Contacts of the helix formed by residues 165 - 171 (chain E) in PDB entry 3Q2K
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 PRO 165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163E THR* 4.1 6.1 - - + -
164E ARG* 1.3 89.9 - - - +
166E GLN* 1.3 67.7 + - - +
167E GLU* 3.0 28.2 + - + +
168E TYR* 3.1 20.1 + - + +
169E TYR* 3.4 9.7 - - - -
215E ARG* 3.6 9.9 - - - +
550E HP7 3.1 28.0 - - - +
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Residues in contact with GLN 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E PRO* 1.3 70.3 - - - +
167E GLU* 1.3 75.9 + - - +
169E TYR* 3.1 18.2 + - - +
170E ASP* 3.0 39.0 + - - +
214E ALA 4.8 0.4 + - - -
215E ARG* 3.1 30.8 - - - +
216E ARG* 2.7 64.8 + - - +
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Residues in contact with GLU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E PRO* 3.4 24.2 - - + +
166E GLN* 1.3 91.3 + - - +
168E TYR* 1.3 62.9 + - - +
170E ASP* 2.9 22.2 + - + +
171E ALA* 3.1 13.3 + - - +
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Residues in contact with TYR 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 4.4 11.4 - - - -
164E ARG* 3.8 17.5 - - - -
165E PRO* 3.1 28.2 + - + +
167E GLU* 1.3 80.3 - - - +
169E TYR* 1.3 83.6 + + - +
171E ALA* 3.7 8.1 - - - +
175E ARG* 3.2 43.1 + - + -
181E ASP* 5.6 0.7 - - - -
187E ASN* 3.8 3.4 + - - -
188E GLN* 3.1 23.7 + - - -
550E HP7 2.1 77.6 + - - +
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Residues in contact with TYR 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ARG* 3.6 28.6 - - + +
165E PRO 3.4 14.1 - - - -
166E GLN* 3.1 11.7 + - - +
168E TYR* 1.3 95.8 - + - +
170E ASP* 1.3 59.4 + - - +
171E ALA 3.2 3.8 - - - -
172E ALA 3.3 19.8 - - - +
173E ARG 5.3 0.2 - - - +
175E ARG* 3.8 16.7 - - + +
176E GLY* 4.2 18.6 - - - -
181E ASP* 5.0 1.3 - - - -
183E GLY* 5.9 2.9 - - - -
184E ALA* 5.5 0.5 + - - +
188E GLN* 3.9 20.8 + - - -
215E ARG* 3.8 23.4 - - + +
217E ILE* 3.5 46.7 - - + +
220E GLU 5.5 0.5 + - - -
221E ASP* 4.9 2.9 - - - +
241E MET* 3.9 11.4 - - - +
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Residues in contact with ASP 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLN* 3.0 46.9 - - - +
167E GLU* 2.9 16.0 + - + +
169E TYR* 1.3 79.3 - - - +
171E ALA* 1.3 54.8 - - - +
172E ALA* 3.2 12.2 + - - -
216E ARG* 5.2 5.2 + - - +
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Residues in contact with ALA 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 6.5 1.8 - - - -
167E GLU 3.1 8.9 + - - +
168E TYR* 3.7 16.2 - - - +
169E TYR 3.2 0.8 - - - -
170E ASP* 1.3 75.3 - - - +
172E ALA* 1.3 63.1 + - - +
175E ARG* 4.1 9.8 + - - +
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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