Contacts of the helix formed by residues 193 - 198 (chain K) in PDB entry 2ZHX
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 193 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K SER* 3.3 11.4 + - - -
191K HIS* 2.8 22.1 + - - -
192K PRO* 1.3 75.7 - - - +
194K PRO* 1.3 67.9 - - - +
195K LEU* 3.5 9.4 + - - +
196K SER* 2.9 11.6 + - - -
197K ALA 2.6 32.7 + - - -
20L GLU* 3.8 3.8 + - - -
22L ILE* 4.3 8.2 - - - +
24L MET* 5.1 3.6 - - - -
43L VAL* 4.1 11.1 - - - +
45L THR* 3.8 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K ARG* 3.6 24.2 - - + -
93K SER 4.4 1.6 - - - +
96K ASN* 3.5 18.2 - - - +
192K PRO 3.4 0.6 - - - +
193K SER* 1.3 90.6 - - - +
195K LEU* 1.3 61.2 + - - +
196K SER 3.0 1.4 + - - -
197K ALA* 3.6 7.7 + - + +
198K SER* 4.7 4.9 + - - -
20L GLU* 4.4 3.6 - - - +
45L THR* 3.9 20.0 - - + -
54L ASN* 3.3 31.4 - - + +
56L MET* 4.0 10.1 - - - -
73L GLN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K SER* 3.2 4.8 + - - +
194K PRO* 1.3 78.0 - - - +
196K SER* 1.3 57.5 + - - +
198K SER* 5.6 0.5 + - - -
199K ARG* 4.1 3.5 - - - +
24L MET* 4.2 10.5 - - - -
28L GLU 6.2 0.2 - - - -
29L VAL* 5.1 9.6 - - + -
32L VAL* 3.3 46.8 - - + +
33L ILE* 4.4 17.5 - - + -
43L VAL* 3.7 36.3 - - + -
56L MET* 3.5 24.1 - - + -
58L LEU* 3.9 16.2 - - + -
71L VAL* 4.5 16.6 - - + -
73L GLN* 4.4 4.1 + - - +
79L ASN* 5.1 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K PRO* 4.0 10.2 - - - +
191K HIS* 2.4 45.7 + - - +
193K SER* 2.9 6.5 + - - -
195K LEU* 1.3 80.7 - - - +
197K ALA* 1.3 65.3 + - - +
198K SER 3.3 2.7 - - - -
199K ARG* 2.8 29.6 + - - +
24L MET* 3.6 25.1 - - - +
32L VAL* 5.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K ASN* 3.3 31.2 - - + +
191K HIS 3.6 8.3 - - - -
192K PRO* 3.5 7.6 - - + +
193K SER 2.6 15.4 + - - +
194K PRO* 3.6 4.9 + - + +
196K SER* 1.3 70.6 + - - +
198K SER* 1.3 58.2 - - - +
201K PHE* 2.9 30.9 + - + -
202K PHE* 3.0 31.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.1 8.5 - - - -
54A THR 5.3 2.0 - - - +
55A PHE* 5.1 0.7 - - - -
56A PRO* 3.0 29.6 - - - +
194K PRO 4.7 5.5 + - - -
195K LEU 5.6 0.5 + - - -
196K SER 3.3 0.4 - - - -
197K ALA* 1.3 75.4 - - - +
199K ARG* 1.3 66.5 + - - +
200K GLY 3.1 8.8 + - - -
202K PHE* 3.6 20.6 - - - +
73L GLN* 5.8 1.0 + - - -
77L GLY* 5.6 1.8 + - - -
----------------------------------------------------------
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