Contacts of the helix formed by residues 199 - 207 (chain A) in PDB entry 4UT2
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 GLY 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 4.0 13.0 - - - -
196A PRO* 5.5 0.7 - - - -
198A GLN* 1.3 77.2 - - - +
200A LEU* 1.3 66.3 + - - -
201A LEU 3.4 2.0 - - - -
202A CYS* 3.2 3.2 + - - +
203A ASP* 3.0 33.4 + - - +
225A PHE* 6.2 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 3.6 31.4 - - - +
179A ASP* 4.1 11.6 + - + -
180A LEU* 3.8 24.7 - - + +
185A GLN* 3.7 48.9 - - + +
186A ILE* 4.2 5.4 - - + +
189A ILE* 4.3 11.4 - - + -
199A GLY* 1.3 70.9 - - - -
201A LEU* 1.3 63.4 + - - +
203A ASP* 3.3 2.3 + - - +
204A LEU* 3.0 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 4.6 3.1 - - - +
161A ILE* 3.5 42.8 - - + -
189A ILE* 4.4 22.8 - - + +
193A THR* 3.8 28.9 - - + -
194A ASP 4.0 3.4 - - - +
195A VAL* 4.1 12.8 - - + -
196A PRO* 3.7 29.1 - - + +
199A GLY 3.4 0.8 - - - -
200A LEU* 1.3 78.0 - - - +
202A CYS* 1.3 63.5 + - - +
204A LEU* 3.4 3.7 + - - +
205A LEU* 3.4 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.1 10.8 - - - -
196A PRO* 3.4 22.0 - - - +
197A ASP 3.6 12.1 - - - -
198A GLN* 3.8 12.8 - - - +
199A GLY 3.2 10.8 + - - +
201A LEU* 1.3 78.8 - - - +
203A ASP* 1.3 63.4 + - - +
205A LEU 3.1 3.5 + - - -
206A TRP* 3.0 35.4 + - - +
223A VAL* 3.5 32.8 - - - -
224A SER* 4.4 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY 3.6 2.3 - - - +
176A LEU 3.7 3.6 - - - +
177A SER* 2.4 42.1 + - - +
178A PRO* 3.3 15.4 - - - +
179A ASP* 4.7 2.6 - - - +
198A GLN* 5.9 0.2 - - - -
199A GLY* 3.0 22.3 + - - +
200A LEU 3.3 1.5 + - - +
202A CYS* 1.3 76.8 - - - +
204A LEU* 1.3 62.8 + - - +
207A SER* 3.1 30.8 + - - -
224A SER* 2.8 31.4 + - - +
225A PHE* 3.5 16.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
161A ILE* 3.6 23.8 - - + -
162A ALA* 5.5 0.4 - - + -
170A PHE* 4.3 23.6 - - + -
172A CYS* 3.8 14.8 - - + +
173A HIS 3.8 2.1 + - - -
174A GLY* 2.9 21.7 + - - -
175A GLY 3.4 19.9 + - - +
176A LEU* 4.9 1.6 - - - -
177A SER* 5.1 2.0 - - - +
180A LEU* 4.3 15.3 - - + -
186A ILE* 3.9 23.6 - - + -
189A ILE* 4.5 4.9 - - + -
200A LEU* 3.0 34.3 + - + +
201A LEU* 3.7 5.8 - - - +
202A CYS 3.3 0.2 - - - -
203A ASP* 1.3 76.8 - - - +
205A LEU* 1.3 66.6 + - + +
206A TRP 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 3.5 34.1 - - + +
123A GLY* 3.7 22.9 - - - +
124A ASN* 3.4 22.2 - - - +
161A ILE* 4.1 21.1 - - + +
173A HIS* 3.5 16.4 - - + -
174A GLY* 3.9 8.5 - - - +
195A VAL* 3.7 28.9 - - + -
201A LEU* 3.4 19.0 + - + +
202A CYS 3.1 5.0 + - - +
204A LEU* 1.3 92.2 - - + +
206A TRP* 1.3 65.3 + - + +
248A HIS* 3.6 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 3.3 41.8 + - + +
130A ILE* 3.7 32.1 - - + -
195A VAL* 4.3 13.4 - - + +
196A PRO 5.5 0.2 + - - -
202A CYS* 3.0 38.2 + - - +
203A ASP 3.3 0.2 + - - -
204A LEU 3.6 0.2 - - - -
205A LEU* 1.3 85.6 - - + +
207A SER* 1.3 66.1 + - - +
208A ASP* 3.8 0.7 - - - +
219A ASN* 4.0 2.3 + - - -
221A ARG* 3.7 40.9 + - + -
223A VAL* 3.3 36.0 - - + +
224A SER* 3.7 17.8 - - - -
248A HIS* 2.9 20.7 + + - -
501A PO4 5.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY 3.3 12.3 - - - -
175A GLY* 3.1 20.5 - - - +
176A LEU 2.9 25.6 + - - -
203A ASP* 3.1 7.9 + - - -
206A TRP* 1.3 80.7 - - - +
208A ASP* 1.3 59.4 + - - +
216A TRP* 5.2 1.3 - - - -
219A ASN* 4.2 0.4 - - - +
224A SER* 3.4 12.9 + - - -
225A PHE* 3.3 21.5 - - - -
227A PHE* 3.4 7.9 - - - -
246A ARG* 3.2 15.4 + - - -
248A HIS* 3.5 0.5 - - - -
----------------------------------------------------------
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