Contacts of the helix formed by residues 198 - 208 (chain B) in PDB entry 4TR8
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 ARG 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER 5.0 1.6 + - - -
146B MET* 3.6 48.4 + - + +
147B ALA 3.1 28.0 + - - -
148B GLN* 3.6 42.7 + - - +
149B GLN 5.2 0.7 - - - +
156B ASN* 3.0 26.2 + - + +
157B GLY* 3.4 1.4 - - - -
197B PRO* 1.3 71.1 - - + +
199B LYS* 1.4 65.9 + - + +
201B ILE* 3.4 0.9 - - - +
202B LEU* 3.1 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL 5.8 0.6 + - - -
22B GLU* 4.7 17.4 - - - +
48B ASP* 3.7 25.9 + - - +
50B GLU* 4.3 15.3 - - - +
51B VAL* 5.2 3.1 - - + -
197B PRO* 3.3 2.0 - - - +
198B ARG* 1.4 81.9 - - + +
200B GLY* 1.3 61.8 - - - +
202B LEU* 3.5 6.5 + - - +
203B GLU* 3.2 24.1 + - + +
206B ARG* 4.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 5.0 1.0 + - - -
51B VAL* 3.6 29.6 - - - +
196B VAL* 4.2 2.7 - - - -
197B PRO* 3.1 10.7 + - - +
199B LYS* 1.3 74.6 - - - +
201B ILE* 1.3 58.8 + - - +
203B GLU* 3.3 3.4 + - - +
204B LEU* 2.9 23.7 + - - +
233B PHE* 3.2 16.4 - - - -
235B SER* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 6.1 0.9 - - + -
139B ILE* 3.7 40.4 - - + +
146B MET* 3.6 31.2 - - + -
158B MET* 3.8 19.5 - - + -
160B LEU* 3.9 17.3 - - + -
196B VAL* 3.7 29.3 - - + +
197B PRO 3.0 13.9 + - - +
198B ARG* 3.4 10.5 - - - +
200B GLY* 1.3 76.0 - - - +
202B LEU* 1.4 64.6 + - - +
204B LEU* 3.3 16.2 + - + +
205B ALA 3.1 18.7 + - - -
224B ILE* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 5.2 1.1 - - + -
143B SER* 3.6 35.9 - - - +
146B MET* 3.9 7.9 - - + -
198B ARG* 3.1 50.6 + - - +
199B LYS* 4.0 5.4 - - - +
200B GLY 3.4 0.2 - - - -
201B ILE* 1.4 75.9 - - - +
203B GLU* 1.4 61.5 + - - +
205B ALA* 3.5 6.8 + - + +
206B ARG* 3.3 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 4.4 4.0 - - - +
19B GLY* 4.6 9.9 - - - +
20B VAL* 3.6 32.4 - - + +
51B VAL* 5.2 4.0 - - + -
53B LEU* 4.4 2.3 - - - +
199B LYS* 3.2 18.2 + - + +
200B GLY* 3.6 6.1 - - - +
201B ILE 3.3 0.2 - - - -
202B LEU* 1.4 73.2 - - - +
204B LEU* 1.4 63.3 + - - +
206B ARG* 3.0 37.7 + - - +
207B LEU* 3.1 50.7 + - + +
233B PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.4 16.2 - - + -
139B ILE* 4.4 3.4 - - + -
196B VAL* 5.8 0.7 - - + -
200B GLY 2.9 17.1 + - - +
201B ILE* 3.3 24.2 + - + +
203B GLU* 1.4 75.0 - - - +
205B ALA* 1.4 60.7 + - - +
207B LEU* 3.1 22.8 + - + +
208B LEU* 3.3 35.9 + - + +
217B ILE* 5.5 0.4 - - + -
224B ILE* 4.9 15.7 - - + -
226B ALA* 3.7 21.8 - - + -
233B PHE* 3.6 38.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 3.1 31.6 + - + +
139B ILE* 3.7 33.3 - - + +
140B ASP* 3.6 24.0 - - - +
201B ILE 3.1 6.5 + - - -
202B LEU* 3.7 10.5 - - + +
203B GLU 3.3 0.2 - - - -
204B LEU* 1.4 74.8 - - - +
206B ARG* 1.4 62.5 + - + +
208B LEU* 3.2 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 5.9 1.9 - - - +
136B ARG* 4.0 14.5 + - - +
199B LYS* 4.9 3.6 + - - +
202B LEU* 3.3 32.0 + - - +
203B GLU* 3.0 44.9 + - - +
205B ALA* 1.4 78.7 - - + +
207B LEU* 1.3 60.7 + - + +
209B THR* 3.6 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 37.1 - - + +
53B LEU* 3.9 27.8 - - + -
132B GLN* 4.5 2.3 - - - +
203B GLU* 3.1 37.5 + - + +
204B LEU* 3.1 13.7 + - + +
206B ARG* 1.3 75.8 - - - +
208B LEU* 1.3 59.6 + - + +
209B THR* 3.0 16.2 + - - -
228B THR* 5.8 2.4 - - - +
233B PHE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 3.6 45.3 - - + +
133B SER* 5.8 0.7 - - - -
135B LEU* 3.8 21.3 - - + -
136B ARG* 3.2 54.9 + - + +
139B ILE* 4.2 4.7 - - + -
204B LEU* 3.4 30.7 - - + +
205B ALA* 3.2 6.6 + - - +
207B LEU* 1.3 73.7 - - + +
209B THR* 1.3 60.6 + - - +
215B VAL* 3.9 25.6 - - + -
228B THR* 4.9 4.0 - - + -
----------------------------------------------------------
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