Contacts of the helix formed by residues 178 - 185 (chain M) in PDB entry 2GLJ
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 LEU 178 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176M ASP 3.4 3.4 + - - -
177M ILE* 1.3 85.8 - - + +
179M VAL* 1.3 67.0 + - - +
180M HIS* 3.4 37.5 - - + +
181M LEU* 3.0 27.8 + - + -
182M ALA* 3.0 9.4 + - - +
345P ALA* 3.5 34.8 - - + -
355P MET* 5.6 4.5 - - + -
408P LEU* 4.4 6.1 - - + -
439P ASN* 4.7 3.2 - - - +
440P MSE 3.8 42.4 - - + +
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Residues in contact with VAL 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M ILE 3.7 0.6 + - - -
178M LEU* 1.3 72.4 - - - +
180M HIS* 1.3 82.0 + - + +
181M LEU 3.1 1.2 + - - -
182M ALA* 3.2 18.5 + - - +
183M SER* 4.3 3.6 + - - -
134P GLY 4.0 15.9 - - - +
135P ILE* 3.3 27.1 - - - +
136P LYS* 3.6 18.9 - - + +
137P LYS* 3.4 24.7 - - + +
440P MSE 4.8 3.0 + - - +
441P HIS* 4.3 18.2 - - + +
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Residues in contact with HIS 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178M LEU* 3.0 27.1 + - + -
179M VAL* 1.3 87.1 - - + +
181M LEU* 1.3 71.2 + - + +
183M SER* 5.0 4.4 + - - -
408P LEU* 4.4 13.2 - - + -
414P GLY* 3.1 22.5 - - - -
415P GLY 3.9 12.1 + - - +
440P MSE 3.0 31.7 - - + +
441P HIS* 3.4 26.6 + + - -
6031P MN 4.3 4.0 - - - -
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Residues in contact with LEU 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M ILE* 4.3 7.0 - - + +
178M LEU* 3.0 23.3 + - + -
180M HIS* 1.3 94.5 - - + +
182M ALA* 1.3 57.2 + - - +
183M SER* 3.1 10.3 + - - +
184M GLU* 4.3 4.5 + - - +
345P ALA* 5.6 0.2 - - + -
354P VAL* 3.5 46.9 - - + +
355P MET* 4.1 7.4 - - + -
408P LEU* 3.7 28.0 - - + -
409P GLY* 3.6 26.5 - - - +
413P GLN* 3.9 11.4 + - + +
414P GLY* 3.9 19.3 - - - +
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Residues in contact with ALA 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M ILE* 4.4 5.4 - - + +
178M LEU 3.0 10.6 + - - +
179M VAL* 3.2 11.9 + - - +
181M LEU* 1.3 76.8 - - - +
183M SER* 1.3 59.2 + - - +
184M GLU 3.3 2.2 - - - -
185M GLN* 2.8 38.1 + - - +
137P LYS* 3.3 38.6 - - + +
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Residues in contact with SER 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M VAL 4.3 4.0 + - - -
180M HIS 5.3 3.1 - - - -
181M LEU* 3.1 6.5 - - - -
182M ALA* 1.3 78.3 - - - +
184M GLU* 1.3 62.4 + - - +
185M GLN 3.1 1.0 + - - -
186M LEU* 3.9 20.4 - - - +
413P GLN* 5.1 14.1 - - - -
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Residues in contact with GLU 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M LEU 4.3 6.0 + - - +
182M ALA 3.3 0.6 - - - -
183M SER* 1.3 78.5 + - - +
185M GLN* 1.3 57.3 + - - +
186M LEU* 3.3 17.6 + - - +
187M GLU* 4.7 1.0 + - - +
192M LYS* 5.1 4.9 - - - +
353P ASN* 5.4 2.9 - - - +
354P VAL* 6.1 1.1 - - + -
413P GLN* 3.8 24.7 - - - +
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Residues in contact with GLN 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M ASP* 3.7 7.1 + - - -
177M ILE* 3.2 24.2 - - + +
182M ALA* 2.8 19.0 + - - +
184M GLU* 1.3 75.0 - - - +
186M LEU* 1.3 59.2 + - - +
192M LYS* 2.9 49.8 + - + +
193M VAL* 3.4 18.4 - - - +
137P LYS* 2.6 35.8 + - - -
189P LYS* 4.1 14.1 - - + +
190P ALA* 4.8 3.3 + - - -
351P TYR* 4.5 4.4 + - - -
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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