Contacts of the strand formed by residues 158 - 162 (chain C) in PDB entry 4IRQ
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 TYR 158 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS* 3.8 20.4 + - + +
94C ARG 3.4 24.0 - - - -
95C LEU* 3.4 21.1 - - + -
96C ALA 2.8 24.8 + - - -
124C ILE* 3.5 17.8 - - - +
156C THR* 3.2 7.3 - - - +
157C ASP* 1.3 82.8 - - + +
159C ILE* 1.3 69.6 + - - +
175C TYR 2.8 22.8 + - - -
176C GLY* 3.3 29.3 - - - -
177C PHE* 3.7 17.4 + + + -
178C PRO* 3.4 15.9 - - + -
205C LEU* 4.1 6.1 - - + -
206C LEU 3.2 14.1 - - - +
207C SER* 3.7 7.6 - - - -
208C LYS 4.1 3.8 - - - +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.6 4.2 - - - +
96C ALA* 3.3 15.7 - - + +
98C LEU* 3.7 31.4 - - + -
145C ILE* 4.8 0.7 - - + -
149C PHE* 3.9 28.0 - - + -
152C SER* 5.0 3.4 - - - +
156C THR* 4.2 7.0 - - + -
158C TYR* 1.3 81.4 - - - +
160C ALA* 1.3 60.9 + - - +
161C MET* 4.0 20.9 - - + +
204C LEU 4.4 3.1 - - - +
205C LEU* 3.3 6.4 - - - +
206C LEU* 3.0 49.0 + - + +
208C LYS* 5.2 0.7 - - + -
211C TYR* 4.1 26.2 - - + -
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Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.3 17.9 - - + +
96C ALA 2.9 8.0 + - - +
97C VAL* 3.6 5.9 - - + -
98C LEU* 2.7 32.5 + - - -
159C ILE* 1.3 73.3 - - - +
161C MET* 1.3 61.6 + - - +
162C HIS* 3.4 18.5 + - + +
175C TYR* 5.0 1.6 - - + -
204C LEU 3.7 3.8 - - - -
205C LEU* 3.5 27.6 - - + -
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Residues in contact with MET 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.8 6.5 - - - -
141C ARG* 4.0 20.2 - - - +
145C ILE* 3.6 30.5 - - + -
159C ILE* 4.0 6.7 - - + +
160C ALA* 1.3 69.0 - - - +
162C HIS* 1.3 57.8 + - - +
202C GLY 3.5 2.8 - - - +
203C ILE* 3.1 6.6 - - - +
204C LEU* 2.9 47.6 + - + +
206C LEU* 3.9 17.9 - - + -
211C TYR* 4.0 13.0 - - + -
217C MET* 3.7 30.1 - - - +
231C PHE* 3.8 25.8 - - + -
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Residues in contact with HIS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 4.0 17.0 - - + -
98C LEU 3.0 10.0 + - - +
99C VAL* 3.6 10.9 - - - +
100C PRO* 3.4 17.3 - - - +
111C PHE* 3.5 19.3 - + + -
115C MET* 3.7 12.0 - - + +
141C ARG* 4.7 0.4 - - - +
160C ALA* 3.9 13.5 - - + +
161C MET* 1.3 74.4 - - - +
163C ASP* 1.3 85.2 + - - +
164C VAL 3.5 0.9 + - - -
166C LEU 3.2 27.6 - - - -
168C PRO* 4.2 3.4 - - + -
175C TYR* 2.7 35.7 + + - -
202C GLY 3.6 1.1 - - - -
203C ILE* 3.4 29.5 - - + +
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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