Contacts of the helix formed by residues 185 - 191 (chain A) in PDB entry 2G4C
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA* 5.7 0.9 - - + -
182A ARG* 3.3 45.1 - - - +
184A ASN* 1.3 74.2 - - - +
186A LEU* 1.3 59.1 - - - +
187A HIS 3.5 1.3 - - - -
188A GLY* 3.8 3.5 + - - +
189A ALA* 3.2 22.3 + - - +
210A GLN* 3.2 59.7 + - + +
212A GLY* 3.6 17.0 - - - +
214A CYS* 4.0 12.3 - - - -
236A GLU* 3.6 11.8 + - + +
238A SER* 3.5 22.6 + - - -
339A ASN* 4.7 3.8 - - - +
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Residues in contact with LEU 186 (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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184A ASN* 3.4 16.9 - - + +
185A LEU* 1.3 75.7 - - - +
187A HIS* 1.3 68.7 + - - +
189A ALA* 3.1 6.8 + - - +
190A LEU* 3.0 50.1 + - + +
238A SER* 4.5 2.7 + - - +
240A VAL* 4.5 12.3 - - + -
282A GLU* 4.7 9.9 - - - +
306A LEU* 3.6 28.7 - - + -
310A GLU* 5.0 2.7 - - + +
337A SER* 3.4 25.8 - - - +
339A ASN* 5.2 4.0 - - - +
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Residues in contact with HIS 187 (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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134A LYS* 4.1 30.1 - - + -
184A ASN* 3.8 15.8 + - - +
185A LEU 3.5 0.2 - - - -
186A LEU* 1.3 79.8 - - - +
188A GLY* 1.3 67.0 + - - +
189A ALA 2.9 1.0 + - - -
190A LEU* 3.0 6.9 + - - +
191A GLU* 2.8 57.4 + - + +
314A MET* 3.6 24.8 - - + +
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Residues in contact with GLY 188 (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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130A ALA* 3.7 26.0 - - - -
184A ASN 5.1 1.6 + - - -
185A LEU* 3.8 6.2 + - - +
186A LEU 3.4 0.2 - - - -
187A HIS* 1.3 79.7 - - - +
189A ALA* 1.3 59.1 + - - +
191A GLU* 3.7 12.5 + - - +
192A HIS* 2.8 33.3 + - - -
210A GLN* 4.7 2.0 - - - -
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Residues in contact with ALA 189 (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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128A VAL* 4.9 3.4 - - + -
185A LEU 3.2 14.1 + - - +
186A LEU 3.1 9.4 + - - +
187A HIS 2.9 0.6 - - - -
188A GLY* 1.3 75.6 - - - +
190A LEU* 1.3 62.4 + - - +
192A HIS* 2.8 28.9 + - - +
193A TYR* 3.4 3.8 + - - -
208A LEU* 3.7 20.1 - - + +
210A GLN* 4.7 6.1 - - - +
240A VAL* 3.5 34.8 - - + -
242A PHE* 4.6 1.5 - - - -
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Residues in contact with LEU 190 (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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186A LEU* 3.0 39.4 + - + +
187A HIS* 3.5 2.2 - - - +
189A ALA* 1.3 73.5 - - - +
191A GLU* 1.3 52.0 + - - +
192A HIS 2.7 8.5 + - - -
193A TYR* 3.0 12.3 + - - +
240A VAL* 4.2 4.9 - - + -
242A PHE* 4.2 12.3 - - + -
310A GLU* 3.8 33.9 - - + +
311A LEU* 4.5 7.6 - - + +
314A MET* 3.3 28.0 - - + -
315A TYR* 2.4 30.9 + - - -
335A VAL* 4.0 31.0 - - + -
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Residues in contact with GLU 191 (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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134A LYS* 5.1 3.3 - - - +
187A HIS* 2.8 52.7 + - - +
188A GLY* 3.8 12.7 - - - +
189A ALA 3.2 0.2 - - - -
190A LEU* 1.3 75.6 - - - +
192A HIS* 1.3 60.3 + - + +
195A ASN* 3.8 12.5 + - - -
314A MET* 3.7 12.6 - - + -
315A TYR* 3.0 14.4 + - - -
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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