Contacts of the helix formed by residues 173 - 177 (chain C) in PDB entry 2PCB
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 GLY 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C ALA 3.0 7.9 + - - -
171C LEU 2.7 2.8 + - - -
172C MET* 1.3 74.5 - - - +
174C ALA* 1.3 55.7 + - - +
175C HIS 2.8 11.7 + - - -
176C ALA* 3.2 20.4 + - - +
198C PHE* 5.2 0.9 - - - -
199C THR 4.7 0.9 - - - +
200C ASN* 6.0 0.2 - - - -
202C PHE* 4.1 10.1 - - - +
203C TYR* 3.2 34.4 + - - -
258C PHE* 4.2 13.2 - - - -
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Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.4 6.3 - - + -
170C ALA 4.3 0.6 + - - -
171C LEU 2.9 16.2 + - - +
172C MET 4.3 0.2 - - - +
173C GLY* 1.3 73.8 - - - +
175C HIS* 1.3 57.5 - - - +
176C ALA* 3.1 7.6 + - - -
177C LEU* 3.4 24.8 + - + +
198C PHE* 4.6 10.3 - - - -
262C PHE* 4.2 11.5 - - + -
295C HEM 3.4 45.7 - - + +
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Residues in contact with HIS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C MET* 2.9 17.5 + - - +
173C GLY 2.8 1.2 - - - -
174C ALA* 1.3 75.9 - - - +
176C ALA* 1.3 58.3 + - - +
177C LEU 3.4 1.6 - - - -
191C TRP* 2.9 55.9 + + + +
202C PHE* 3.5 18.9 - - + -
232C LEU* 3.8 17.7 - - + -
235C ASP* 2.6 32.3 + - - -
295C HEM 2.1 76.5 + + + -
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY 3.2 15.5 + - - +
174C ALA 3.1 0.2 - - - -
175C HIS* 1.3 78.5 - - - +
177C LEU* 1.3 69.2 + - + +
178C GLY 4.5 0.7 - - - +
191C TRP* 5.1 1.3 - - - +
192C GLY* 4.9 9.0 + - - +
194C ALA 3.8 4.1 - - - +
195C ASN* 3.2 24.3 + - - +
197C VAL 5.0 0.9 - - - +
198C PHE* 5.4 1.6 - - + -
199C THR* 4.0 29.2 - - - +
201C GLU* 4.9 4.5 - - + +
202C PHE* 4.4 16.8 - - + +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PRO* 3.7 13.7 - - + -
47C VAL* 3.9 22.9 - - + -
116C VAL* 5.0 0.2 - - + -
119C MET* 3.8 27.1 - - + -
174C ALA* 3.4 19.0 - - - +
176C ALA* 1.3 78.7 - - + +
178C GLY* 1.3 68.1 + - - +
191C TRP* 3.5 15.8 - - - -
195C ASN 3.8 4.3 - - - -
196C ASN 4.8 0.4 - - - +
197C VAL 4.0 10.5 - - - +
198C PHE* 3.8 56.1 - - + +
295C HEM 3.5 11.4 - - + +
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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