Contacts of the strand formed by residues 193 - 197 (chain H) in PDB entry 6H25
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 ALA 193 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H ASP* 4.8 0.2 - - - -
189H LEU* 3.3 32.2 + - - +
191H CYS* 3.8 1.8 - - - +
192H GLY* 1.3 79.2 - - - +
194H SER* 1.3 62.3 + - - +
205H ILE* 4.6 4.9 - - + -
206H TYR 3.9 6.3 - - - +
207H PRO* 4.5 0.2 - - - -
208H THR* 4.4 2.7 - - - +
233H VAL* 4.6 7.2 - - + -
234H ILE* 3.9 26.7 - - + -
237H LEU* 3.9 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H HIS 3.4 8.7 - - - -
188H ASP* 3.3 21.7 - - - +
193H ALA* 1.3 74.0 - - - +
195H VAL* 1.3 62.7 + - - +
205H ILE* 3.7 3.3 - - - +
206H TYR* 2.9 68.6 + - - +
208H THR* 3.6 19.3 + - - +
209H PRO* 5.0 1.2 - - - +
237H LEU* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H HIS 3.8 1.9 - - - +
186H PHE* 3.9 3.6 - - - +
187H HIS* 2.9 49.6 + - + +
189H LEU* 4.8 15.9 - - + -
193H ALA 5.3 0.4 - - - +
194H SER* 1.3 75.9 - - - +
196H ILE* 1.3 65.6 + - - +
197H LEU* 3.7 29.6 - - + -
203H ILE* 3.9 13.2 - - + -
204H TRP 3.3 13.0 - - - +
205H ILE* 4.1 10.8 - - + -
206H TYR* 4.6 1.4 - - - -
237H LEU* 5.7 4.5 - - + -
241H ILE* 4.9 5.8 - - + -
256H ILE* 5.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ILE* 4.8 8.3 - - + -
85H VAL* 3.9 22.4 - - + +
142H SER* 4.6 17.9 - - - +
166H LEU* 4.7 7.4 - - + -
185H HIS* 4.6 2.0 - - + -
186H PHE* 3.6 38.1 - - + -
195H VAL* 1.3 73.9 - - - +
197H LEU* 1.3 64.8 + - - +
198H GLY* 3.6 7.5 + - - +
203H ILE* 3.5 5.9 - - - -
204H TRP* 2.9 56.5 + - + +
206H TYR* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ILE* 3.5 14.6 - - - +
179H VAL* 5.5 5.6 - - + -
185H HIS* 3.5 33.5 + - + +
187H HIS* 4.0 23.8 - - + +
195H VAL* 3.7 24.0 - - + -
196H ILE* 1.3 71.1 - - - +
198H GLY* 1.3 67.3 + - - +
202H PHE 4.4 2.5 - - - -
203H ILE* 3.7 14.4 - - + -
251H LEU* 3.7 34.5 - - + +
252H TYR* 4.5 13.2 - - - -
253H ASP 4.8 0.4 - - - +
256H ILE* 4.3 17.7 - - + -
----------------------------------------------------------
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