Contacts of the helix formed by residues 173 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.0 25.4 + - - +
136A ILE* 5.8 0.2 - - - -
167A MET* 3.0 39.3 + - - -
170A ARG* 3.0 19.1 + - - -
171A PRO* 4.3 1.4 - - - +
172A GLU* 1.3 75.6 - - - +
174A THR* 1.3 65.3 + - - +
175A ASN 3.4 0.7 - - - -
176A MET* 3.3 6.0 + - - +
177A LEU* 3.0 33.3 + - - +
462A ASN* 5.8 0.2 + - - -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PRO* 2.5 23.6 + - - +
172A GLU 3.1 1.4 - - - -
173A SER* 1.3 78.0 + - - +
175A ASN* 1.3 64.0 + - - +
177A LEU* 3.0 13.9 + - - +
178A MET* 3.0 20.9 + - + +
420A ASN 3.7 10.3 - - - -
421A PHE* 3.7 14.1 - - + -
424A ALA* 3.9 15.0 - - + -
462A ASN* 3.9 30.3 + - + +
463A PHE* 4.2 21.0 - - + -
466A ALA* 4.4 3.4 - - + -
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 3.8 11.8 - - + +
172A GLU 4.2 7.9 + - - +
173A SER 3.4 0.6 - - - -
174A THR* 1.3 77.4 - - - +
176A MET* 1.3 55.1 + - - +
178A MET* 3.2 11.4 + - - +
179A HIS* 2.7 31.5 + - - -
281A THR* 2.7 30.9 + - - +
282A LYS* 4.8 0.6 - - + +
420A ASN 4.5 2.8 + - - +
423A GLN* 3.3 25.1 + - - +
424A ALA* 3.3 34.7 - - + +
427A VAL* 3.3 18.5 - - - +
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Residues in contact with MET 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 3.8 20.4 - - + -
129A ASN* 5.2 1.1 - - - +
131A LEU* 3.9 26.5 - - + -
133A VAL* 3.3 38.0 - - + +
134A PHE* 3.6 27.4 + - + +
135A PHE* 3.5 52.5 - - + +
172A GLU 5.0 0.2 + - - -
173A SER 3.3 9.2 + - - +
175A ASN* 1.3 73.4 - - - +
177A LEU* 1.3 66.8 + - - +
179A HIS* 2.9 5.8 + - - +
180A ILE* 2.9 26.0 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.8 27.1 - - + -
163A TYR* 6.6 0.2 - - + -
164A TRP* 3.6 35.4 - - + -
167A MET* 4.2 18.6 - - + +
173A SER* 3.0 33.8 + - - +
174A THR* 3.2 13.0 - - + +
176A MET* 1.3 75.8 - - - +
178A MET* 1.3 59.9 + - - +
180A ILE* 4.2 4.0 - - + -
181A PHE* 3.2 44.8 + - + +
439A LEU* 4.1 1.0 - - - +
443A LEU* 5.0 0.2 - - - +
463A PHE* 3.7 19.5 - - + -
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR* 3.0 16.7 + - + +
175A ASN 3.2 10.5 - - - +
176A MET 3.2 0.4 - - - -
177A LEU* 1.3 76.6 - - - +
179A HIS* 1.3 56.1 + - - +
182A THR* 3.3 21.8 - - - +
424A ALA* 3.8 23.8 - - + +
427A VAL* 4.2 16.2 - - + -
428A TYR* 4.0 15.3 - - + -
431A MET* 3.4 8.8 - - + +
439A LEU* 3.4 23.5 - - - +
463A PHE* 3.5 28.0 - - + -
466A ALA* 3.7 26.9 - - + -
467A ASP 5.2 0.4 - - - +
470A LEU* 3.6 25.4 - - + -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.2 19.3 - - + +
132A PRO* 3.8 30.4 - - + +
133A VAL* 3.6 22.9 - - + +
175A ASN* 2.7 42.4 + - - -
176A MET* 2.9 9.4 + - - +
178A MET* 1.3 74.6 - - - +
180A ILE* 1.3 62.9 + - - +
181A PHE 3.3 2.2 - - - -
182A THR* 2.7 27.5 + - - -
184A GLU* 4.3 5.6 - - - +
185A GLY 4.2 5.0 + - - -
194A ARG* 4.6 8.5 - - - -
283A ASP* 4.8 3.6 + - + -
427A VAL* 3.7 28.3 - - + +
431A MET* 5.3 0.9 - - + -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.0 42.7 + - + +
109A ASP* 3.9 23.8 - - - +
110A PRO* 3.9 11.9 - - + -
131A LEU* 3.5 24.7 - - + -
135A PHE* 4.4 16.2 - - + -
176A MET* 2.9 17.2 + - + +
177A LEU* 4.0 8.5 - - + +
179A HIS* 1.3 77.5 - - - +
181A PHE* 1.3 89.8 + - + +
182A THR 3.4 0.2 - - - +
185A GLY* 3.3 13.8 - - - -
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.7 26.9 - - - +
163A TYR* 4.5 10.1 - + - -
164A TRP* 3.6 24.5 - + - -
177A LEU* 3.2 23.9 + - + +
180A ILE* 1.3 100.6 - - + +
182A THR* 1.3 55.7 + - - +
439A LEU* 3.3 27.9 - - + -
442A ASN* 2.7 45.5 + - + +
443A LEU* 3.6 18.6 - - + -
446A ASP* 3.4 40.4 - - + -
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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