Contacts of the helix formed by residues 178 - 185 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176O ASP 3.4 3.1 + - - -
177O ILE* 1.3 86.6 - - + +
179O VAL* 1.3 66.6 + - - +
180O HIS* 3.0 35.4 - - + +
181O LEU* 3.0 29.0 + - + +
182O ALA* 3.0 9.1 + - - +
345R ALA* 3.6 34.3 - - + -
355R MET* 5.7 4.7 - - + -
408R LEU* 4.3 7.2 - - + -
439R ASN* 4.9 2.3 - - - +
440R MSE 3.9 42.4 - - + +
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Residues in contact with VAL 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE 3.7 0.8 + - - -
178O LEU* 1.3 72.2 - - - +
180O HIS* 1.3 86.8 + - + +
181O LEU 3.1 0.9 + - - -
182O ALA* 3.2 19.2 + - - +
183O SER* 4.3 3.8 + - - -
134R GLY 4.0 15.9 - - - +
135R ILE* 3.3 27.4 - - - +
136R LYS* 3.5 21.6 - - + +
137R LYS* 3.4 22.4 - - + -
440R MSE 5.0 2.8 + - - +
441R HIS* 4.4 12.1 - - + +
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Residues in contact with HIS 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O LEU* 3.0 29.3 - - + -
179O VAL* 1.3 87.8 - - + +
181O LEU* 1.3 71.1 + - + +
183O SER* 5.1 4.2 + - - -
134R GLY 5.9 0.2 - - - -
408R LEU* 4.5 5.2 - - + -
413R GLN 4.7 0.3 - - - +
414R GLY* 3.0 21.7 - - - -
415R GLY 3.9 19.6 + - - +
440R MSE 3.3 29.2 - - + +
441R HIS* 3.4 26.1 + + - -
6035R MN 4.5 3.6 - - - -
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Residues in contact with LEU 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE* 4.3 6.3 - - + +
178O LEU* 3.0 23.5 + - + -
180O HIS* 1.3 95.5 - - + +
182O ALA* 1.3 57.4 + - - +
183O SER* 3.1 9.3 + - - -
184O GLU* 4.3 4.7 + - - +
345R ALA* 5.7 0.2 - - + -
354R VAL* 3.5 45.9 - - + +
355R MET* 4.3 5.6 - - + -
408R LEU* 3.8 23.6 - - + -
409R GLY* 3.6 27.4 - - - +
413R GLN* 3.8 13.1 + - - +
414R GLY* 3.6 22.9 - - - +
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Residues in contact with ALA 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE* 4.4 5.4 - - + +
178O LEU 3.0 9.3 + - - +
179O VAL* 3.2 12.5 + - - +
181O LEU* 1.3 77.2 - - - +
183O SER* 1.3 57.9 + - - +
184O GLU 3.3 2.2 - - - -
185O GLN* 2.8 42.1 + - - +
137R LYS* 3.3 35.7 - - + +
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Residues in contact with SER 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179O VAL 4.3 3.6 + - - -
180O HIS 5.3 2.9 - - - -
181O LEU* 3.1 6.1 - - - -
182O ALA* 1.3 77.9 - - - +
184O GLU* 1.3 63.6 + - - +
185O GLN 3.1 1.0 + - - -
186O LEU* 3.9 20.4 - - - +
413R GLN* 5.2 13.2 - - - -
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Residues in contact with GLU 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O LEU 4.3 5.4 + - - +
182O ALA 3.3 0.8 - - - -
183O SER* 1.3 78.7 + - - +
185O GLN* 1.3 56.4 + - - +
186O LEU* 3.3 15.6 + - - +
187O GLU* 4.7 1.0 + - - +
192O LYS* 5.1 4.7 - - - +
353R ASN 5.6 1.4 - - - +
413R GLN* 3.9 23.9 - - - +
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Residues in contact with GLN 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O ASP* 3.7 7.7 + - - -
177O ILE* 3.2 24.5 - - + +
182O ALA* 2.8 20.1 + - - +
184O GLU* 1.3 76.4 - - - +
186O LEU* 1.3 57.7 + - - +
192O LYS* 2.9 48.5 + - + +
193O VAL* 3.4 19.0 - - - +
137R LYS* 2.8 33.8 + - - -
189R LYS* 4.1 13.5 - - + +
190R ALA* 4.7 4.0 + - - -
351R TYR* 4.6 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