Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 4TLG
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 LEU 197 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.2 17.3 - - + +
159A SER* 3.3 44.9 - - - +
160A LEU* 3.5 25.4 - - + +
163A LEU* 4.2 11.0 - - + -
195A PRO* 3.1 6.9 - - + +
196A LYS* 1.3 78.7 - - - +
198A PHE* 1.3 64.7 + - - +
199A PRO* 3.4 0.7 - - - -
200A VAL* 3.1 27.4 + - + -
201A ALA* 3.1 15.9 + - + +
300A GLY 5.8 0.2 - - - +
302A VAL* 4.1 9.9 - - + -
354A THR* 5.5 1.8 - - + +
512A EDO 5.8 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
155A MET* 4.0 28.0 - - + -
158A LEU* 3.9 10.3 - - + +
191A VAL* 3.9 30.1 - - + -
194A ALA* 3.8 15.7 - - + -
195A PRO* 3.0 21.6 + - + +
197A LEU* 1.3 76.5 - - - +
199A PRO* 1.4 64.7 - - + +
201A ALA* 3.1 2.4 + - + +
202A PHE* 2.7 52.9 + + + +
217A ILE* 5.7 1.6 - - + -
219A ILE* 3.9 16.8 - - + -
390A SER* 3.7 22.4 - - - -
394A LEU* 4.1 10.8 - - + -
518A 11A 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS 3.3 15.3 - - - +
197A LEU 3.6 0.7 - - - -
198A PHE* 1.4 93.9 - - + +
200A VAL* 1.3 60.2 + - - +
202A PHE* 3.6 0.4 + - + -
203A ASN 3.1 14.7 + - - -
386A PRO* 3.7 19.7 - - + -
387A ASP* 3.0 32.1 + - - +
390A SER* 4.0 13.0 - - - -
391A GLU* 3.4 34.1 - - - +
394A LEU* 3.7 16.8 - - + -
512A EDO 4.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.2 10.1 - - + -
197A LEU* 3.1 25.8 + - + +
199A PRO* 1.3 76.8 - - - +
201A ALA* 1.3 65.0 + - - +
203A ASN* 3.3 14.4 + - - +
204A LEU* 3.6 10.4 + - + +
300A GLY 3.8 22.2 - - - +
302A VAL* 4.2 9.2 - - + -
384A LEU* 3.9 30.4 - - + +
385A LEU 3.8 9.2 - - - +
386A PRO* 3.7 26.2 - - + -
512A EDO 4.4 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.0 21.3 - - + -
163A LEU* 3.9 28.3 - - + -
197A LEU* 3.1 12.0 + - + +
198A PHE* 3.1 7.5 + - + +
200A VAL* 1.3 77.0 - - - +
202A PHE* 1.3 63.9 + - - +
204A LEU* 3.1 20.6 + - - +
205A VAL 3.9 2.3 + - - -
518A 11A 4.0 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 2.7 40.0 + + + +
199A PRO 4.0 2.2 - - - +
201A ALA* 1.3 72.9 - - - +
203A ASN* 1.3 62.3 + - - +
205A VAL* 3.0 10.4 + - + +
206A LYS* 3.0 44.8 + - + +
209A MET* 3.9 21.3 - - + -
214A ARG* 4.9 6.7 - - + -
217A ILE* 3.5 34.5 - - + -
387A ASP* 3.7 20.6 - - - -
390A SER* 3.5 18.8 - - - +
518A 11A 3.9 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO 3.1 14.5 + - - +
200A VAL 3.6 4.0 - - - +
201A ALA 3.2 0.2 - - - -
202A PHE* 1.3 77.2 - - - +
204A LEU* 1.3 62.6 + - + +
205A VAL 3.3 0.6 + - - -
206A LYS* 2.7 47.3 + - - +
207A SER* 5.0 2.6 + - - -
385A LEU* 3.3 36.9 + - - +
386A PRO 4.4 1.6 + - - -
387A ASP* 3.7 14.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
163A LEU* 3.9 28.7 - - + -
168A VAL* 4.0 30.3 - - + -
172A GLN* 2.9 29.2 + - - +
200A VAL 3.7 12.6 - - - +
201A ALA 3.4 9.4 - - - +
202A PHE 3.1 1.0 + - - -
203A ASN* 1.3 80.1 - - + +
205A VAL* 1.3 59.4 + - + +
207A SER* 5.0 1.2 + - - -
208A PHE* 3.9 5.9 - - - -
304A ARG* 4.3 15.5 - - - +
384A LEU* 4.0 35.7 - - + -
518A 11A 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.7 3.8 - - + -
171A TYR* 4.3 21.8 - - + -
172A GLN* 4.3 15.3 - - + +
175A PHE* 4.2 12.2 - - + -
201A ALA 4.7 0.4 - - - +
202A PHE* 3.0 15.4 + - + +
204A LEU* 1.3 82.2 - - + +
206A LYS* 1.3 66.9 + - - +
207A SER 3.3 3.1 - - - -
208A PHE* 3.0 25.6 + - + +
209A MET* 3.7 24.0 + - + +
518A 11A 4.1 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.0 33.9 + - + +
203A ASN* 2.7 36.0 + - - +
204A LEU 3.7 0.8 - - - -
205A VAL* 1.3 77.8 - - - +
207A SER* 1.3 64.4 + - - +
209A MET* 3.3 15.8 + - - +
214A ARG* 2.7 36.5 + - - +
387A ASP* 2.9 31.8 + - - +
388A LYS 5.1 0.8 - - - +
----------------------------------------------------------
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