Contacts of the helix formed by residues 210 - 214 (chain G) in PDB entry 3DV0
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173G ASP* 3.5 28.7 - - + +
201G ASN* 3.7 24.7 - - - +
203G ARG* 2.9 46.7 + - - +
208G THR 3.7 0.8 + - - -
209G PRO* 1.3 69.1 - - - +
211G GLU* 1.3 70.7 + - - +
213G GLN* 3.5 18.9 - - + +
214G THR* 3.8 10.6 + - - +
219G LEU* 4.2 14.8 - - + -
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Residues in contact with GLU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ALA* 5.5 1.7 - - - +
203G ARG* 3.1 34.8 + - - +
204G PHE* 5.5 0.5 - - - -
209G PRO* 3.0 33.8 - - + +
210G VAL* 1.3 94.9 + - - +
212G LYS* 1.3 60.8 + - + +
213G GLN 3.2 4.7 - - - -
214G THR 3.4 16.7 + - - +
215G VAL* 4.9 6.8 - - - +
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Residues in contact with LYS 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ALA* 3.8 11.8 - - - +
191E PHE* 6.1 0.2 - - - -
32F VAL* 6.1 4.9 - - - +
49F GLU* 5.6 5.4 - - - -
54F ASP* 4.5 29.2 - - + +
55F THR* 4.8 1.9 - - - +
56F PRO* 3.8 17.5 - - - +
208G THR* 4.0 10.5 - - + -
209G PRO* 2.9 39.6 + - + +
211G GLU* 1.3 77.9 - - + +
213G GLN* 1.3 64.5 + - - +
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Residues in contact with GLN 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASN* 3.2 20.8 + - - -
190E ALA* 3.8 2.0 - - - +
55F THR 5.1 0.2 + - - -
56F PRO* 3.1 15.9 - - - +
57F LEU* 2.4 36.4 + - - +
173G ASP* 3.9 21.6 + - - +
174G GLY* 3.6 19.1 - - - +
176G THR* 4.4 3.8 - - - +
177G SER* 2.7 20.3 + - - +
205G ALA* 3.7 17.6 - - - +
208G THR* 3.8 17.2 + - - +
209G PRO 3.5 3.0 + - - -
210G VAL* 3.5 21.5 - - + +
211G GLU 3.2 0.2 - - - -
212G LYS* 1.3 82.1 - - - +
214G THR* 1.3 63.4 + - + +
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Residues in contact with THR 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASN* 2.8 26.5 + - - -
190E ALA* 4.4 6.5 - - - -
226E ALA 3.6 7.3 + - - -
176G THR* 4.9 1.3 - - - +
177G SER* 5.5 0.9 - - - -
210G VAL 3.8 10.4 + - - +
211G GLU* 3.4 14.3 - - - +
212G LYS 3.6 0.2 - - - -
213G GLN* 1.3 79.2 - - + +
215G VAL* 1.3 63.9 + - - +
216G ALA* 3.3 20.9 + - + +
219G LEU* 3.8 17.0 - - + -
222G LYS* 3.2 29.9 + - - +
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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