Contacts of the helix formed by residues 211 - 219 (chain A) in PDB entry 6DWM
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 HIS 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 TYR* 3.5 37.6 - + + -
208A ASP* 3.0 34.1 + - + +
209A HIS 3.6 0.4 - - - -
210A ASN* 1.3 74.8 - - - +
212A GLN* 1.3 65.2 + - - +
213A GLU* 3.4 40.7 + - + -
214A LEU* 3.6 8.4 + - + +
215A LEU* 3.2 27.2 + - - +
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Residues in contact with GLN 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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210A ASN 4.0 9.6 - - - +
211A HIS* 1.3 73.0 - - - +
213A GLU* 1.3 66.4 + - - +
215A LEU* 4.3 4.5 - - - +
216A SER* 3.2 24.3 + - - -
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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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205A ARG* 5.9 0.2 + - - -
207A TYR* 4.0 14.4 + - - -
211A HIS* 3.4 24.9 + - + -
212A GLN* 1.3 78.9 - - - +
214A LEU* 1.3 63.4 + - - +
216A SER* 3.3 8.4 + - - -
217A LEU* 3.2 19.8 + - + +
257A LYS* 3.9 9.8 + - - +
261A PHE* 4.2 21.1 - - + -
264A LYS* 3.1 37.6 + - - +
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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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192A VAL* 3.9 36.3 - - + -
195A THR* 3.8 25.1 - - + -
196A ASN* 4.3 4.9 - - - +
199A CYS* 5.8 0.2 - - - -
207A TYR* 3.7 44.2 - - + -
208A ASP 4.6 2.5 - - - +
211A HIS* 3.6 18.7 + - + +
212A GLN 3.4 0.4 - - - -
213A GLU* 1.3 79.6 + - - +
215A LEU* 1.3 54.7 + - + +
217A LEU* 2.6 33.0 + - + +
218A VAL* 2.9 26.7 + - + +
261A PHE* 5.6 3.1 - - + -
315A PHE* 5.0 5.8 - - + -
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Residues in contact with LEU 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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188A ARG* 3.6 37.5 - - - +
192A VAL* 3.8 29.6 - - + -
208A ASP 5.6 0.4 - - - +
209A HIS 3.8 9.4 - - - +
210A ASN* 4.0 9.6 - - - +
211A HIS 3.2 18.4 + - - +
212A GLN* 4.3 4.3 - - - +
214A LEU* 1.3 78.8 - - + +
216A SER* 1.3 57.9 + - - +
218A VAL* 4.6 2.0 - - + -
219A ASN* 3.0 58.3 + - + +
220A LEU* 3.6 1.1 - - - +
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Residues in contact with SER 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 GLN 3.2 20.7 + - - -
213A GLU* 3.4 7.4 - - - -
214A LEU 3.1 0.8 - - - -
215A LEU* 1.3 76.7 - - - +
217A LEU* 1.3 57.1 + - - +
220A LEU* 3.4 41.1 - - - +
254A LEU* 5.9 1.0 - - - +
257A LYS* 3.2 29.3 - - - +
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Residues in contact with LEU 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* 3.2 11.3 + - + +
214A LEU* 2.6 21.9 + - + +
216A SER* 1.3 72.8 - - - +
218A VAL* 1.3 60.4 + - + +
219A ASN 3.6 0.4 - - - -
220A LEU 5.2 0.2 - - - +
222A ASN* 3.3 18.9 + - - +
254A LEU* 4.3 2.4 - - - +
257A LYS* 3.4 44.4 - - + +
258A PHE* 3.3 39.2 - - + -
261A PHE* 3.7 45.8 - - + -
315A PHE* 4.2 16.6 - - + -
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Residues in contact with VAL 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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187A TYR* 4.6 6.1 + - - -
191A VAL* 3.9 29.8 - - + +
192A VAL* 5.4 0.2 - - + -
195A THR* 4.1 21.3 - - + +
214A LEU* 2.9 42.2 + - + +
215A LEU* 4.6 2.7 - - + -
217A LEU* 1.3 82.3 - - + +
219A ASN* 1.3 63.9 + - + +
222A ASN* 3.0 16.5 - - - +
258A PHE* 4.7 1.1 - - + -
315A PHE* 4.5 5.4 - - + -
319A PHE* 3.6 41.2 - - + -
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Residues in contact with ASN 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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187A TYR* 3.9 19.3 - - - -
188A ARG* 3.6 35.0 + - - +
191A VAL* 4.4 14.4 - - + -
215A LEU* 3.0 33.3 + - + +
218A VAL* 1.3 80.8 - - + +
220A LEU* 1.3 59.7 + - - +
221A ASN 4.2 0.4 - - - -
222A ASN* 3.6 2.0 - - - -
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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