Contacts of the helix formed by residues 177 - 183 (chain H) in PDB entry 1B6C
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 LEU 177 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H THR* 1.3 75.2 - - - +
178H LYS* 1.3 57.5 + - - +
180H LEU* 3.4 9.7 - - + +
181H ILE* 2.9 35.1 + - - +
193H LEU* 4.7 0.8 - - + +
201H ILE* 3.6 26.5 - - + -
224H TRP* 3.2 54.9 - - + -
227H GLU* 2.9 26.0 + - + +
229H VAL* 4.4 9.4 - - + -
263H ILE* 4.2 37.7 - - + -
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Residues in contact with LYS 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H THR* 3.1 10.5 + - - +
177H LEU* 1.3 77.4 - - - +
179H ASP* 1.3 64.1 - - - +
181H ILE* 3.4 13.1 + - + +
182H TYR* 3.1 21.5 + - - +
227H GLU* 4.7 0.4 + - - -
281H ASP* 5.7 6.1 - - - +
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Residues in contact with ASP 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H THR* 3.2 24.3 - - + +
176H THR* 2.5 43.4 + - - +
178H LYS* 1.3 74.8 - - - +
180H LEU* 1.3 54.3 + - - +
182H TYR* 2.8 12.1 + - - +
183H ASP* 2.8 43.6 + - - +
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Residues in contact with LEU 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 6.6 0.2 - - - -
175H THR* 5.4 6.1 - - - +
176H THR 2.9 12.0 + - - +
177H LEU* 3.4 32.3 - - + +
179H ASP* 1.3 77.2 - - - +
181H ILE* 1.3 63.5 + - - +
183H ASP* 3.1 12.0 + - + +
184H MET* 3.0 59.8 + - + +
193H LEU* 4.5 1.6 - - + -
197H VAL* 5.4 0.9 - - + -
201H ILE* 4.1 10.8 - - + -
224H TRP* 4.0 17.3 - - + -
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Residues in contact with ILE 181 (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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177H LEU 2.9 25.3 + - - +
178H LYS* 3.7 13.0 - - + +
179H ASP 3.2 0.2 - - - -
180H LEU* 1.3 76.6 - - - +
182H TYR* 1.3 53.4 + - - +
184H MET* 4.1 2.1 - - - +
185H THR* 2.6 31.7 + - - -
191H SER 3.4 21.8 - - - +
192H GLY* 3.9 7.9 - - - +
193H LEU* 3.6 26.2 - - + +
255H ARG* 3.4 19.7 + - - +
262H PHE 3.6 22.7 - - - +
263H ILE* 4.2 21.1 - - + -
281H ASP* 6.1 0.4 - - - +
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Residues in contact with TYR 182 (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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178H LYS 3.1 11.8 + - - +
179H ASP* 2.8 12.9 + - - +
181H ILE* 1.3 76.9 - - - +
183H ASP* 1.3 77.6 + - - +
185H THR* 3.2 23.7 + - + +
255H ARG* 4.5 12.1 - - - +
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Residues in contact with ASP 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ARG* 5.2 7.4 - - - +
175H THR* 5.2 3.3 + - - -
179H ASP* 2.8 32.2 + - - +
180H LEU* 3.8 12.1 + - + +
182H TYR* 1.3 86.4 - - - +
184H MET* 1.3 62.9 + - + +
185H THR 3.1 8.5 + - - +
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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
------------------------------------------------------------
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