Contacts of the helix formed by residues 164 - 173 (chain H) in PDB entry 2BDI
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D GLU* 3.4 16.1 + - - -
96E ARG* 5.7 4.0 - - - -
97E PRO* 6.0 0.9 - - - +
132H ALA* 4.0 21.6 - - - +
163H VAL* 1.3 76.9 - - - +
165H GLU* 1.3 67.4 + - - +
166H GLU* 4.2 1.7 + - - +
167H VAL* 3.2 26.3 + - - +
168H CYS* 2.9 22.5 + - - +
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Residues in contact with GLU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D SER* 3.4 17.9 - - - -
165D GLU* 3.4 25.4 + - - +
166D GLU* 3.0 35.4 + - + +
163H VAL 3.6 1.7 + - - -
164H SER* 1.3 73.8 - - - +
166H GLU* 1.3 64.6 + - - +
168H CYS* 3.0 6.1 + - - +
169H SER* 2.8 26.2 + - - -
176H TYR* 3.7 25.8 + - + +
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLU* 2.7 26.4 + - + +
166D GLU* 5.3 0.9 - - - +
169D SER* 3.6 18.2 - - - +
176D TYR* 2.7 43.3 + - - +
178D PRO* 4.6 10.0 - - - +
174E PRO* 5.7 1.9 - - + +
164H SER* 4.2 2.1 + - - +
165H GLU* 1.3 74.5 - - - +
167H VAL* 1.3 74.0 + - + +
168H CYS 2.8 1.0 + - - -
169H SER* 3.2 7.1 + - - -
170H LYS* 3.1 47.8 + - + +
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Residues in contact with VAL 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E PRO* 5.1 14.4 - - + -
98E LEU* 4.9 6.1 - - + +
174E PRO* 4.1 21.9 - - + +
175E LEU* 4.3 19.5 - - + -
163H VAL* 4.0 18.4 - - + -
164H SER* 3.2 19.6 + - - +
166H GLU* 1.3 86.6 - - + +
168H CYS* 1.3 58.0 + - - +
171H LEU* 2.8 52.7 + - + +
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Residues in contact with CYS 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H VAL* 4.6 2.2 - - + +
164H SER 2.9 18.0 + - - +
165H GLU* 3.4 7.6 - - - +
166H GLU 2.8 1.8 + - - -
167H VAL* 1.3 81.6 - - - +
169H SER* 1.3 62.5 + - - +
171H LEU* 4.6 0.9 - - - -
172H TYR* 3.1 31.1 + - - +
176H TYR* 4.4 13.7 - - + -
181H PHE* 4.0 7.2 - - - -
182H CYS* 2.1 66.4 - - + -
227H VAL* 6.0 0.7 - - - -
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Residues in contact with SER 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU* 3.8 26.2 - - - +
169D SER* 5.0 0.9 + - - -
170D LYS* 4.0 8.9 + - - -
165H GLU 2.8 15.9 + - - -
166H GLU* 3.2 8.0 + - - -
168H CYS* 1.3 77.1 - - - +
170H LYS* 1.3 61.6 + - - +
173H ASP* 2.8 31.5 + - - +
176H TYR* 3.3 38.7 - - - +
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Residues in contact with LYS 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D SER* 3.8 26.0 + - - -
170D LYS* 4.3 22.0 - - - +
173D ASP* 2.9 32.2 + - - +
176D TYR* 5.4 0.4 - - - +
173E ASP* 4.8 5.8 - - - +
174E PRO* 3.8 30.7 - - + +
166H GLU* 3.1 38.5 + - + +
169H SER* 1.3 85.5 + - - +
171H LEU* 1.3 67.9 + - - +
172H TYR 3.0 0.9 + - - -
173H ASP* 3.4 15.0 + - - +
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Residues in contact with LEU 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E LEU* 5.4 0.2 - - + -
173E ASP 5.6 0.2 - - - +
174E PRO* 4.0 22.6 - - + +
175E LEU* 4.8 7.2 - - + -
167H VAL* 2.8 34.3 + - + +
168H CYS 3.8 3.6 - - - +
170H LYS* 1.3 79.9 - - - +
172H TYR* 1.3 65.8 + - + +
173H ASP 3.6 1.3 - - - +
217H LYS* 3.1 33.2 + - - +
223H GLY 3.4 15.5 - - - +
224H VAL* 5.4 5.4 - - + -
225H PRO* 3.4 34.3 - - + -
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Residues in contact with TYR 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H CYS* 3.1 20.1 + - - +
169H SER 3.7 0.9 - - - -
171H LEU* 1.3 85.7 - - + +
173H ASP* 1.3 64.0 + - - +
175H LEU* 2.9 30.1 + - + +
176H TYR* 3.0 19.5 + - + +
180H MET* 6.3 0.4 - - - -
182H CYS* 4.2 16.2 - - - -
215H PHE* 3.8 23.1 - + + -
216H GLY* 3.5 5.0 - - - -
217H LYS* 3.4 44.6 + - + +
224H VAL* 4.3 5.7 - - + +
225H PRO* 2.7 36.5 + - + -
227H VAL* 3.6 22.1 - - + +
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Residues in contact with ASP 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 5.0 8.5 - - - +
170D LYS* 2.9 29.0 + - - +
170G LYS* 4.7 6.3 + - - +
169H SER 2.8 17.7 + - - +
170H LYS* 3.4 12.4 + - - +
171H LEU 4.9 1.2 - - - +
172H TYR* 1.3 79.7 - - - +
174H PRO* 1.3 79.2 - - - +
176H TYR* 4.4 2.9 - - - +
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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