Contacts of the helix formed by residues 216 - 227 (chain A) in PDB entry 6OZE
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASP 4.0 12.3 - - - -
31A ARG* 4.5 1.8 - - - -
32A ASP* 2.8 40.6 + - - +
211A VAL* 3.7 1.1 - - - -
215A MET* 1.3 75.8 - - - +
217A LEU* 1.3 61.4 + - - +
218A GLU* 3.8 6.5 + - - +
219A ALA* 3.2 16.5 + - - +
220A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 217 (chain A).
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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30A ASP 5.1 0.4 + - - -
192A VAL* 3.9 19.3 - - + +
193A LEU 4.8 2.0 - - - -
194A GLY* 3.8 19.3 - - - +
195A MET* 3.7 26.0 - - + -
209A ILE* 3.7 26.0 - - + +
210A SER* 4.1 11.2 - - - -
211A VAL* 3.4 19.2 - - + +
216A SER* 1.3 73.5 - - - +
218A GLU* 1.3 63.8 + - + +
220A ALA* 3.2 2.4 + - + +
221A VAL* 3.0 39.7 + - + +
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Residues in contact with GLU 218 (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 MET* 5.4 9.6 - - - -
216A SER* 3.3 6.9 + - - +
217A LEU* 1.3 79.5 - - + +
219A ALA* 1.3 62.3 + - - +
221A VAL* 3.4 5.5 + - - +
222A ARG* 3.1 30.7 + - + +
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Residues in contact with ALA 219 (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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32A ASP* 3.5 16.8 - - - +
37A GLN 3.8 17.7 - - - +
42A PHE* 3.7 4.5 - - + -
215A MET* 3.6 15.4 - - + +
216A SER* 3.2 18.9 + - - +
218A GLU* 1.3 76.2 - - - +
220A ALA* 1.3 60.3 + - - +
222A ARG* 3.3 11.3 + - - +
223A LEU* 2.8 31.2 + - - +
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Residues in contact with ALA 220 (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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151A VAL* 3.7 31.0 - - + +
209A ILE* 4.2 7.2 - - + -
210A SER 5.0 3.6 - - - +
211A VAL* 5.0 3.6 - - + -
215A MET* 3.9 15.6 - - + +
216A SER 2.9 18.3 + - - +
217A LEU* 3.2 9.8 + - + +
219A ALA* 1.3 75.7 - - - +
221A VAL* 1.3 57.3 + - - +
223A LEU* 3.4 2.4 + - - +
224A THR* 2.9 33.6 + - - -
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Residues in contact with VAL 221 (chain A).
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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180A GLY 5.4 1.8 - - - +
182A SER* 4.2 17.9 - - - +
195A MET* 3.7 35.4 - - + -
197A LEU* 3.9 27.7 - - + +
209A ILE* 3.8 21.8 - - + -
217A LEU* 3.0 23.2 + - + +
218A GLU* 3.8 4.7 - - - +
220A ALA* 1.3 75.3 - - - +
222A ARG* 1.3 65.3 + - + +
224A THR* 3.3 4.7 + - - -
225A SER* 3.0 22.1 + - - -
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Residues in contact with ARG 222 (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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37A GLN 4.4 5.9 + - - -
38A ARG 5.4 0.6 - - - -
39A ASP 3.1 26.3 + - - -
40A PRO* 2.7 29.2 + - - +
42A PHE* 3.6 23.5 - - + -
218A GLU* 3.1 20.9 + - + +
219A ALA* 3.7 7.9 - - - +
221A VAL* 1.3 79.2 - - + +
223A LEU* 1.3 56.5 + - - +
225A SER* 3.3 7.9 + - - -
226A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 223 (chain A).
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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36A TRP* 4.4 2.9 - - + -
42A PHE* 3.5 18.3 - - + -
45A LEU* 3.6 27.4 - - + -
48A VAL* 4.6 1.6 - - + -
72A PHE* 4.2 7.4 - - + -
122A VAL* 3.8 37.2 - - + -
124A LEU* 4.1 15.9 - - + -
151A VAL* 4.6 1.1 - - + -
215A MET* 3.9 16.2 - - + -
219A ALA 2.8 17.2 + - - +
220A ALA 3.7 3.8 - - - +
222A ARG* 1.3 76.3 - - - +
224A THR* 1.3 64.4 + - - +
226A ALA* 3.1 1.8 + - - +
227A CYS* 2.9 40.8 + - - -
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Residues in contact with THR 224 (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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124A LEU* 4.5 6.8 - - + +
151A VAL* 3.9 17.2 - - - +
153A VAL* 4.2 6.2 - - + +
197A LEU* 3.8 12.1 - - + -
207A LEU* 4.0 3.4 - - + -
209A ILE* 3.7 25.8 - - + +
220A ALA 2.9 19.9 + - - -
221A VAL 3.7 4.9 - - - -
222A ARG 3.3 0.4 - - - -
223A LEU* 1.3 76.8 - - - +
225A SER* 1.3 60.0 + - - +
227A CYS* 3.2 13.5 + - - +
228A SER* 2.8 21.0 + - - -
233A PRO* 3.5 25.7 - - + +
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Residues in contact with SER 225 (chain A).
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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179A ARG* 2.8 40.6 + - - +
180A GLY* 3.5 28.1 + - - -
197A LEU* 3.9 12.2 - - - +
199A SER* 5.5 1.3 - - - +
221A VAL 3.0 13.7 + - - -
222A ARG* 3.6 10.3 - - - -
223A LEU 3.3 0.2 - - - -
224A THR* 1.3 76.3 - - - +
226A ALA* 1.3 58.7 + - - +
228A SER* 3.1 12.8 + - - -
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Residues in contact with ALA 226 (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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42A PHE* 4.4 7.4 - - + -
72A PHE* 4.0 28.0 - - + -
73A PRO 5.5 0.7 - - - +
75A LEU* 4.0 2.9 - - - +
179A ARG* 3.9 5.2 - - - +
222A ARG 2.9 17.4 + - - +
223A LEU* 3.1 7.8 + - - +
225A SER* 1.3 76.5 - - - +
227A CYS* 1.3 57.2 + - - +
303A GOL 2.5 26.6 + - - -
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Residues in contact with CYS 227 (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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48A VAL* 4.2 11.2 - - - -
72A PHE* 4.0 15.3 - - - -
75A LEU* 3.6 19.3 - - + +
124A LEU* 4.1 19.3 - - + -
223A LEU* 2.9 36.4 + - - +
224A THR 3.2 5.8 + - - +
225A SER 3.1 0.4 - - - -
226A ALA* 1.3 77.5 - - - +
228A SER* 1.3 57.0 + - - +
229A ARG 3.6 0.6 + - - -
233A PRO* 4.2 1.3 - - + -
234A GLU* 2.8 33.4 + - - +
235A PRO* 3.9 15.0 - - + -
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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