Contacts of the helix formed by residues 198 - 202 (chain A) in PDB entry 1HS6
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 PRO 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 3.9 16.2 - - + +
152A VAL 3.4 13.5 - - - +
153A LYS* 3.9 6.7 - - + -
197A ILE* 1.4 95.8 - - + +
199A CYS* 1.4 64.4 + - - +
200A TYR* 3.1 44.6 + - + +
201A LEU* 3.2 27.8 + - + +
304A ASN 4.6 3.1 - - - +
307A THR* 3.8 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 4.2 1.0 - - - +
140A CYS* 3.6 23.6 - - - +
146A CYS* 4.1 9.9 - - + -
147A GLN 3.4 24.5 - - - +
148A ASP* 3.3 31.0 - - - -
149A THR 4.1 7.3 + - - -
152A VAL 4.3 4.4 + - - -
154A LEU* 4.6 14.8 - - + +
197A ILE* 3.7 2.7 + - - -
198A PRO* 1.4 65.9 - - - +
200A TYR* 1.3 56.7 + - - +
201A LEU 3.0 6.1 - - - -
202A ILE* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 3.8 13.1 + - - +
136A GLN* 3.6 51.2 + - + +
137A ALA 3.6 23.1 - - - +
140A CYS* 5.0 1.1 - - - -
148A ASP* 5.2 1.6 - - - +
149A THR 5.8 0.4 - - - -
150A PRO* 3.9 13.0 - - + -
198A PRO* 3.1 38.8 - - + -
199A CYS* 1.3 81.2 - - - +
201A LEU* 1.3 78.2 + - + +
202A ILE 3.3 1.5 + - - +
270A MET* 4.1 5.4 - - + +
271A GLU* 4.4 3.7 + - - -
272A ASN* 4.3 2.6 + - - -
303A GLY 3.5 17.5 + - - -
304A ASN* 4.6 0.9 + - - -
307A THR* 3.7 3.0 - - + +
311A TRP* 3.5 26.5 - + + -
317A ASN* 3.0 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER* 2.7 25.8 + - - -
197A ILE* 4.1 8.5 - - + -
198A PRO* 3.5 35.2 - - + +
199A CYS 3.0 1.0 - - - -
200A TYR* 1.3 105.5 - - + +
202A ILE* 1.4 54.7 + - - +
270A MET* 3.8 13.7 - - + -
271A GLU* 3.7 17.9 - - + +
272A ASN* 3.8 6.9 + - - +
273A PRO* 3.2 28.1 - - + +
304A ASN* 3.2 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.1 26.9 - - + -
133A SER* 4.1 0.3 + - - -
135A CYS* 3.2 28.3 + - - +
140A CYS* 4.0 24.2 - - - -
143A ILE* 5.5 6.1 - - + -
144A LEU* 5.0 10.1 - - + -
154A LEU* 4.9 7.4 - - + -
156A TYR* 4.2 22.2 - - + -
170A MET* 4.4 17.5 - - + -
171A SER* 3.6 3.8 - - - -
197A ILE* 4.3 5.8 - - + -
199A CYS* 3.0 25.7 + - + +
200A TYR 4.3 1.0 - - - +
201A LEU* 1.4 77.5 - - - +
203A ALA* 1.3 65.6 + - - +
204A LEU* 6.3 0.2 - - + -
272A ASN* 4.7 0.9 + - - -
----------------------------------------------------------
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