Contacts of the helix formed by residues 164 - 173 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132K ALA* 4.1 20.7 - - - +
163K VAL* 1.3 80.1 - - - +
165K GLU* 1.3 64.4 + - - +
166K GLU* 4.2 1.6 + - - +
167K VAL* 3.3 25.5 + - - +
168K CYS* 2.9 20.1 + - - +
96L ARG* 5.6 5.4 - - - -
97L PRO* 6.1 0.2 - - - +
165M GLU* 3.4 16.5 + - - -
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Residues in contact with GLU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K VAL 3.6 1.2 + - - -
164K SER* 1.3 74.0 - - - +
166K GLU* 1.3 63.9 + - - +
168K CYS* 3.1 6.6 + - - +
169K SER* 2.8 25.9 + - - -
176K TYR* 3.8 24.6 + - + +
164M SER* 3.3 18.1 - - - -
165M GLU* 3.4 25.9 + - + +
166M GLU* 3.0 34.6 + - + +
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Residues in contact with GLU 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K SER* 4.2 1.9 + - - +
165K GLU* 1.3 75.9 - - - +
167K VAL* 1.3 71.7 + - + +
169K SER* 3.2 6.4 + - - -
170K LYS* 3.1 50.4 + - + +
174L PRO* 5.8 1.8 - - + +
165M GLU* 2.5 34.3 + - + +
169M SER* 3.9 15.7 - - - +
176M TYR* 2.6 43.0 + - - +
178M PRO* 4.2 13.7 - - - +
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Residues in contact with VAL 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163K VAL* 3.9 18.4 - - + -
164K SER* 3.2 19.8 + - - +
166K GLU* 1.3 85.8 - - + +
168K CYS* 1.3 56.9 + - - +
170K LYS* 4.0 0.3 - - - +
171K LEU* 2.8 51.4 + - + +
97L PRO* 4.9 13.9 - - + -
98L LEU* 4.5 10.3 - - + +
174L PRO* 4.2 16.9 - - + +
175L LEU* 4.2 21.8 - - + -
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Residues in contact with CYS 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K VAL* 4.6 0.8 - - - +
164K SER 2.9 13.2 + - - +
165K GLU* 3.4 11.7 - - - +
167K VAL* 1.3 77.4 - - - +
169K SER* 1.3 66.2 + - - +
171K LEU* 4.5 2.0 - - - -
172K TYR* 3.2 30.4 + - - +
176K TYR* 3.9 20.5 - - + +
181K PHE* 4.0 2.9 - - - -
182K CYS* 2.0 65.3 - - + +
227K VAL* 5.5 2.7 - - - -
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Residues in contact with SER 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K GLU 2.8 20.3 + - - -
166K GLU* 3.2 8.1 + - - -
168K CYS* 1.3 74.4 - - - +
170K LYS* 1.3 67.6 + - - +
173K ASP* 2.9 31.0 + - - +
176K TYR* 3.3 36.6 - - - +
166M GLU* 4.0 25.2 - - - +
169M SER* 5.0 1.0 + - - -
170M LYS* 4.3 6.7 + - - -
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Residues in contact with LYS 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K GLU* 3.1 39.4 + - + +
169K SER* 1.3 85.6 + - - +
171K LEU* 1.3 66.5 + - - +
172K TYR 3.0 1.4 + - - -
173K ASP* 3.4 16.2 + - - +
173L ASP* 4.8 4.7 - - - +
174L PRO* 3.5 36.5 - - + +
169M SER* 3.8 30.7 + - - +
170M LYS* 4.8 13.7 - - - +
173M ASP* 3.4 27.7 + - - +
176M TYR* 5.0 1.8 + - - +
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Residues in contact with LEU 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K VAL* 2.8 35.1 + - + +
168K CYS* 4.2 0.7 - - - +
170K LYS* 1.3 77.9 - - - +
172K TYR* 1.3 67.4 + - + +
173K ASP 4.9 1.4 - - - +
217K LYS* 3.1 33.1 + - - +
223K GLY 3.3 26.9 - - - +
224K VAL* 4.7 4.7 - - + -
225K PRO* 3.4 24.2 - - + -
98L LEU* 5.0 0.4 - - + -
174L PRO* 4.0 22.4 - - + +
175L LEU* 4.5 9.2 - - + -
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Residues in contact with TYR 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K CYS* 3.2 21.1 + - - +
169K SER 3.7 1.1 - - - -
170K LYS 3.0 0.4 - - - -
171K LEU* 1.3 88.0 - - + +
173K ASP* 1.3 64.8 + - - +
175K LEU* 2.9 29.7 + - + +
176K TYR* 3.0 17.6 + - + +
180K MET* 6.3 0.2 - - - -
182K CYS* 4.1 15.9 - - - -
215K PHE* 3.8 22.7 - + + -
216K GLY* 3.6 4.3 - - - -
217K LYS* 3.5 46.2 + - + +
224K VAL* 4.3 5.7 - - + +
225K PRO* 2.7 37.3 + - + -
227K VAL* 3.6 21.9 - - + +
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Residues in contact with ASP 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J LYS* 4.8 6.0 + - - +
169K SER 2.9 19.0 + - - +
170K LYS* 3.4 14.1 + - - +
171K LEU 4.9 1.0 - - - +
172K TYR* 1.3 80.5 - - - +
174K PRO* 1.3 80.7 - - - +
176K TYR* 4.3 2.5 - - - +
170M LYS* 3.0 29.9 + - - +
173N ASP* 5.4 3.6 - - - +
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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
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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