Contacts of the helix formed by residues 130 - 134 (chain A) in PDB entry 2HA7
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE* 5.8 0.7 - - - -
85A MET 3.9 22.0 - - - +
86A TRP* 3.9 22.7 - - + +
87A ASN 3.2 28.0 - - - +
89A ASN* 3.8 16.4 - - + +
126A GLY* 5.2 2.5 - - - -
127A ALA* 3.5 25.1 - - + +
128A ALA 3.5 1.8 - - - +
129A SER* 1.3 79.7 - - - +
131A ASP* 1.3 66.6 + - - +
132A VAL* 4.4 4.7 - - + +
133A TYR* 3.1 54.4 + - + +
134A ASP* 3.9 1.9 + - - +
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Residues in contact with ASP 131 (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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85A MET 5.4 1.4 + - - -
89A ASN* 4.4 2.4 + - - +
129A SER 4.5 1.0 - - - +
130A LEU* 1.3 73.1 - - - +
132A VAL* 1.3 63.6 + - + +
133A TYR 3.3 1.0 + - - -
134A ASP* 3.3 22.4 - - - +
457A LEU* 3.7 15.9 - - + +
495B SER* 3.3 34.1 + - - -
496B LYS* 4.8 9.9 - - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.3 34.1 + - + +
86A TRP* 3.8 22.0 - - + -
130A LEU* 4.4 8.5 - - + -
131A ASP* 1.3 77.9 - - + +
133A TYR* 1.3 83.2 + - + +
134A ASP 3.4 1.6 - - - -
451A ILE* 3.9 9.8 - - + +
452A GLU* 4.2 21.5 - - + +
455A PHE* 3.4 26.9 - - - +
457A LEU* 3.9 16.0 - - + +
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Residues in contact with TYR 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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86A TRP* 3.5 18.7 - - - -
102A TRP* 4.0 14.4 - - - -
117A TRP* 3.2 49.0 - + + +
119A TYR* 3.7 20.8 - - + +
120A GLY 4.3 4.7 + - - -
127A ALA 3.2 29.6 - - - -
128A ALA* 4.2 12.6 - - - +
130A LEU* 3.1 36.6 + - + +
132A VAL* 1.3 94.8 - - + +
134A ASP* 1.3 62.8 + - - +
135A GLY 3.2 3.5 + - - -
146A LEU* 5.0 1.0 - - - +
148A SER* 5.2 1.8 + - - +
202A GLU* 5.2 0.2 + - - -
451A ILE* 3.9 15.1 - - + +
455A PHE* 3.4 16.8 - + + -
908A ETM 4.3 10.6 - - - -
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Residues in contact with ASP 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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65A PHE* 6.2 1.8 - - - -
102A TRP* 3.6 16.7 + - - -
130A LEU 3.9 2.0 + - - +
131A ASP* 3.3 20.7 + - - +
132A VAL 3.4 2.6 + - - -
133A TYR* 1.3 74.0 - - - +
135A GLY* 1.3 61.9 + - - +
136A ARG* 2.8 56.0 + - - +
137A PHE* 3.9 25.1 - - + -
455A PHE* 3.5 15.0 - - - +
457A LEU* 4.7 1.3 - - + +
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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