Contacts of the helix formed by residues 200 - 210 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D GLY* 4.6 12.9 - - - -
177D PRO* 5.3 4.0 - - - +
199D SER* 1.3 85.6 + - - +
201D PRO* 1.3 73.6 - - + +
202D VAL* 4.6 11.7 - - + +
203D CYS* 3.0 41.7 + - + +
204D VAL* 2.9 19.8 + - - +
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Residues in contact with PRO 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D SER 3.5 8.5 - - - +
200D ARG* 1.3 84.7 - - + +
202D VAL* 1.3 58.5 + - - +
204D VAL* 3.8 8.7 - - + +
205D ASP* 2.9 30.8 + - - +
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ARG* 4.7 15.3 - - + +
201D PRO* 1.3 79.7 - - - +
203D CYS* 1.3 75.6 + - - +
205D ASP* 3.7 7.5 + - + +
206D ALA* 3.3 21.7 + - - +
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Residues in contact with CYS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.2 38.5 - - + +
176D GLY* 4.7 1.8 - - - -
177D PRO* 6.0 0.7 - - - -
180D LEU* 3.5 10.7 - - - +
200D ARG* 3.0 50.9 + - + +
202D VAL* 1.3 87.9 - - - +
204D VAL* 1.3 59.6 + - - +
206D ALA* 3.3 4.7 + - - +
207D ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 4.0 12.3 - - + -
198D GLY 4.0 13.9 - - - +
199D SER* 4.2 8.5 - - - +
200D ARG 2.9 19.5 + - - +
201D PRO* 3.3 8.0 + - + +
203D CYS* 1.3 75.4 - - - +
205D ASP* 1.3 62.4 + - - +
207D ALA* 3.3 3.2 + - - +
208D LYS* 3.1 38.5 + - - +
215D ILE* 3.7 43.0 - - + +
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Residues in contact with ASP 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PRO 2.9 16.6 + - - +
202D VAL* 3.9 8.1 - - - +
204D VAL* 1.3 80.5 - - - +
206D ALA* 1.3 63.4 + - - +
208D LYS* 3.4 11.2 + - - +
209D TYR* 3.2 20.7 + - - +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.7 27.8 - - + -
202D VAL 3.3 14.6 + - - +
203D CYS 3.3 0.6 + - - +
205D ASP* 1.3 78.6 - - - +
207D ALA* 1.3 65.0 + - - +
209D TYR* 3.1 8.9 + - - +
210D TYR* 3.0 38.6 + - + -
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 4.2 9.0 - - + -
180D LEU* 3.5 16.7 - - + +
183D VAL* 3.7 7.1 - - + +
196D ALA* 4.1 15.5 - - + -
203D CYS 2.9 18.3 + - - +
204D VAL 3.6 5.8 - - - +
205D ASP 3.3 0.4 - - - -
206D ALA* 1.3 76.4 - - - +
208D LYS* 1.3 59.6 + - - +
210D TYR* 3.2 3.8 + - - -
211D GLY 3.2 6.6 + - - -
212D ALA* 2.9 36.0 + - + +
215D ILE* 4.2 2.7 - - + -
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D VAL* 3.1 35.6 + - - +
205D ASP* 3.7 11.4 - - - +
207D ALA* 1.3 76.1 - - - +
209D TYR* 1.3 62.8 + - - +
211D GLY* 3.3 11.6 + - - -
212D ALA* 3.9 17.8 + - - +
215D ILE* 3.9 19.7 - - + -
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Residues in contact with TYR 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ASP* 3.2 13.5 + - - +
206D ALA* 3.1 12.6 + - + +
208D LYS* 1.3 77.8 - - - +
210D TYR* 1.3 99.0 + + - +
211D GLY* 3.5 1.0 + - - -
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Residues in contact with TYR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.9 33.0 - - + +
181D MET* 3.6 24.0 - - + +
183D VAL* 3.6 19.2 - - + +
184D ALA* 3.7 28.2 - - + +
187D LYS* 3.9 13.2 - - - +
206D ALA* 3.0 37.8 + - + +
207D ALA* 3.2 2.2 + - - -
209D TYR* 1.3 107.0 - + - +
211D GLY* 1.3 57.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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