Contacts of the helix formed by residues 211 - 227 (chain A) in PDB entry 6H60
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 ASP 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A SER 5.0 0.4 - - - -
209A VAL 3.5 3.6 + - - -
210A VAL* 1.3 74.5 - - - +
212A ASP* 1.3 67.5 + - - +
213A GLU 3.2 2.9 - - - -
214A LEU* 2.8 19.4 + - - +
215A ALA* 2.9 11.6 + - - +
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Residues in contact with ASP 212 (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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210A VAL 4.1 1.2 + - - -
211A ASP* 1.3 70.4 - - - +
213A GLU* 1.3 57.0 + - - +
215A ALA* 3.4 1.6 + - - -
216A THR* 2.9 24.4 + - - -
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Residues in contact with GLU 213 (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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211A ASP 3.2 0.4 - - - -
212A ASP* 1.3 72.8 - - - +
214A LEU* 1.3 66.6 + - - +
216A THR* 3.6 2.8 - - - +
217A ARG* 2.9 21.1 + - - -
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Residues in contact with LEU 214 (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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78A VAL* 6.0 5.2 - - - +
211A ASP* 2.8 15.8 + - - +
213A GLU* 1.3 77.8 - - - +
215A ALA* 1.3 55.9 + - - +
217A ARG* 3.3 1.6 + - - -
218A PHE* 2.9 24.1 + - - -
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Residues in contact with ALA 215 (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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210A VAL* 5.7 1.2 - - - +
211A ASP 2.9 11.8 + - - +
212A ASP* 3.9 2.2 - - - +
214A LEU* 1.3 74.5 - - - +
216A THR* 1.3 62.0 + - - +
218A PHE* 2.9 3.2 + - - +
219A LEU* 2.9 23.7 + - - -
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Residues in contact with THR 216 (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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212A ASP 2.9 16.4 + - - -
213A GLU* 3.2 6.0 + - - +
215A ALA* 1.3 76.6 - - - +
217A ARG* 1.3 55.1 + - - +
219A LEU* 4.4 0.2 - - - -
220A LYS* 2.9 25.6 + - - -
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Residues in contact with ARG 217 (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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213A GLU 2.9 14.0 + - - -
214A LEU 3.7 3.6 - - - -
216A THR* 1.3 73.3 - - - +
218A PHE* 1.3 61.0 + - - +
220A LYS* 4.2 0.7 - - - +
221A SER* 2.9 28.9 + - - +
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Residues in contact with PHE 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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71A THR* 5.8 5.1 - - - +
214A LEU 2.9 14.8 + - - -
215A ALA* 2.9 5.9 + - - +
217A ARG* 1.3 76.7 - - - +
219A LEU* 1.3 56.2 + - - +
222A PHE* 2.9 25.1 + - - -
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Residues in contact with LEU 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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37A ALA* 6.1 0.3 - - - -
215A ALA 2.9 14.3 + - - -
216A THR 4.0 0.4 - - - -
218A PHE* 1.3 71.1 - - - +
220A LYS* 1.3 59.1 + - - +
222A PHE* 3.6 2.2 - - - +
223A LYS* 2.9 22.9 + - - -
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Residues in contact with LYS 220 (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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216A THR 2.9 21.2 + - - -
217A ARG* 3.8 1.3 - - - +
218A PHE 3.2 0.4 - - - -
219A LEU* 1.3 73.0 - - - +
221A SER* 1.3 57.9 + - - +
222A PHE 2.9 3.6 - - - -
223A LYS* 3.0 5.9 + - - -
224A ALA* 2.9 22.9 + - - -
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Residues in contact with SER 221 (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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71A THR* 5.8 5.4 - - - -
217A ARG* 2.9 17.8 + - - +
218A PHE 3.9 0.7 - - - -
220A LYS* 1.3 71.4 - - - +
222A PHE* 1.3 56.3 + - - +
224A ALA* 3.7 6.3 - - - +
225A ASN* 2.9 23.2 + - - -
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Residues in contact with PHE 222 (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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67A ALA 5.6 6.5 - - - -
71A THR* 6.2 2.7 - - - +
218A PHE 2.9 21.3 + - - -
219A LEU* 3.7 3.4 - - - +
220A LYS 2.9 0.6 - - - -
221A SER* 1.3 75.6 - - - +
223A LYS* 1.3 58.5 + - - +
225A ASN* 3.3 1.6 + - - +
226A LEU* 2.9 25.1 + - - -
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Residues in contact with LYS 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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39A CYS* 5.4 12.7 - - - +
219A LEU 2.9 14.8 + - - -
220A LYS 3.0 3.5 + - - -
222A PHE* 1.3 75.5 - - - +
224A ALA* 1.3 51.5 + - - +
226A LEU* 3.3 1.5 + - - +
227A GLU* 2.6 32.6 + - - -
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Residues in contact with ALA 224 (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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220A LYS 2.9 14.4 + - - -
221A SER* 4.0 4.5 - - - +
222A PHE 3.2 0.2 - - - -
223A LYS* 1.3 73.7 - - - +
225A ASN* 1.3 64.2 + - - +
227A GLU* 3.0 15.2 + - - +
228A ASN 3.6 4.7 + - - +
231A ARG* 5.9 0.2 - - - -
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Residues in contact with ASN 225 (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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67A ALA* 6.5 0.9 - - - -
221A SER 2.9 18.8 + - - -
222A PHE* 3.3 1.8 + - - +
224A ALA* 1.3 73.8 - - - +
226A LEU* 1.3 55.7 - - - +
228A ASN 2.4 29.1 - - - +
229A PRO* 3.8 4.3 - - - +
231A ARG* 4.9 13.7 - - - +
232A LEU* 4.3 5.8 + - - +
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Residues in contact with LEU 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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40A ASP 3.7 17.0 - - - +
44A VAL* 6.2 0.2 - - - -
222A PHE 2.9 15.5 + - - -
223A LYS* 3.5 3.8 - - - +
225A ASN* 1.3 72.4 - - - +
227A GLU* 1.3 58.1 + - - +
228A ASN* 2.9 14.3 + - - -
229A PRO* 4.7 0.9 - - - -
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Residues in contact with GLU 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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40A ASP* 4.9 6.5 - - - +
223A LYS 2.6 20.3 + - - -
224A ALA* 3.0 8.7 + - - +
226A LEU* 1.3 72.7 - - - +
228A ASN* 1.4 54.9 + - - +
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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