Contacts of the helix formed by residues 173 - 181 (chain C) in PDB entry 2J2M
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 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.1 24.7 + - - +
136C ILE* 5.7 0.2 - - - -
167C MET* 2.7 58.0 + - - +
170C ARG* 2.7 11.5 + - - -
171C PRO 4.1 0.7 - - - -
172C GLU* 1.3 76.7 - - - +
174C THR* 1.3 65.3 + - - +
175C ASN 3.3 0.4 - - - -
176C MET* 3.1 6.8 + - - +
177C LEU* 2.9 28.2 + - - +
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Residues in contact with THR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PRO* 2.6 24.1 + - - +
172C GLU 3.2 1.0 - - - -
173C SER* 1.3 76.7 + - - +
175C ASN* 1.3 63.6 + - - +
177C LEU* 3.1 13.7 + - - +
178C MET* 3.0 22.2 + - + +
420C ASN 3.7 11.2 - - - -
421C PHE* 3.7 14.5 - - + -
424C ALA* 4.0 14.1 - - + -
462C ASN* 3.8 30.1 + - + +
463C PHE* 4.1 20.8 - - + -
466C ALA* 4.4 3.6 - - + -
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Residues in contact with ASN 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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133C VAL* 3.9 12.0 - - + +
172C GLU 4.1 6.7 + - - +
173C SER 3.3 0.6 - - - -
174C THR* 1.3 77.9 - - - +
176C MET* 1.3 57.6 + - - +
178C MET* 3.1 10.7 + - - +
179C HIS* 2.7 41.7 + - - -
281C THR* 3.0 25.7 + - - +
282C LYS* 4.9 1.5 - - - +
420C ASN 4.6 2.6 + - - +
423C GLN* 2.8 31.7 + - + +
424C ALA* 3.4 33.2 - - + +
427C VAL* 3.4 8.4 - - - +
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Residues in contact with MET 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PRO* 3.7 31.2 - - + -
129C ASN* 5.2 1.1 - - - +
131C LEU* 3.9 23.3 - - + -
133C VAL* 3.2 38.2 - - + +
134C PHE* 3.7 29.0 + - + +
135C PHE* 3.4 42.6 - - + +
173C SER 3.1 9.4 + - - +
175C ASN* 1.3 78.0 - - - +
177C LEU* 1.3 58.1 + - - +
179C HIS* 3.1 5.0 + - - +
180C ILE* 2.9 28.3 + - + +
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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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135C PHE* 4.0 23.8 - - + -
163C TYR* 6.2 2.5 - - + -
164C TRP* 3.8 31.9 - - + -
167C MET* 4.0 16.4 - - + +
173C SER* 2.9 40.0 + - - +
174C THR* 3.1 11.4 + - - +
176C MET* 1.3 75.7 - - - +
178C MET* 1.3 61.4 + - - +
180C ILE* 4.4 2.5 - - + -
181C PHE* 3.2 49.2 + - + +
439C LEU* 4.0 1.4 - - - +
443C LEU* 4.7 0.2 - - - +
463C PHE* 3.9 17.5 - - + -
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Residues in contact with MET 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C THR* 3.0 16.9 + - + +
175C ASN* 3.1 9.8 + - - +
177C LEU* 1.3 75.8 - - - +
179C HIS* 1.3 60.5 + - - +
182C THR* 3.2 20.1 - - - +
424C ALA* 3.5 32.8 - - + +
427C VAL* 4.2 15.9 - - + -
428C TYR* 4.1 10.8 - - + -
431C MET* 3.5 5.9 - - + +
439C LEU* 3.4 25.8 - - - +
463C PHE* 3.7 20.2 - - + +
466C ALA* 3.8 22.7 - - + -
467C ASP 5.2 0.7 - - - +
470C LEU* 3.6 33.2 - - + -
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Residues in contact with HIS 179 (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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131C LEU* 4.3 19.7 - - + -
132C PRO* 3.8 34.0 - - + +
133C VAL* 3.7 20.7 - - + +
175C ASN* 2.7 44.5 + - - -
176C MET* 3.1 8.5 + - - +
178C MET* 1.3 75.0 - - - +
180C ILE* 1.3 66.0 + - - +
181C PHE 3.2 0.2 - - - -
182C THR* 2.8 29.6 + - - +
184C GLU* 4.5 5.1 - - - +
185C GLY 4.2 3.6 + - - -
194C ARG* 4.6 7.6 - - - -
283C ASP* 4.7 3.8 + - - -
427C VAL* 3.6 28.5 - - + +
431C MET* 5.2 1.1 - - + -
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Residues in contact with ILE 180 (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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108C ARG* 3.1 29.6 + - + -
109C ASP* 3.6 40.4 - - - +
110C PRO* 3.6 6.1 - - + -
131C LEU* 3.6 21.8 - - + -
135C PHE* 4.1 23.1 - - + -
176C MET* 2.9 18.7 + - + +
177C LEU* 4.2 8.3 - - + +
179C HIS* 1.3 77.0 - - - +
181C PHE* 1.3 88.4 + - + +
185C GLY* 3.3 15.2 - - - -
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Residues in contact with PHE 181 (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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108C ARG* 3.6 26.5 - - - +
163C TYR* 4.4 9.0 - + - -
164C TRP* 3.8 17.9 - + - -
177C LEU* 3.2 31.1 + - + +
179C HIS 3.2 0.6 - - - -
180C ILE* 1.3 100.5 - - + +
182C THR* 1.3 59.0 + - - +
439C LEU* 3.3 25.2 - - + -
442C ASN* 2.8 43.4 + - + +
443C LEU* 3.8 18.8 - - + -
446C ASP* 3.0 44.4 - - + -
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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