Contacts of the helix formed by residues 210 - 214 (chain A) in PDB entry 3R9X
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 VAL 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A THR* 3.4 31.2 - - + +
207A ARG 3.2 15.7 - - - +
209A GLU* 1.3 85.5 - - - +
211A PRO* 1.3 60.6 - - + +
213A SER* 2.6 35.7 + - - -
214A ILE* 3.5 12.9 + - + +
244A LEU* 4.1 28.7 - - + -
247A ILE* 4.2 12.3 - - + -
248A ILE* 4.7 5.8 - - + -
1530C G 4.6 0.2 - - - +
1531C A 3.5 19.7 - - + +
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Residues in contact with PRO 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 4.0 19.7 - - + -
39A ARG* 4.4 0.9 + - - -
199A ARG* 5.6 0.3 - - - +
203A MET* 3.7 43.9 - - + +
206A THR* 3.3 33.7 - - - +
207A ARG 3.2 15.3 - - - +
208A GLU 3.3 12.8 - - - +
209A GLU 3.6 0.9 - - - -
210A VAL* 1.3 92.0 - - + +
212A THR* 1.3 58.6 + - - +
213A SER 3.3 2.3 + - - -
214A ILE* 3.5 22.1 + - + +
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Residues in contact with THR 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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34A LYS* 5.5 0.7 - - + -
35A ALA 3.3 26.5 - - - +
36A GLY* 3.9 20.9 - - - +
39A ARG* 2.9 22.8 + - - +
203A MET* 4.3 4.5 - - + -
208A GLU 5.4 0.4 + - - -
209A GLU* 3.8 10.2 + - - -
210A VAL 3.2 0.6 - - - -
211A PRO* 1.3 76.6 - - + +
213A SER* 1.3 58.6 + - - +
214A ILE 3.3 1.6 - - - -
288A ARG* 2.8 30.1 + - - -
1506C C 5.6 1.6 + - - -
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU* 2.8 24.3 + - - +
210A VAL 2.6 19.6 + - - -
212A THR* 1.3 71.7 - - - +
214A ILE* 1.3 56.5 + - - +
238A ILE 3.6 4.3 - - - +
239A VAL* 3.6 6.9 - - - -
240A ASP* 3.4 11.4 + - - -
241A ARG* 5.0 0.9 + - - -
244A LEU* 3.4 26.4 - - - +
287A TRP* 3.1 24.7 + - - -
288A ARG* 3.1 22.5 + - - +
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Residues in contact with ILE 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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39A ARG* 2.6 33.6 + - - -
199A ARG* 3.7 9.7 - - + +
202A ALA* 3.9 40.2 - - + +
203A MET* 4.6 1.1 - - + +
206A THR* 3.9 4.7 - - - +
210A VAL* 3.5 24.2 - - + +
211A PRO* 3.5 16.2 + - + +
212A THR 3.3 1.0 - - - -
213A SER* 1.3 81.3 - - - +
215A ALA* 1.3 68.7 + - - +
216A VAL* 4.3 9.4 - - + -
237A ILE* 4.0 17.3 - - + -
238A ILE 3.4 3.4 - - - -
239A VAL* 4.3 2.5 - - + -
248A ILE* 3.9 22.2 - - + -
287A TRP* 3.8 1.6 - - - -
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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
------------------------------------------------------------
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