Contacts of the helix formed by residues 164 - 173 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ARG* 5.3 6.1 - - - +
97A PRO* 5.7 2.4 - - - +
132D ALA* 4.0 20.8 - - - +
163D VAL* 1.3 79.1 - - - +
165D GLU* 1.3 67.0 + - - +
166D GLU* 4.2 2.1 + - - +
167D VAL* 3.2 25.5 + - - +
168D CYS* 3.0 19.4 + - - +
165H GLU* 3.4 16.5 + - - -
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Residues in contact with GLU 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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163D VAL 3.6 1.9 + - - -
164D SER* 1.3 74.0 - - - +
166D GLU* 1.3 57.9 + - - +
168D CYS* 3.1 7.2 + - - +
169D SER* 2.8 31.9 + - - -
176D TYR* 3.8 23.8 + - + +
164H SER* 3.4 15.5 - - - -
165H GLU* 3.4 25.8 + - - +
166H GLU* 2.7 40.8 + - + +
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Residues in contact with GLU 166 (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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174A PRO* 5.7 2.4 - - + +
164D SER* 4.2 3.0 + - - +
165D GLU* 1.3 73.6 - - - +
167D VAL* 1.3 75.3 + - + +
168D CYS 3.0 0.2 + - - -
169D SER* 3.3 6.1 + - - -
170D LYS* 3.0 53.7 + - + +
165H GLU* 3.0 19.8 + - + +
166H GLU* 5.3 1.3 - - - +
169H SER* 3.8 19.5 - - - +
176H TYR* 2.9 36.9 + - - +
178H PRO* 4.8 8.8 - - - +
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Residues in contact with VAL 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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97A PRO* 4.8 18.4 - - + -
98A LEU* 4.6 7.0 - - + +
174A PRO* 4.3 20.4 - - + +
175A LEU* 4.2 19.1 - - + -
163D VAL* 4.0 18.4 - - + -
164D SER* 3.2 19.4 + - - +
166D GLU* 1.3 87.0 - - + +
168D CYS* 1.3 57.3 + - - +
170D LYS* 4.1 0.3 - - - +
171D LEU* 2.8 51.4 + - + +
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Residues in contact with CYS 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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163D VAL* 4.9 1.6 - - + +
164D SER 3.0 16.4 + - - +
165D GLU* 3.6 7.0 - - - +
167D VAL* 1.3 74.9 - - - +
169D SER* 1.3 66.9 + - - +
171D LEU* 4.5 2.9 - - - -
172D TYR* 3.2 28.4 + - - +
176D TYR* 3.9 21.2 - - + +
181D PHE* 4.0 3.8 - - - -
182D CYS* 2.0 66.9 - - + +
227D VAL* 5.5 1.8 - - - -
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Residues in contact with SER 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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165D GLU 2.8 18.6 + - - -
166D GLU* 3.3 7.6 + - - -
168D CYS* 1.3 77.6 - - - +
170D LYS* 1.3 60.9 + - - +
172D TYR 3.7 0.2 - - - -
173D ASP* 2.8 32.1 + - - +
176D TYR* 3.3 36.6 - - - +
166H GLU* 3.6 25.4 - - - +
169H SER* 5.0 1.0 + - - -
170H LYS* 3.8 9.8 + - - -
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Residues in contact with LYS 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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173A ASP* 4.7 5.1 + - - +
174A PRO* 3.7 34.9 - - + +
166D GLU* 3.0 46.0 + - + +
169D SER* 1.3 76.0 - - - +
171D LEU* 1.3 68.8 + - - +
172D TYR 3.0 1.2 + - - -
173D ASP* 3.4 15.0 + - - +
169H SER* 4.0 16.1 + - - -
170H LYS* 4.3 23.6 - - - +
173H ASP* 2.9 32.2 + - - +
176H TYR* 5.5 0.4 - - - +
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Residues in contact with LEU 171 (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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98A LEU* 4.8 0.7 - - + -
174A PRO* 4.1 18.5 - - + +
175A LEU* 4.8 9.6 - - + -
167D VAL* 2.8 41.1 + - + +
168D CYS* 4.2 0.7 - - - +
170D LYS* 1.3 74.3 - - - +
172D TYR* 1.3 66.9 + - + +
173D ASP 4.9 1.1 - - - +
217D LYS* 3.1 32.5 + - - +
223D GLY 3.4 16.2 - - - +
224D VAL* 5.4 4.0 - - + -
225D PRO* 3.4 35.0 - - + -
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Residues in contact with TYR 172 (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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168D CYS 3.2 13.7 + - - +
169D SER 3.7 1.1 - - - -
170D LYS 3.1 0.4 - - - -
171D LEU* 1.3 86.2 - - + +
173D ASP* 1.3 64.0 + - - +
175D LEU* 2.9 30.3 + - + +
176D TYR* 3.1 18.3 + - + +
180D MET* 6.3 0.2 - - - -
182D CYS* 3.7 28.9 - - - -
215D PHE* 3.9 22.2 - + + -
216D GLY* 3.5 4.9 - - - -
217D LYS* 3.4 46.5 + - + +
224D VAL* 4.3 4.8 - - + +
225D PRO* 2.7 37.1 + - + -
227D VAL* 3.6 16.7 - - + +
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Residues in contact with ASP 173 (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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170C LYS* 4.9 5.9 - - - +
169D SER 2.8 18.3 + - - +
170D LYS* 3.4 13.5 + - - +
171D LEU 4.9 1.0 - - - +
172D TYR* 1.3 80.2 - - - +
174D PRO* 1.3 79.2 - - - +
176D TYR* 4.4 2.5 - - - +
173E ASP* 5.2 6.1 - - - +
170H LYS* 2.9 27.6 + - - +
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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