Contacts of the helix formed by residues 210 - 216 (chain A) in PDB entry 4TLG
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.0 25.8 + - - +
209A MET* 1.3 77.1 - - - +
211A GLU* 1.3 58.5 + - - +
212A GLU* 3.6 8.8 + - - +
213A THR* 3.1 26.0 + - - -
214A ARG* 2.9 28.5 + - - +
501A EDO 4.6 0.5 + - - -
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Residues in contact with GLU 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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210A SER* 1.3 71.9 - - - +
212A GLU* 1.3 58.2 + - - +
214A ARG* 2.8 40.6 + - - +
215A ARG* 2.9 73.6 + - - +
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Residues in contact with GLU 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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184A GLU* 4.9 13.9 - - + +
210A SER* 3.2 8.4 + - - +
211A GLU* 1.3 80.0 - - - +
213A THR* 1.3 61.6 + - - +
215A ARG* 3.3 25.2 + - - +
216A LYS* 3.4 41.9 + - - +
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Residues in contact with THR 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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175A PHE* 5.3 4.3 - - + -
178A LEU* 5.6 1.3 - - + -
179A GLU* 2.6 31.3 + - - +
186A LEU* 5.4 0.2 - - + -
189A LEU* 3.9 29.4 - - + +
209A MET* 4.1 15.5 - - + -
210A SER* 3.1 13.3 + - - -
212A GLU* 1.3 72.9 - - - +
214A ARG* 1.3 67.3 + - - +
216A LYS* 3.0 26.2 + - - +
217A ILE* 3.7 6.4 + - - +
501A EDO 3.5 22.8 + - - -
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Residues in contact with ARG 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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202A PHE* 4.9 4.3 - - + -
206A LYS* 2.7 37.3 + - - +
207A SER* 4.1 12.3 + - - +
209A MET* 2.7 39.6 + - + -
210A SER* 2.9 14.4 + - - +
211A GLU* 2.8 55.0 + - - +
213A THR* 1.3 75.2 - - - +
215A ARG* 1.3 62.1 + - - +
217A ILE* 3.1 32.6 + - + +
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Residues in contact with ARG 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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211A GLU* 2.9 54.1 + - - +
212A GLU* 3.7 19.9 + - - +
213A THR 3.2 0.2 - - - -
214A ARG* 1.3 75.3 - - - +
216A LYS* 1.3 59.6 + - + +
217A ILE 3.3 5.7 + - - +
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Residues in contact with LYS 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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148A MET* 4.4 7.8 - - - +
184A GLU* 3.9 25.8 - - - +
186A LEU 2.7 29.9 + - - +
187A LYS* 3.7 18.4 - - - +
188A ASN* 2.9 22.0 - - - +
189A LEU* 3.0 24.9 + - + -
212A GLU* 3.5 38.3 + - - +
213A THR* 3.0 17.1 + - - +
215A ARG* 1.3 77.2 - - + +
217A ILE* 1.3 61.3 + - - +
218A VAL* 3.6 1.8 + - - -
501A EDO 4.3 8.2 + - - +
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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