Contacts of the helix formed by residues 164 - 170 (chain D) in PDB entry 2ORE
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 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D ILE* 3.6 16.3 - - - +
163D GLU* 1.3 78.8 - - - +
165D TYR* 1.3 85.7 + - - +
166D ALA* 3.3 7.3 + - - +
167D ASP* 3.2 23.8 + - - -
168D SER* 3.2 12.1 + - - -
205D GLN* 4.8 1.9 + - - -
301D SAH 3.4 21.3 + - - -
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PRO* 4.1 6.7 - - + -
35D PHE* 3.6 28.0 - + + -
164D SER* 1.3 83.1 + - - +
166D ALA* 1.3 79.9 + - + -
168D SER* 3.1 8.2 + - - -
169D MET* 3.1 29.7 + - - +
201D PHE* 3.9 16.8 - + - -
205D GLN* 3.3 49.3 + - + +
208D HIS* 2.7 40.6 + + + -
209D LEU* 4.1 17.9 - - + -
212D ILE* 3.9 15.3 - - + -
301D SAH 2.9 31.9 + + - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER* 3.3 5.2 + - - +
165D TYR* 1.3 92.7 - - + +
167D ASP* 1.3 65.7 + - - +
169D MET* 3.7 2.0 + - - +
170D ALA* 3.3 22.3 + - - +
208D HIS* 4.2 10.8 - - + +
212D ILE* 3.9 24.8 - - + +
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Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D GLU* 3.6 23.0 - - + +
164D SER* 3.2 21.4 + - - +
166D ALA* 1.3 81.1 - - - +
168D SER* 1.3 62.8 + - - +
170D ALA* 3.3 17.7 + - - +
171D ARG* 3.9 8.0 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 4.1 12.5 - - - +
34D PRO* 3.4 22.4 + - - +
51D ILE* 5.5 1.8 - - - -
53D ALA* 3.5 23.4 - - - +
163D GLU* 2.9 20.3 + - - -
164D SER 3.2 10.4 + - - -
165D TYR* 3.1 9.9 + - - -
167D ASP* 1.3 73.5 - - - +
169D MET* 1.3 56.8 + - - -
170D ALA 2.9 4.3 - - - -
171D ARG* 2.8 38.2 + - - +
172D ALA 4.1 0.9 + - - -
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Residues in contact with MET 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 4.7 8.1 - - - -
34D PRO* 3.2 23.1 - - + +
165D TYR* 3.1 23.2 + - - +
166D ALA 4.1 3.1 - - - +
168D SER* 1.3 74.8 + - - +
170D ALA* 1.3 57.0 + - - +
171D ARG 3.1 4.2 + - - -
172D ALA* 3.4 18.0 + - - +
178D VAL* 4.1 12.1 - - + -
180D CYS* 3.6 15.9 - - - -
209D LEU* 3.2 40.8 - - + +
212D ILE* 4.0 29.2 - - + -
213D ALA* 4.5 4.3 - - + +
216D LEU* 3.8 27.9 - - + +
223D VAL* 4.6 5.2 - - + -
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA 3.3 14.3 + - - +
167D ASP* 3.3 15.3 - - - +
168D SER 2.8 1.8 + - - -
169D MET* 1.3 76.1 - - - +
171D ARG* 1.3 60.4 - - - +
172D ALA 3.5 2.9 - - - +
216D LEU* 5.6 0.7 - - - -
219D ARG* 5.2 7.4 + - - +
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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