Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 5FHT
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 ILE 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 3.8 15.3 - - + +
164A THR 3.9 1.6 - - - -
191A LYS* 3.7 0.4 - - - +
192A VAL* 2.8 37.3 + - + -
193A THR* 2.9 39.7 + - + +
195A GLY* 1.3 82.6 - - - +
197A SER* 1.3 57.8 + - - +
198A PHE* 3.6 31.0 - - + -
240A ILE* 4.3 4.3 - - + -
243A GLU* 3.5 41.7 - - + +
247A ARG* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE 3.8 0.3 - - - +
163A GLN* 3.4 5.5 - - - +
164A THR* 2.9 34.4 + - - +
165A ASP 5.6 0.2 - - - -
166A ALA 3.4 21.7 + - - -
167A ALA* 3.7 3.5 - - - -
168A ILE* 3.1 33.2 + - - +
190A MET 3.3 9.6 - - - -
191A LYS* 3.6 15.8 - - - +
195A GLY 5.6 0.2 - - - -
196A ILE* 1.3 76.8 + - - +
198A PHE* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.4 44.6 - + + -
162A ILE 3.5 1.8 - - - -
163A GLN* 3.4 37.9 - - + -
164A THR* 5.6 0.2 - - - -
168A ILE* 3.5 6.7 - - - +
189A THR* 2.9 27.1 + - + +
190A MET* 2.7 26.2 + - + +
192A VAL* 3.6 16.8 - - + -
196A ILE* 3.6 13.9 - - + -
197A SER* 1.3 82.4 - - - +
199A ALA* 1.3 60.3 + - - +
234A LEU* 3.7 23.8 - - + -
240A ILE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.6 9.5 - - - -
162A ILE* 2.9 35.5 + - + +
164A THR* 5.7 0.2 - - + -
168A ILE* 4.7 1.8 - - + -
177A LEU* 3.8 29.2 - - + -
186A GLY* 4.2 3.8 - - - -
187A VAL 3.1 25.4 - - - +
188A ASN* 4.0 6.5 - - - +
189A THR* 3.9 0.7 - - - -
198A PHE* 1.3 75.6 - - - +
200A ILE* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS 5.4 0.2 - - - +
94A ALA* 3.0 34.5 - - + +
95A ASP* 4.4 6.1 - - + +
96A ILE* 4.3 16.6 - - + -
159A VAL* 4.3 4.0 - - + -
161A TYR* 3.6 28.3 - - + +
186A GLY* 3.0 4.1 - - - -
187A VAL* 2.9 45.0 + - + +
189A THR* 3.8 16.8 - - + -
199A ALA* 1.3 70.0 - - - +
201A PRO* 1.3 82.4 - - + +
204A ARG* 4.2 20.2 - - + -
205A LEU* 5.1 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.5 18.8 - - - +
159A VAL* 4.0 12.3 - - + -
160A GLU 3.3 26.0 - - - +
161A TYR* 4.3 0.2 - - - -
162A ILE* 4.1 11.7 - - + -
185A ILE 3.6 6.5 - - - +
199A ALA 3.7 5.4 - - - +
200A ILE* 1.3 93.0 - - + +
202A SER* 1.3 66.8 + - - +
203A ASP* 4.3 1.6 - - + +
204A ARG* 3.1 10.7 + - + +
205A LEU* 3.1 17.5 + - - +
402A CL 3.6 20.9 - - + -
----------------------------------------------------------
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