Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 7UUT
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 200 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY* 4.4 14.8 - - - +
177B PRO* 5.2 2.2 - - - +
199B SER* 1.3 83.1 + - - +
201B PRO* 1.3 66.8 - - + +
203B CYS* 3.0 38.9 + - + +
204B VAL* 2.9 26.7 + - - +
340B LYS* 4.2 30.1 - - - +
341B PRO 3.9 10.3 + - - -
342B LYS* 3.9 45.1 + - + +
344B LEU 3.0 24.5 + - - -
345B ILE* 5.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B SER 3.6 8.1 - - - +
200B ARG* 1.3 85.8 - - + +
202B VAL* 1.3 57.6 + - - +
204B VAL* 3.8 7.6 - - + +
205B ASP* 2.9 31.2 + - - +
342B LYS* 4.9 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 4.6 2.5 - - + -
201B PRO* 1.3 78.4 - - - +
203B CYS* 1.3 71.0 + - - +
205B ASP* 4.0 7.0 - - + +
206B ALA* 3.3 21.0 + - - +
318B LYS* 6.0 0.3 - - - -
321B THR* 4.3 7.2 - - + -
342B LYS 3.1 25.3 + - - +
343B ASP* 3.9 28.3 - - + +
344B LEU 4.3 2.7 - - - +
345B ILE* 3.7 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 3.3 39.3 - - + +
176B GLY* 4.8 1.6 - - - -
180B LEU* 3.6 4.7 - - - +
200B ARG* 3.0 51.4 + - + +
202B VAL* 1.3 87.9 - - - +
204B VAL* 1.3 54.4 + - - +
205B ASP 3.2 0.2 - - - -
206B ALA* 3.2 4.4 + - - -
207B ALA* 2.7 35.9 + - - +
345B ILE* 4.4 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.1 14.6 - - + -
198B GLY 4.1 9.4 - - - +
199B SER* 4.1 9.9 - - - +
200B ARG 2.9 19.2 + - - +
201B PRO* 3.8 7.6 - - + +
203B CYS* 1.3 75.6 - - - +
205B ASP* 1.3 62.5 + - - +
207B ALA* 3.3 4.1 + - - +
208B LYS* 3.1 38.5 + - - +
215B ILE* 3.8 41.5 - - + -
217B ASN* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO 2.9 17.6 + - - +
202B VAL* 4.0 7.8 - - - +
204B VAL* 1.3 78.8 - - - +
206B ALA* 1.3 60.8 + - - +
208B LYS* 3.5 9.9 + - - +
209B TYR* 3.2 19.2 + - - +
318B LYS* 2.9 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.7 27.4 - - + -
202B VAL 3.3 15.2 + - - +
203B CYS 3.2 1.6 + - - +
205B ASP* 1.3 76.4 - - - +
207B ALA* 1.3 64.2 + - - +
209B TYR* 3.1 8.1 + - - +
210B TYR* 3.0 32.8 + - + -
318B LYS* 4.1 22.7 - - + +
345B ILE* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.3 6.1 - - + -
180B LEU* 3.5 16.1 - - + +
183B VAL* 3.9 6.2 - - + +
196B ALA* 4.2 10.5 - - + -
203B CYS 2.7 21.0 + - - +
204B VAL* 3.3 7.4 + - - +
206B ALA* 1.3 74.1 - - - +
208B LYS* 1.3 59.3 + - - +
210B TYR* 3.3 4.8 + - - -
211B GLY 3.2 6.1 + - - -
212B ALA* 2.9 29.0 + - + +
215B ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 3.1 34.8 + - - +
205B ASP* 3.8 9.2 - - - +
207B ALA* 1.3 75.3 - - - +
209B TYR* 1.3 64.1 + - - +
211B GLY* 3.2 13.0 + - - -
212B ALA 3.9 17.8 + - - +
215B ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 5.2 5.7 + - - -
205B ASP 3.2 13.5 + - - +
206B ALA 3.1 8.6 + - - +
208B LYS* 1.3 78.4 - - - +
210B TYR* 1.3 93.0 + + - +
211B GLY* 3.5 0.5 + - - -
315B ASP* 3.5 32.9 + - + +
318B LYS* 3.9 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.9 28.9 - - + +
181B MET* 3.5 22.0 - - + +
183B VAL* 3.7 11.9 - - + +
184B ALA* 3.7 35.1 - - + +
187B LYS* 3.7 15.1 - - - +
206B ALA* 3.0 30.3 + - + +
207B ALA 3.3 1.1 + - - -
208B LYS 3.2 0.6 - - - -
209B TYR* 1.3 90.2 - + - +
211B GLY* 1.3 56.4 + - - +
314B VAL* 4.6 2.5 - - + -
315B ASP 2.7 36.8 + - - -
316B PRO* 3.4 11.1 - - - +
318B LYS* 3.2 28.5 + - + +
319B LEU* 3.7 16.1 + - + -
----------------------------------------------------------
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