Contacts of the helix formed by residues 200 - 212 (chain A) in PDB entry 4O0Z
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 SER 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 3.3 3.6 + - - +
199A SER* 1.3 81.9 + - - +
201A GLN* 1.3 58.9 + - - +
202A GLU 3.5 2.3 + - - -
203A THR* 3.2 16.6 + - - -
204A ALA* 2.9 28.6 + - - +
154B GLN* 3.6 15.9 + - - -
200B SER* 3.3 6.1 + - - -
202B GLU* 3.5 19.8 + - - -
203B THR* 2.9 21.1 + - - -
206B ILE* 3.8 11.4 - - - -
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Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 2.6 32.5 + - - -
200A SER* 1.3 74.0 - - - +
202A GLU* 1.3 63.7 + - - +
204A ALA* 3.1 14.6 + - - +
205A GLY* 3.2 11.1 + - - -
222A ALA* 4.5 5.4 - - - +
9B PHE* 3.8 19.0 - - + -
14B ALA* 4.0 0.3 - - - +
69B TYR* 3.5 44.1 - - + +
151B ILE* 3.6 27.2 - - - +
154B GLN* 2.9 29.5 + - - +
202B GLU* 3.4 2.4 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 2.9 30.6 + - - +
68A LYS* 4.6 4.0 - - - -
69A TYR* 2.6 33.8 + - - -
200A SER 3.3 0.2 - - - -
201A GLN* 1.3 77.7 - - - +
203A THR* 1.3 62.8 + - - +
205A GLY* 3.2 1.7 + - - -
206A ILE* 3.1 31.3 + - + +
226A LEU* 5.1 0.2 - - - +
200B SER* 3.7 11.3 - - - +
201B GLN* 3.4 4.6 + - - +
202B GLU* 2.9 48.9 + - + +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TYR* 3.6 21.1 - - + +
198A VAL* 3.7 20.2 - - + -
199A SER* 4.0 4.7 - - - +
200A SER* 3.2 13.2 + - - -
202A GLU* 1.3 77.2 - - - +
204A ALA* 1.3 54.5 + - - +
206A ILE* 3.3 4.1 + - - -
207A GLY* 2.7 34.0 + - - -
388A GLN* 4.8 2.2 - - - +
199B SER* 2.6 34.8 + - - +
200B SER* 2.9 13.7 + - - -
203B THR* 2.9 14.1 + - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR* 3.4 39.0 - - + -
198A VAL* 3.7 15.9 - - + +
200A SER 2.9 14.2 + - - +
201A GLN 3.1 10.5 + - - +
203A THR* 1.3 75.6 - - - +
205A GLY* 1.3 57.0 + - - +
207A GLY* 3.9 0.2 - - - -
208A ALA* 2.8 33.4 + - - +
220A THR* 3.7 10.7 - - + +
222A ALA* 4.2 0.7 - - + -
387A LEU* 4.6 1.2 - - - +
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN 3.2 9.0 + - - -
202A GLU* 3.2 2.9 + - - -
204A ALA* 1.3 77.9 - - - +
206A ILE* 1.3 61.7 + - - +
209A SER* 3.1 25.6 + - - -
222A ALA* 3.7 31.0 - - - +
223A GLY* 3.5 5.5 - - - -
226A LEU* 3.5 10.8 - - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.7 0.2 - - - -
64A TYR* 3.5 36.8 - - + +
157A TYR* 3.9 8.7 - - + -
158A PRO* 3.9 35.7 - - + -
202A GLU* 3.1 27.4 + - + +
203A THR 3.7 2.5 - - - +
205A GLY* 1.3 75.3 - - - +
207A GLY* 1.3 62.2 + - - +
209A SER* 2.6 21.0 + - - +
210A ALA* 3.2 9.0 + - - +
226A LEU* 3.5 20.6 - - + +
199B SER 4.2 5.2 - - - +
200B SER* 4.1 14.4 - - - -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TYR* 3.5 30.3 - - - -
161A VAL* 3.7 0.8 - - - +
203A THR 2.7 16.9 + - - -
204A ALA 3.9 0.2 - - - -
206A ILE* 1.3 72.6 - - - +
208A ALA* 1.3 61.6 + - - +
210A ALA* 3.2 16.2 + - - +
211A HIS 3.2 9.7 + - - -
387A LEU* 3.5 20.6 - - - +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASP* 3.5 23.9 - - - +
204A ALA 2.8 19.5 + - - +
207A GLY* 1.3 75.6 - - - +
209A SER* 1.3 61.7 + - - +
211A HIS* 3.4 5.6 + - - +
212A LEU* 3.2 28.6 + - + +
218A THR* 4.5 3.5 + - - +
220A THR* 3.6 26.2 - - + +
223A GLY* 3.7 11.2 - - - -
387A LEU* 4.1 1.2 - - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 2.9 23.6 + - - -
205A GLY 3.1 13.7 + - - -
206A ILE* 2.6 24.3 + - - +
208A ALA* 1.3 75.2 - - - +
210A ALA* 1.3 61.6 + - - +
212A LEU* 3.3 4.5 + - - -
213A VAL* 3.5 1.2 + - - +
223A GLY* 4.3 3.3 - - - -
226A LEU* 4.1 10.9 - - - +
227A ILE* 3.7 27.8 - - - -
473A PHE* 3.3 26.5 - - - -
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.5 15.0 - - + -
158A PRO* 3.5 31.2 - - + +
161A VAL* 3.8 8.3 - - + -
162A ALA* 3.6 22.2 - - - +
206A ILE 3.2 8.0 + - - +
207A GLY 3.2 10.2 + - - +
209A SER* 1.3 77.5 + - - +
211A HIS* 1.3 65.7 + - - +
213A VAL* 3.3 18.9 + - - +
214A ASN* 3.9 1.2 - - - +
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 4.2 4.2 - - + +
165A SER* 3.1 22.7 + - - -
190A LEU* 2.7 35.1 + - + -
192A ASP* 3.9 14.9 + - + +
207A GLY 3.2 9.2 + - - +
208A ALA* 3.5 12.1 - - - +
209A SER 3.3 0.2 - - - -
210A ALA* 1.3 79.8 - - - +
212A LEU* 1.3 61.1 + - + +
213A VAL 3.0 0.2 - - - -
214A ASN* 2.8 22.9 + - - +
215A PHE* 3.1 37.4 + + + +
217A GLY 3.8 17.3 + - - -
218A THR* 5.2 0.2 - - - -
386A LEU* 3.4 39.2 - - + +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA* 3.2 19.6 + - + +
209A SER* 3.7 7.0 - - - +
210A ALA 3.2 1.0 - - - -
211A HIS* 1.3 74.2 - - + +
213A VAL* 1.3 61.2 + - - +
214A ASN 3.1 2.0 - - - -
215A PHE 3.3 20.0 - - - +
216A LYS 4.0 9.0 - - - -
217A GLY 4.5 1.8 - - - +
218A THR* 4.0 19.1 - - + +
223A GLY* 4.8 4.9 - - - -
224A LEU* 4.2 21.3 - - + -
227A ILE* 3.7 19.3 - - + -
238A PRO* 3.8 17.0 - - + +
239A GLY* 3.8 11.4 - - - -
473A PHE* 3.6 10.3 - - + -
477A ARG* 2.8 36.4 + - - +
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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