Contacts of the helix formed by residues 161 - 166 (chain C) in PDB entry 5L26
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 VAL 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ALA* 3.4 47.3 - - + +
144C MET* 3.6 22.9 - - + -
145C SER* 4.1 11.0 - - - -
158C PRO* 3.1 21.7 + - + +
160C VAL* 1.3 80.6 - - + +
162C ARG* 1.3 64.1 + - - +
163C PRO* 3.4 4.3 - - - -
164C TYR* 3.0 25.0 + - + +
165C ILE* 3.2 17.5 + - + +
168C MET* 5.0 4.9 - - + -
176C VAL* 5.4 1.3 - - + -
231C ALA* 5.7 1.3 - - + -
232C GLU 4.8 4.5 - - - +
233C VAL* 5.9 0.7 - - - -
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Residues in contact with ARG 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PRO 2.9 10.3 + - - +
159C LEU* 3.3 24.5 - - + +
160C VAL 3.4 0.6 - - - -
161C VAL* 1.3 76.0 - - - +
163C PRO* 1.3 70.6 - - + +
164C TYR 3.1 1.0 + - - -
165C ILE* 3.2 23.1 + - - +
166C ARG* 4.3 2.1 + - - +
382C MET* 4.1 24.2 - - + +
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Residues in contact with PRO 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU 4.9 0.7 - - - +
160C VAL 4.6 5.2 - - - +
161C VAL* 3.5 5.6 - - - -
162C ARG* 1.3 93.8 - - + +
164C TYR* 1.3 77.3 + - + +
165C ILE 3.3 0.2 - - - -
166C ARG* 4.1 11.9 + - + +
167C ARG* 4.9 3.3 + - - +
234C LEU* 6.1 6.5 - - + -
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Residues in contact with TYR 164 (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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141C ALA* 4.2 20.2 - - + -
160C VAL 5.3 0.2 - - - -
161C VAL* 3.0 23.7 + - + +
163C PRO* 1.3 95.6 - - + +
165C ILE* 1.3 58.8 + - - +
166C ARG 3.3 1.3 - - - -
167C ARG* 3.6 5.7 + - - +
168C MET* 3.1 31.6 + - + +
228C GLN* 5.4 11.0 - - + -
230C ASP 4.3 5.8 + - - -
231C ALA* 3.5 20.5 - - + -
232C GLU* 2.8 51.2 + - + +
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PRO* 3.5 35.4 - - + +
161C VAL* 3.2 16.8 - - + +
162C ARG* 3.2 9.8 + - - +
164C TYR* 1.3 77.2 - - - +
166C ARG* 1.3 63.8 + - - +
168C MET* 3.2 29.1 + - + +
173C LEU* 4.2 16.1 - - + +
176C VAL* 5.4 1.6 - - + -
379C LEU* 3.9 22.4 - - + +
382C MET* 3.6 24.5 - - + -
383C ALA* 3.9 20.3 - - + +
386C ARG* 3.6 8.8 + - + +
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Residues in contact with ARG 166 (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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162C ARG 4.3 1.6 + - - -
163C PRO 4.1 10.6 + - - +
164C TYR 3.3 0.6 - - - -
165C ILE* 1.3 80.8 - - - +
167C ARG* 1.3 58.4 + - + +
382C MET 5.2 3.6 - - - +
383C ALA* 4.0 18.2 - - + +
386C ARG* 3.6 20.5 + - - +
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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