Contacts of the helix formed by residues 52 - 61 (chain A) in PDB entry 1G82
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 THR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP* 1.3 61.0 + - - +
54A LEU* 3.3 9.7 + - - +
55A ASP* 3.2 46.0 + - + +
56A HIS* 3.2 18.5 + - - +
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Residues in contact with ASP 53 (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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52A THR* 1.3 70.3 - - - +
54A LEU* 1.3 53.9 + - - +
56A HIS* 3.4 5.6 + - - +
57A LEU* 2.7 38.6 + - - +
202A LYS 4.1 11.7 - - - +
203A ASP* 3.7 31.9 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 3.3 8.6 + - - +
53A ASP* 1.3 77.2 - - - +
55A ASP* 1.3 64.7 + - - +
57A LEU* 3.2 16.6 + - + +
58A LYS* 2.9 69.6 + - + +
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Residues in contact with ASP 55 (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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52A THR* 3.2 31.2 + - + +
54A LEU* 1.3 87.5 - - - +
56A HIS* 1.3 65.4 + - - +
58A LYS* 3.4 15.8 + - - +
59A GLY* 3.2 17.3 + - - -
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Residues in contact with HIS 56 (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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52A THR 3.2 19.2 + - - +
53A ASP* 3.4 5.8 - - - +
54A LEU 3.2 0.4 - - - -
55A ASP* 1.3 78.8 - - - +
57A LEU* 1.3 64.8 + - - +
59A GLY* 3.3 3.7 + - - -
60A ILE* 3.1 37.3 + - + +
63A ARG* 4.4 7.8 + - - -
199A GLU* 4.1 18.4 - - + +
202A LYS* 6.0 0.7 - - + -
203A ASP* 2.5 36.2 + - - +
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Residues in contact with LEU 57 (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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53A ASP 2.7 21.9 + - - +
54A LEU* 3.2 15.7 - - + +
56A HIS* 1.3 72.7 - - - +
58A LYS* 1.3 56.6 + - + +
60A ILE* 2.7 27.7 + - + +
61A LEU* 2.9 25.0 + - + +
200A LEU* 4.3 10.3 - - + -
203A ASP* 3.3 19.5 + - + +
204A ILE* 5.8 1.8 - - + -
57D LEU* 4.0 40.2 - - + -
61D LEU* 4.9 2.7 - - + -
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Residues in contact with LYS 58 (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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54A LEU* 2.9 57.4 + - + +
55A ASP* 3.7 17.9 + - - +
56A HIS 3.3 0.6 - - - -
57A LEU* 1.3 77.5 - - + +
59A GLY* 1.3 60.0 + - - +
61A LEU* 3.4 15.1 + - + -
62A ARG* 2.8 46.0 + - - +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP 3.2 13.1 + - - -
56A HIS 3.6 5.2 - - - -
57A LEU 3.1 0.4 - - - -
58A LYS* 1.3 76.2 - - - +
60A ILE* 1.3 64.9 + - - +
62A ARG* 3.0 14.7 + - - -
63A ARG* 3.4 14.0 + - - +
96A GLU* 3.9 29.7 - - - +
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Residues in contact with ILE 60 (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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56A HIS* 3.1 20.2 + - + +
57A LEU* 2.7 16.5 + - + +
59A GLY* 1.3 70.4 - - - +
61A LEU* 1.3 63.6 + - - +
62A ARG 3.1 1.0 + - - -
63A ARG* 3.1 43.1 + - + +
64A ARG* 5.2 0.2 + - - -
197A VAL* 3.7 23.1 - - + -
199A GLU* 4.5 1.6 - - + -
200A LEU* 4.2 18.8 - - + -
203A ASP* 3.7 21.5 - - - +
61D LEU* 3.4 40.1 - - + +
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Residues in contact with LEU 61 (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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57A LEU* 2.9 25.9 + - + +
58A LYS* 3.5 23.1 - - + +
60A ILE* 1.3 76.0 - - - +
62A ARG* 1.3 64.7 + - - +
64A ARG* 3.2 18.5 + - - -
57D LEU* 5.6 1.1 - - + -
60D ILE* 3.9 28.9 - - + +
61D LEU* 4.1 19.5 - - + -
192D VAL 4.4 5.7 - - - +
194D PRO* 3.9 16.9 - - + +
201D TYR* 4.1 21.3 - - + -
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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