Contacts of the helix formed by residues 159 - 170 (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 ASP 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C SER 4.5 1.1 + - - +
150C LYS 5.0 1.8 + - - -
152C ASP* 4.7 7.2 - - + +
155C THR* 5.8 0.2 - - - +
157C ILE 3.4 6.9 + - - +
158C GLN* 1.3 77.8 - - - +
160C PRO* 1.4 61.7 - - - +
161C ASP* 2.8 18.2 + - - +
162C ARG* 2.8 52.6 + - - +
163C TYR* 3.4 9.8 + - - -
449C GLN 4.3 1.2 - - - +
451C ARG* 2.8 41.9 + - - -
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Residues in contact with PRO 160 (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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158C GLN* 3.8 7.6 - - + +
159C ASP* 1.4 89.9 - - - +
161C ASP* 1.3 56.3 + - - +
163C TYR* 3.5 33.1 - - + +
164C TRP* 2.9 42.1 + - + +
446C ASP* 3.9 24.0 - - - +
449C GLN* 3.8 38.6 - - + +
450C VAL* 4.2 2.2 - - + -
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Residues in contact with ASP 161 (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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387B ARG* 3.0 47.5 + - - -
388B TYR* 4.6 1.2 + - - -
159C ASP* 2.8 16.7 + - - +
160C PRO* 1.3 78.8 - - - +
162C ARG* 1.3 59.0 + - - +
164C TRP* 4.8 0.4 - - - +
165C ASP* 3.4 6.6 + - - +
449C GLN 4.2 2.9 + - - +
450C VAL* 3.6 12.5 - - - +
451C ARG* 2.8 53.8 + - - +
452C HIS* 2.9 28.0 + - - -
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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
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380B SER* 2.8 25.1 + - - -
382B ASN* 2.6 31.7 + - - -
383B TYR* 3.6 31.3 - - + +
387B ARG* 5.2 0.4 - - - +
147C HIS 2.9 20.0 + - - -
148C SER* 3.2 20.1 + - - +
150C LYS 3.4 12.9 + - - -
152C ASP* 3.7 33.7 + - - +
153C PRO* 3.4 11.7 - - - +
159C ASP* 2.8 28.0 + - - +
161C ASP* 1.3 80.3 - - + +
163C TYR* 1.3 60.6 + - - +
165C ASP* 3.1 21.1 - - - +
166C PHE 3.3 4.9 + - - -
451C ARG* 5.6 0.4 - - - +
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Residues in contact with TYR 163 (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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148C SER* 3.3 33.9 - - - +
149C LEU* 3.8 27.8 - - + +
158C GLN* 3.7 33.1 + - + -
159C ASP 3.4 13.8 + - - -
160C PRO* 3.5 24.9 - - + +
162C ARG* 1.3 76.4 - - - +
164C TRP* 1.3 78.0 + + - +
166C PHE* 3.4 0.9 + - - +
167C MET* 2.9 40.5 + - + +
177C LEU* 6.2 2.0 - - + -
181C PHE* 4.4 10.0 - + - -
446C ASP* 2.6 38.1 + - - -
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Residues in contact with TRP 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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160C PRO* 2.9 32.2 + - + +
163C TYR* 1.3 85.6 - + - +
165C ASP* 1.3 54.0 + - - +
167C MET* 4.4 6.3 - - + +
168C THR* 2.7 60.8 + - + +
177C LEU* 3.8 24.7 - - + -
181C PHE* 3.8 21.1 - + - -
443C LEU* 3.9 10.1 - - + -
446C ASP* 2.9 27.4 + - + +
447C LEU* 3.7 18.0 - - + +
450C VAL* 3.7 22.0 - - + -
455C THR* 3.5 15.5 - - + -
459C ALA* 3.8 20.4 - - + -
463C PHE* 3.7 29.4 - + - -
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Residues in contact with ASP 165 (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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383B TYR* 2.6 26.4 + - - +
385B PRO 4.9 0.4 - - - -
386B ASN* 3.6 1.5 - - - +
387B ARG* 3.1 66.0 + - - +
161C ASP 3.4 5.8 + - - +
162C ARG 3.1 14.7 + - - +
164C TRP* 1.3 78.5 - - - +
166C PHE* 1.3 59.8 + - - +
168C THR* 3.0 16.4 + - - -
169C LEU* 3.1 21.5 + - - +
455C THR* 3.6 10.0 + - - +
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Residues in contact with PHE 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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383B TYR* 3.9 7.3 - + + -
384B GLU 3.6 18.8 - - - -
385B PRO* 4.0 21.6 - - + +
136C ILE* 4.0 22.7 - - + -
141C LYS* 4.0 7.9 - - + -
144C ASP* 3.6 31.6 - - + -
145C MET* 3.6 30.7 - - + -
148C SER* 3.4 31.0 - - - +
162C ARG 3.3 3.2 + - - -
163C TYR 3.9 0.7 - - - +
164C TRP 3.4 0.2 - - - -
165C ASP* 1.3 79.4 - - - +
167C MET* 1.3 76.5 + - - +
169C LEU* 3.2 3.0 + - - +
170C ARG* 2.9 40.3 + - + +
173C SER* 5.8 0.2 - - - -
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Residues in contact with MET 167 (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* 3.3 48.2 - - + -
145C MET* 3.8 9.4 - - + -
148C SER* 4.8 0.9 - - - +
149C LEU* 3.8 33.4 - - + -
163C TYR* 2.9 31.2 + - + +
164C TRP* 4.1 9.0 - - + +
166C PHE* 1.3 85.7 - - + +
168C THR* 1.3 62.9 + - - +
170C ARG 3.0 13.1 - - - +
171C PRO* 3.8 1.9 - - - +
173C SER* 2.7 35.5 + - - +
177C LEU* 4.0 21.2 - - + +
462C ASN* 4.9 0.7 + - - -
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Residues in contact with THR 168 (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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164C TRP* 2.7 48.2 + - + +
165C ASP* 3.0 9.5 + - - -
167C MET* 1.3 72.5 - - - +
169C LEU* 1.3 66.2 + - - +
170C ARG 3.1 0.6 + - - -
171C PRO* 3.8 8.1 - - - +
455C THR* 3.4 32.0 + - + +
458C LEU* 3.7 24.5 - - - +
459C ALA* 3.5 20.2 - - - +
462C ASN* 3.6 19.3 + - - +
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Residues in contact with LEU 169 (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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385B PRO* 3.8 25.4 - - + +
386B ASN* 3.4 42.0 - - - +
387B ARG* 4.2 3.6 - - + +
165C ASP* 3.1 25.5 + - - +
166C PHE 3.6 0.4 - - - +
168C THR* 1.3 80.6 + - - +
170C ARG* 1.3 63.1 + - - +
171C PRO* 3.4 9.8 - - - +
458C LEU* 3.8 25.8 - - + -
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Residues in contact with ARG 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PRO* 3.7 24.6 - - - +
136C ILE* 4.6 3.6 - - + -
137C ARG* 5.8 0.8 - - - +
141C LYS* 4.3 19.6 - - - +
166C PHE* 2.9 33.4 + - + +
167C MET 3.2 2.5 - - - +
169C LEU* 1.3 83.4 + - - +
171C PRO* 1.4 54.9 - - - +
172C GLU* 2.7 69.7 + - - +
173C SER* 2.7 29.2 + - - -
414C GLU* 5.1 10.9 + - - -
20D GLN* 3.7 39.5 + - - +
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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
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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