Contacts of the helix formed by residues 178 - 185 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C ALA* 3.6 33.0 - - + -
355C MET* 5.6 5.8 - - + -
408C LEU* 4.3 7.4 - - + -
439C ASN* 4.9 2.3 - - - +
440C MSE 4.0 41.1 - - + +
176F ASP 3.4 3.0 + - - -
177F ILE* 1.3 86.9 - - + +
179F VAL* 1.3 67.3 + - - +
180F HIS* 3.5 36.1 - - + +
181F LEU* 3.0 28.2 + - + +
182F ALA* 3.0 9.5 + - - +
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Residues in contact with VAL 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C GLY 4.1 11.7 - - - +
135C ILE* 3.4 20.2 - - - +
136C LYS* 3.5 26.1 - - + +
137C LYS* 3.3 28.9 - - + -
440C MSE 5.0 3.6 + - - +
441C HIS* 4.5 11.9 - - + +
177F ILE 3.7 0.8 + - - -
178F LEU* 1.3 73.1 - - - +
180F HIS* 1.3 87.5 + - + +
181F LEU 3.1 0.7 + - - -
182F ALA* 3.2 19.1 + - - +
183F SER* 4.3 3.6 + - - -
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Residues in contact with HIS 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C LEU* 4.4 11.0 - - + -
413C GLN 4.6 0.2 - - - +
414C GLY* 3.0 22.7 - - - -
415C GLY 3.9 14.5 + - - +
440C MSE 3.3 29.5 - - + +
441C HIS* 3.5 25.1 + + + -
6005C MN 4.7 3.6 - - - -
178F LEU* 3.0 27.6 - - + -
179F VAL* 1.3 87.9 - - + +
181F LEU* 1.3 71.6 + - + +
183F SER* 5.1 4.4 + - - -
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Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C ALA* 5.8 0.2 - - + -
354C VAL* 3.4 46.8 - - + +
355C MET* 4.3 6.1 - - + -
408C LEU* 3.9 22.4 - - + +
409C GLY* 3.6 28.0 - - - +
413C GLN* 3.8 12.0 + - + +
414C GLY* 3.7 21.5 - - - +
177F ILE* 4.3 6.6 - - + +
178F LEU* 3.0 23.5 + - + -
180F HIS* 1.3 96.1 - - + +
182F ALA* 1.3 58.0 + - - +
183F SER* 3.1 9.8 + - - +
184F GLU* 4.3 5.2 + - - +
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LYS* 3.3 35.4 - - + +
177F ILE* 4.4 5.4 - - + +
178F LEU 3.0 10.6 + - - +
179F VAL* 3.2 11.2 + - - +
181F LEU* 1.3 76.6 - - - +
183F SER* 1.3 64.4 + - - +
184F GLU 3.3 2.2 - - - -
185F GLN* 2.8 36.0 + - + +
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C GLN* 5.2 13.2 - - - -
179F VAL 4.3 3.4 + - - -
180F HIS 5.3 2.9 - - - -
181F LEU* 3.1 5.7 - - - -
182F ALA* 1.3 78.3 - - - +
184F GLU* 1.3 62.1 + - - +
185F GLN 3.1 1.0 + - - -
186F LEU* 3.9 20.8 - - - +
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Residues in contact with GLU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C ASN 5.6 1.7 - - - +
354C VAL* 6.6 0.2 - - + -
413C GLN* 3.9 23.8 - - - +
181F LEU 4.3 5.8 + - - +
182F ALA 3.3 0.8 - - - -
183F SER* 1.3 78.7 - - - +
185F GLN* 1.3 56.6 + - - +
186F LEU* 3.3 16.0 + - - +
187F GLU* 4.8 1.2 + - - +
192F LYS* 5.0 4.5 - - - +
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Residues in contact with GLN 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LYS* 2.8 33.5 + - - -
189C LYS* 4.1 15.2 - - + +
190C ALA* 4.8 3.3 + - - -
351C TYR* 4.5 4.2 + - - -
176F ASP* 3.7 7.9 + - - -
177F ILE* 3.2 24.0 - - + +
182F ALA* 2.8 19.6 + - - +
184F GLU* 1.3 77.4 - - - +
186F LEU* 1.3 56.9 + - - +
192F LYS* 2.9 48.8 + - + +
193F VAL* 3.4 19.0 - - - +
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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