Contacts of the helix formed by residues 78 - 85 (chain A) in PDB entry 3LRA
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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP* 2.1 26.8 + - - -
77A THR* 1.3 66.8 - - - +
79A LEU* 1.3 59.7 + - - +
80A TYR* 2.8 9.4 + - - -
81A GLU* 2.6 37.7 + - - +
82A LEU* 4.1 2.2 + - - +
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Residues in contact with LEU 79 (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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40A ILE* 3.8 9.4 - - + -
75A SER 5.5 0.4 + - - +
77A THR* 3.2 21.6 + - + +
78A GLY* 1.3 76.0 - - - +
80A TYR* 1.3 71.3 + - - +
81A GLU 3.3 0.2 - - - -
82A LEU* 3.3 36.9 + - + +
83A LEU* 3.7 9.8 + - + +
113A HIS 5.0 0.4 - - - +
116A VAL* 3.3 37.7 - - + +
117A LYS* 4.0 24.2 - - + +
120A GLU* 3.4 31.4 - - + +
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Residues in contact with TYR 80 (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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76A ASP* 5.2 4.5 - - - +
78A GLY 2.8 5.8 + - - -
79A LEU* 1.3 84.8 - - - +
81A GLU* 1.3 88.3 + - + +
83A LEU* 3.6 3.5 + - - +
84A ALA* 3.4 30.0 + - + +
113A HIS* 3.5 44.9 + + + -
117A LYS* 3.5 32.6 - - - +
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Residues in contact with GLU 81 (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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76A ASP* 5.0 5.9 - - - +
78A GLY* 2.6 37.9 + - - +
80A TYR* 1.3 103.6 - - + +
82A LEU* 1.3 54.7 + - - +
84A ALA* 2.9 7.1 + - - -
85A ALA* 2.6 40.9 + - + +
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Residues in contact with LEU 82 (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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33A SER* 3.1 30.7 - - - +
36A ARG* 4.3 27.1 - - + -
37A VAL* 5.4 6.5 - - + -
40A ILE* 6.4 0.2 - - + -
78A GLY 4.1 1.5 + - - +
79A LEU* 3.3 33.3 + - + +
81A GLU* 1.3 79.3 - - - +
83A LEU* 1.3 69.7 + - + +
85A ALA* 3.0 12.6 + - - +
86A LEU* 3.2 18.8 + - + +
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Residues in contact with LEU 83 (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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37A VAL* 3.5 32.3 - - + -
41A PHE* 4.9 2.0 - - + -
79A LEU* 3.7 10.3 + - + +
80A TYR* 3.6 4.1 + - - +
81A GLU 3.4 0.6 - - - -
82A LEU* 1.3 80.7 - - + +
84A ALA* 1.3 61.6 + - - +
86A LEU* 3.4 6.9 + - + +
87A PRO* 3.3 7.8 - - - +
107A PHE* 3.0 52.8 - - + +
112A LEU* 4.8 3.4 - - + -
113A HIS* 3.7 31.9 - - + +
116A VAL* 3.6 40.4 - - + -
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Residues in contact with ALA 84 (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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80A TYR* 3.4 35.1 + - + +
81A GLU* 2.9 9.2 + - - +
83A LEU* 1.3 73.7 - - - +
85A ALA* 1.3 57.5 + - - +
86A LEU 3.0 9.6 + - - -
87A PRO* 3.3 12.6 - - - +
88A ALA* 4.8 1.2 + - - +
104A TRP* 4.7 11.4 - - - -
107A PHE 4.6 5.5 - - - -
113A HIS* 3.9 9.8 - - + +
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Residues in contact with ALA 85 (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 GLU* 2.6 24.4 + - + +
82A LEU* 3.5 6.1 - - - +
84A ALA* 1.3 71.2 - - - +
86A LEU* 1.3 57.5 + - - +
88A ALA* 3.9 10.3 - - + +
89A GLN* 2.8 35.6 + - - +
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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