Contacts of the helix formed by residues 208 - 215 (chain B) in PDB entry 5C1V
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 THR 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ILE* 3.8 9.0 - - - +
207B ASN* 1.3 84.1 - - + +
209B LEU* 1.3 62.8 + - - +
210B ASP* 2.8 29.0 + - + +
211B ASP* 3.0 34.3 + - - +
268B PHE* 4.8 2.5 - - - -
271B HIS* 4.6 11.4 - - - +
272B ASN* 3.5 13.9 - - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 4.3 13.2 - - + -
190B LEU* 4.2 22.9 - - + -
196B LEU* 4.4 10.1 - - + -
208B THR* 1.3 73.2 + - - +
210B ASP* 1.4 57.0 + - - +
212B ILE* 3.0 42.4 + - + +
213B ARG* 3.3 26.5 - - - +
268B PHE* 5.2 0.2 - - + -
272B ASN* 3.7 35.0 - - + +
274B LEU* 4.2 20.2 - - + -
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 2.8 14.2 + - + +
209B LEU* 1.4 77.6 - - - +
211B ASP* 1.3 64.6 + - - +
213B ARG* 3.1 42.2 + - - +
214B LYS* 2.9 47.4 + - - +
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLU 4.5 6.2 - - - +
206B ILE* 4.1 19.0 - - + -
207B ASN* 3.0 27.0 + - - +
208B THR* 3.0 31.2 + - - +
209B LEU 3.1 0.6 - - - -
210B ASP* 1.3 82.5 - - - +
212B ILE* 1.3 62.9 + - - +
214B LYS* 3.2 15.3 + - - +
215B LEU* 3.6 16.1 + - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASN* 3.1 23.4 + - + +
78B LEU* 4.0 28.5 - - + -
187B LEU* 4.9 3.1 - - + -
188B ALA* 3.9 24.7 - - + -
196B LEU* 4.3 22.7 - - + -
198B VAL* 5.9 0.7 - - + -
206B ILE* 3.9 26.5 - - + -
208B THR 4.4 0.4 - - - +
209B LEU* 3.0 24.0 + - + +
211B ASP* 1.3 76.2 - - - +
213B ARG* 1.3 62.8 + - - +
214B LYS 3.3 0.5 + - - -
215B LEU* 3.4 17.6 + - + +
230B ILE* 4.5 14.6 - - + -
268B PHE* 5.3 0.4 - - + -
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASN* 2.9 22.6 + - + +
78B LEU* 3.0 35.8 - - + +
80B ASP* 5.6 3.6 + - - -
209B LEU* 3.3 22.4 + - - +
210B ASP* 3.1 43.6 + - - +
212B ILE* 1.3 79.6 - - - +
214B LYS* 1.3 61.1 + - + +
215B LEU 4.0 0.2 - - - +
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASP* 2.9 39.8 + - - +
211B ASP* 3.2 8.3 + - - +
213B ARG* 1.3 82.5 - - + +
215B LEU* 1.3 62.0 + - - +
216B ASP* 3.8 0.9 + - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 2.6 27.0 + - - +
187B LEU* 3.7 20.2 - - + -
206B ILE* 4.6 3.4 - - + -
211B ASP 3.6 11.6 + - - +
212B ILE* 3.6 17.3 - - - +
213B ARG 3.4 1.7 - - - +
214B LYS* 1.3 78.9 - - - +
216B ASP* 1.3 63.5 + - - +
217B ARG 3.5 1.1 + - - -
226B PRO* 3.4 34.1 - - + -
227B MET* 4.3 17.3 - - + +
230B ILE* 3.7 29.8 - - + -
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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