Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 1D1T
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 CYS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLY 3.6 2.0 + - - -
45A ILE* 1.3 76.6 - - - +
47A ARG* 1.3 70.0 + - - +
48A THR* 3.1 14.1 - - - -
49A ASP* 2.9 28.2 + - - +
50A ASP 3.7 1.7 + - - -
67A HIS* 3.5 10.1 - - + +
68A GLU* 4.0 6.5 - - + +
174A CYS* 3.8 1.6 - - - -
362A LEU* 4.6 2.5 - - - +
369A ARG* 3.3 25.1 - - - +
376A ZN 2.3 37.0 - - - -
501A ACT 3.7 3.1 - - - -
1377A NAD 3.9 11.0 - - - -
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Residues in contact with ARG 47 (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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45A ILE 4.1 1.6 + - - -
46A CYS* 1.3 75.4 - - - +
48A THR* 1.3 63.5 + - - +
50A ASP* 2.9 24.5 + - - -
51A HIS* 3.1 32.1 + - - +
54A LYS* 4.9 1.8 - - - +
269A ILE 5.2 2.9 - - - +
362A LEU* 3.4 43.0 + - + +
363A ASN* 2.8 30.9 + - - +
369A ARG* 4.4 0.4 - - - +
1377A NAD 3.0 71.3 + - - +
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Residues in contact with THR 48 (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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46A CYS* 3.0 6.5 + - - -
47A ARG* 1.3 78.7 - - - +
49A ASP* 1.3 57.2 + - - +
51A HIS* 2.8 37.4 + - - +
52A VAL* 3.5 6.1 + - - +
57A MET* 3.4 29.6 - - + -
67A HIS* 4.0 4.9 - - + -
140A PHE* 4.2 9.0 - - + -
141A LEU* 4.5 1.1 - - + -
294A VAL* 5.3 2.2 - - + -
501A ACT 2.7 40.0 + - - +
1377A NAD 2.7 22.2 + - - +
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Residues in contact with ASP 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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44A GLY 4.0 2.3 - - - +
46A CYS* 2.9 32.6 + - - +
48A THR* 1.3 77.2 - - - +
50A ASP* 1.3 62.8 + - - +
52A VAL* 3.3 20.2 + - - +
53A ILE* 3.7 8.3 + - - +
65A VAL* 4.3 12.0 - - + +
66A GLY* 2.9 31.7 + - - -
67A HIS* 2.9 24.3 + - - -
140A PHE* 3.8 7.8 - - - -
146A PHE* 3.8 11.3 - - - -
359A PHE* 4.1 18.6 - - + -
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Residues in contact with ASP 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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46A CYS 3.7 0.6 + - - -
47A ARG* 2.9 24.9 + - - +
49A ASP* 1.3 77.2 - - - +
51A HIS* 1.3 66.0 + - - +
52A VAL 3.1 0.2 - - - -
53A ILE* 3.2 12.3 + - - +
54A LYS* 2.8 52.0 + - - +
359A PHE* 3.3 24.4 - - + -
362A LEU* 4.4 6.5 - - + -
363A ASN* 2.9 29.4 + - - +
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Residues in contact with HIS 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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47A ARG* 3.1 28.2 + - + +
48A THR* 2.8 25.6 + - - +
50A ASP* 1.3 76.9 - - - +
52A VAL* 1.3 56.5 + - - +
54A LYS* 3.3 4.5 + - + -
55A GLY 2.9 24.6 + - - -
56A THR* 3.0 29.1 + - - +
57A MET* 3.3 20.5 + - + +
269A ILE 5.1 2.2 + - - -
270A GLY* 5.8 1.0 - - - -
294A VAL* 4.2 18.4 + - + +
1377A NAD 2.8 41.6 + - - -
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Residues in contact with VAL 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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14A LEU* 3.9 20.4 - - + -
17A GLN* 4.1 9.9 - - - +
48A THR 4.1 2.0 - - - +
49A ASP 3.5 11.7 - - - +
50A ASP 3.1 0.2 - - - -
51A HIS* 1.3 76.9 - - - +
53A ILE* 1.3 64.4 + - - +
55A GLY* 3.2 11.8 + - - -
57A MET* 3.9 20.8 - - + +
59A SER* 4.0 22.2 - - - +
61A PHE* 4.0 11.9 - - + -
63A VAL* 4.5 0.4 - - + -
65A VAL* 4.1 10.3 - - + -
140A PHE* 3.4 38.4 - - + -
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Residues in contact with ILE 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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14A LEU* 3.8 22.9 - - + -
17A GLN* 5.1 1.3 - - - +
18A LYS* 2.7 35.5 + - - +
19A GLN 3.7 24.5 - - - +
20A PRO* 5.4 2.2 - - + -
21A PHE* 3.5 32.3 - - + +
49A ASP 4.1 6.7 - - - +
50A ASP* 3.2 15.1 + - - +
52A VAL* 1.3 77.2 - - - +
54A LYS* 1.3 66.5 + - + +
55A GLY 3.2 0.7 + - - -
359A PHE* 3.8 23.6 - - + -
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Residues in contact with LYS 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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18A LYS* 3.8 21.3 - - - +
47A ARG* 5.5 1.3 - - - +
50A ASP* 2.8 45.1 + - - +
51A HIS* 3.8 7.4 - - + +
53A ILE* 1.3 79.6 - - + +
55A GLY* 1.3 60.6 + - - +
56A THR* 3.4 17.8 + - + +
363A ASN* 3.1 23.0 + - - +
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Residues in contact with GLY 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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17A GLN* 3.6 26.2 - - - +
18A LYS* 5.1 0.9 - - - -
51A HIS 2.9 5.3 + - - -
52A VAL 3.7 7.2 - - - -
53A ILE 3.1 3.8 - - - -
54A LYS* 1.3 79.6 - - - +
56A THR* 1.3 62.7 + - - +
57A MET 3.2 10.6 + - - +
297A SER* 4.8 2.9 + - - -
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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