Contacts of the helix formed by residues 173 - 181 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 3.0 25.2 + - - +
167B MET* 3.0 38.0 + - - -
170B ARG* 2.9 18.5 + - - -
171B PRO* 4.2 1.6 - - - +
172B GLU* 1.3 77.5 - - - +
174B THR* 1.3 65.6 + - - +
175B ASN 3.3 0.4 - - - -
176B MET* 3.1 8.8 + - - +
177B LEU* 3.1 32.6 + - - +
462B ASN* 5.9 0.2 + - - -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 2.6 24.8 + - - +
172B GLU 3.2 0.8 - - - -
173B SER* 1.3 78.8 + - - +
175B ASN* 1.3 64.3 + - - +
177B LEU* 3.2 12.8 + - - +
178B MET* 3.0 23.8 + - + +
420B ASN 3.7 9.6 - - - -
421B PHE* 3.7 14.7 - - + -
424B ALA* 4.0 14.4 - - + -
462B ASN* 3.9 30.6 + - + +
463B PHE* 4.1 20.6 - - + -
466B ALA* 4.5 0.9 - - + -
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 3.9 10.5 - - + +
172B GLU 4.2 7.0 + - - +
173B SER 3.3 0.4 - - - -
174B THR* 1.3 78.1 - - - +
176B MET* 1.3 55.4 + - - +
178B MET* 3.2 10.3 - - - +
179B HIS* 2.7 30.5 + - - -
281B THR* 2.6 32.3 + - - +
282B LYS* 4.8 1.5 - - - +
420B ASN 4.5 3.7 + - - +
423B GLN* 3.1 26.9 + - - +
424B ALA* 3.4 27.0 - - + +
427B VAL* 3.2 26.0 - - - +
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Residues in contact with MET 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 3.8 20.9 - - + -
129B ASN* 5.2 1.6 - - - +
131B LEU* 3.9 26.7 - - + -
133B VAL* 3.2 38.2 - - + +
134B PHE* 3.7 28.1 + - + +
135B PHE* 3.5 50.3 - - + +
173B SER 3.1 9.4 + - - +
175B ASN* 1.3 73.6 - - - +
177B LEU* 1.3 61.0 + - - +
179B HIS* 2.8 19.2 + - - +
180B ILE* 2.9 14.3 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 3.7 30.7 - - + -
163B TYR* 6.6 0.4 - - + -
164B TRP* 3.7 35.2 - - + -
167B MET* 4.2 17.3 - - + -
173B SER* 3.1 31.2 + - - +
174B THR* 3.3 11.2 - - - +
176B MET* 1.3 75.3 - - - +
178B MET* 1.3 62.6 + - - +
180B ILE* 4.1 3.8 - - + -
181B PHE* 3.1 45.3 + - + +
439B LEU* 4.0 0.9 - - - +
463B PHE* 3.7 19.1 - - + -
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 3.0 18.7 + - + +
175B ASN* 3.2 12.3 - - - +
176B MET 3.2 0.2 - - - -
177B LEU* 1.3 75.0 - - - +
179B HIS* 1.3 57.0 + - - +
182B THR* 3.3 10.9 - - - +
424B ALA* 3.5 29.4 - - + +
427B VAL* 4.2 15.0 - - + -
428B TYR* 4.0 15.3 - - + -
431B MET* 3.3 21.2 - - + +
439B LEU* 3.7 21.1 - - - +
463B PHE* 3.7 16.8 - - + -
466B ALA* 3.6 26.5 - - + -
467B ASP 5.2 0.7 - - - +
470B LEU* 3.7 31.9 - - + -
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Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.5 13.5 - - + -
132B PRO* 3.6 31.4 - - + +
133B VAL* 3.6 22.1 - - + +
175B ASN* 2.7 34.1 + - - -
176B MET* 2.8 14.4 + - - +
178B MET* 1.3 76.0 - - - +
180B ILE* 1.3 66.4 + - - +
181B PHE 3.2 2.2 - - - -
182B THR* 2.6 28.8 + - - -
184B GLU* 4.3 5.8 - - - +
185B GLY 4.2 4.0 + - - -
194B ARG* 4.4 9.6 - - - -
283B ASP* 4.7 4.4 + - - -
427B VAL* 3.6 32.8 - - + +
431B MET* 5.4 0.7 - - - -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 3.0 44.3 + - + +
109B ASP* 3.7 26.9 - - - +
110B PRO* 3.9 10.1 - - + -
131B LEU* 3.5 23.6 - - + -
135B PHE* 4.3 15.5 - - + -
176B MET* 2.9 15.9 + - + +
177B LEU* 3.9 9.2 - - + +
179B HIS* 1.3 78.3 - - - +
181B PHE* 1.3 88.6 + - + +
185B GLY* 3.1 14.0 - - - -
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 3.6 29.2 - - - +
163B TYR* 4.5 9.9 - + - -
164B TRP* 3.6 23.1 - + - -
177B LEU* 3.1 29.9 + - + +
180B ILE* 1.3 100.5 - - + +
182B THR* 1.3 55.5 + - - +
439B LEU* 3.3 24.0 - - + -
442B ASN* 2.7 45.1 + - + +
443B LEU* 3.7 18.6 - - + -
446B ASP* 3.3 41.1 - - + -
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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