Contacts of the helix formed by residues 48 - 59 (chain A) in PDB entry 1R9G
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLN* 3.4 24.7 + - - +
47A GLY* 1.3 76.9 - - - +
49A SER* 1.3 66.8 + - - +
50A THR* 4.0 14.2 + - - -
51A THR* 3.1 27.3 + - - +
52A MSE 3.1 21.0 + - - +
80A ALA* 4.1 2.9 - - - -
106A ARG* 2.6 36.1 + - - -
111A ARG* 5.9 0.5 + - - -
135A ARG* 5.6 4.0 + - - -
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Residues in contact with SER 49 (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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48A GLU* 1.3 73.1 - - - +
50A THR* 1.3 66.1 + - - -
52A MSE 3.4 3.8 + - - +
53A ARG* 3.3 18.6 + - - +
80A ALA* 3.7 13.7 - - - +
83A ILE* 3.5 37.3 - - - +
84A ILE* 4.3 8.8 - - - +
88A GLU* 4.8 2.9 + - - -
96A HIS* 4.3 6.5 + - - -
106A ARG* 2.7 35.4 + - - +
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Residues in contact with THR 50 (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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48A GLU* 3.6 12.6 + - - -
49A SER* 1.3 78.6 + - - +
51A THR* 1.3 64.9 + - - +
53A ARG* 3.3 18.7 - - + +
54A ARG* 3.4 13.1 + - - +
96A HIS* 6.1 0.7 - - - -
106A ARG* 4.4 9.0 + - - -
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Residues in contact with THR 51 (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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10A GLN* 3.5 25.6 - - + +
48A GLU* 3.1 29.5 + - - +
49A SER 3.3 0.6 - - - -
50A THR* 1.3 77.9 - - - +
52A MSE 1.3 65.5 + - - +
53A ARG 3.0 1.4 + - - -
54A ARG* 3.1 48.6 + - - +
55A LEU* 3.1 18.0 + - + +
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Residues in contact with MSE 52 (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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7A LEU* 3.7 30.7 - - + +
9A LEU* 5.1 5.6 - - + -
10A GLN* 4.0 18.8 - - + +
44A LEU* 3.8 20.6 - - + -
45A PRO* 5.0 3.4 - - - -
46A GLY* 3.9 32.5 - - - +
48A GLU 3.1 14.4 + - - +
49A SER* 3.9 3.8 - - - +
51A THR* 1.3 80.4 - - - +
53A ARG* 1.3 59.1 + - - +
55A LEU* 3.6 10.8 - - - +
56A ILE* 2.9 40.9 + - + +
80A ALA* 5.6 0.7 - - + -
81A GLY* 4.9 0.2 - - - -
84A ILE* 3.3 36.6 - - + -
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Residues in contact with ARG 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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49A SER 3.3 11.5 + - - +
50A THR* 3.3 15.3 - - + +
51A THR 3.0 0.6 - - - -
52A MSE 1.3 78.7 - - - +
54A ARG* 1.3 62.7 + - - +
56A ILE* 3.1 20.0 - - - +
57A ASP* 2.6 49.7 + - - +
62A MSE 3.1 29.0 - - - +
84A ILE* 4.6 4.0 - - - +
94A ASN* 2.6 34.0 - - - +
95A PRO 3.0 11.7 + - - -
96A HIS* 2.6 39.5 + - + -
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Residues in contact with ARG 54 (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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50A THR* 3.4 11.1 + - - +
51A THR* 3.1 43.2 + - - +
53A ARG* 1.3 80.8 - - - +
55A LEU* 1.3 79.8 + - - +
57A ASP* 3.3 8.4 + - - +
58A THR* 2.8 29.3 + - - +
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Residues in contact with LEU 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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9A LEU* 3.5 26.2 - - + +
10A GLN* 3.4 39.5 - - + -
51A THR* 3.1 18.8 + - + +
52A MSE 3.6 7.2 - - - +
53A ARG 3.1 0.6 - - - -
54A ARG* 1.3 97.7 - - - +
56A ILE* 1.3 66.0 + - - +
57A ASP 3.2 0.5 + - - -
58A THR* 3.6 6.2 + - - +
59A TYR* 3.2 38.1 + - + +
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Residues in contact with ILE 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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7A LEU* 4.4 12.1 - - + -
9A LEU* 3.5 22.7 - - + -
52A MSE 2.9 29.0 + - + +
53A ARG* 3.1 24.9 - - - +
55A LEU* 1.3 76.3 - - - +
57A ASP* 1.3 63.7 + - - +
59A TYR 3.5 0.2 - - - -
60A GLN 3.2 1.7 + - - -
61A PHE* 2.7 42.1 + - + +
62A MSE 3.2 49.5 + - + +
65A LEU* 5.0 7.2 - - + -
84A ILE* 5.0 9.4 - - + -
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Residues in contact with ASP 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 ARG* 2.6 46.5 + - - +
54A ARG* 3.3 10.6 + - - +
55A LEU 3.1 0.8 - - - -
56A ILE* 1.3 79.3 - - - +
58A THR* 1.3 59.2 + - - +
59A TYR 2.8 9.5 + - - -
60A GLN* 2.9 16.0 + - - +
61A PHE 5.0 0.2 - - - +
62A MSE 4.5 15.1 - - - +
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Residues in contact with THR 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 ARG 2.8 18.6 + - - +
55A LEU* 3.6 10.9 + - - +
57A ASP* 1.3 76.3 - - - +
59A TYR* 1.3 72.6 + - - +
60A GLN* 3.5 0.4 - - - +
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Residues in contact with TYR 59 (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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9A LEU* 3.4 28.3 - - + -
31A LYS* 4.3 11.2 - - + -
33A PRO* 3.4 17.6 - - + +
55A LEU* 3.2 27.5 + - + +
57A ASP 2.8 1.2 - - - -
58A THR* 1.3 96.3 - - - +
60A GLN* 1.3 71.1 + - - +
61A PHE* 3.2 14.6 + + + -
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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