - +
209A VAL* 1.3 59.5 + - - +
211A GLY* 4.0 6.4 + - - -
212A VAL* 4.2 6.9 + - - +
229A LEU* 3.5 35.0 - - + +
230A ILE* 4.0 23.1 - - + -
233A LEU* 4.2 26.9 - - + -
238A GLU 4.2 4.3 - - - +
239A ILE* 5.8 0.2 - - + -
240A PRO* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.9 18.2 - - + -
198A GLY* 3.7 16.4 - - - -
199A VAL 3.9 13.7 - - - +
205A LEU 2.7 22.7 + - - +
206A ALA* 3.7 6.5 - - - +
208A LEU* 1.3 70.5 - - - +
210A SER* 1.3 67.6 + - - +
211A GLY 3.0 4.3 + - - -
212A VAL* 3.1 32.7 + - + +
219A THR* 3.5 33.9 - - + +
221A LEU* 4.2 16.4 - - + -
229A LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 2.6 51.0 + - - -
34A ASP* 4.5 8.9 + - - +
196A CYS* 3.4 24.4 - - - +
197A ALA* 3.7 7.7 - - - +
198A GLY* 3.7 13.0 - - - -
206A ALA 3.0 10.3 + - - -
207A LYS 3.0 10.0 + - - -
209A VAL* 1.3 77.6 - - - +
211A GLY* 1.3 60.6 + - - +
213A PHE 4.7 2.9 + - - +
217A GLN 4.8 0.7 - - - +
218A GLN* 5.7 0.2 - - - -
219A THR* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 6.1 0.9 - - - -
196A CYS* 5.6 0.7 - - - -
207A LYS 4.2 1.4 + - - -
208A LEU 4.0 6.7 + - - -
209A VAL 3.0 1.4 - - - -
210A SER* 1.3 84.1 + - - +
212A VAL* 1.3 64.6 + - - +
213A PHE 3.2 3.3 + - - -
214A LYS* 3.6 33.4 + - - +
----------------------------------------------------------
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