Contacts of the helix formed by residues 132 - 137 (chain A) in PDB entry 5HG1
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 GLU 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP 3.9 8.2 + - - +
129A HIS 4.5 10.1 - - - +
130A ILE* 2.9 2.3 - - - +
131A ALA* 1.3 76.7 - - - +
133A CYS* 1.3 57.5 + - - +
134A LEU* 3.2 5.0 + - - +
135A ALA* 3.8 6.9 + - - +
136A ASN* 3.6 13.6 + - + +
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Residues in contact with CYS 133 (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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92A VAL* 5.7 7.2 - - + -
112A TYR* 3.3 35.9 - - + +
130A ILE* 3.0 42.5 + - - +
131A ALA* 3.0 2.6 - - - -
132A GLU* 1.3 75.8 - - - +
134A LEU* 1.3 58.8 + - - +
136A ASN* 3.1 19.3 - - + -
137A PHE* 2.4 37.3 + - + +
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Residues in contact with LEU 134 (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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81A LEU* 4.7 18.2 - - + -
131A ALA 3.7 10.2 + - - +
132A GLU 3.2 2.2 - - - +
133A CYS* 1.3 77.8 - - - +
135A ALA* 1.3 59.1 + - - +
137A PHE* 4.5 1.1 - - - +
138A MET* 3.7 15.2 + - - +
143A ILE* 4.7 10.4 - - + +
144A LYS* 4.7 20.3 - - + +
146A LYS 6.1 0.7 - - - +
194A GLN* 5.6 8.1 - - - +
201A ILE* 5.0 22.2 - - + +
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Residues in contact with ALA 135 (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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132A GLU 3.8 6.6 + - - +
134A LEU* 1.3 78.1 - - - +
136A ASN* 1.3 61.2 - - - +
137A PHE 3.4 0.4 - - - -
138A MET* 3.4 19.6 + - - +
139A ASP* 3.7 4.9 + - - -
144A LYS* 4.7 13.5 - - + -
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Residues in contact with ASN 136 (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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112A TYR* 4.3 8.5 + - + +
132A GLU 3.6 6.6 + - - +
133A CYS* 2.8 34.5 + - + +
135A ALA* 1.3 80.0 - - - +
137A PHE* 1.3 57.1 + - - +
138A MET 3.3 0.2 - - - -
139A ASP* 3.5 20.0 - - - +
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Residues in contact with PHE 137 (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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81A LEU* 4.7 9.9 - - + -
92A VAL* 3.3 36.1 - - + -
93A LEU 3.9 5.2 - - - -
94A TRP* 3.4 25.1 - + + -
108A GLU* 2.7 34.1 - - + -
109A ASN* 3.3 15.7 - - - -
110A GLN* 3.4 24.2 - - + -
112A TYR* 4.3 7.4 - + - +
133A CYS* 2.4 32.1 + - + +
134A LEU* 4.5 1.3 - - - +
136A ASN* 1.3 66.6 - - - +
138A MET* 1.3 55.3 + - - +
139A ASP* 3.2 6.4 + - - -
140A LYS* 4.0 14.4 + - + +
141A LEU 4.8 0.5 + - - -
143A ILE* 4.8 8.7 - - + +
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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