Contacts of the helix formed by residues 46 - 55 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLY 3.7 1.6 + - - -
45B ILE* 1.3 76.5 - - - +
47B ARG* 1.3 63.9 + - - +
48B THR* 3.6 14.8 - - - -
49B ASP* 2.8 42.8 + - - +
50B ASP* 3.6 2.6 + - - +
67B HIS* 3.5 5.4 - - + +
68B GLU* 4.2 6.3 - - + +
174B CYS* 3.9 1.6 - - - -
362B LEU* 4.6 2.2 - - - -
369B ARG* 3.6 23.8 - - - +
376B ZN 2.3 37.0 - - - -
506B ACT 3.8 1.3 - - - -
2377B NAD 3.9 11.4 - - - -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE 4.2 0.8 + - - -
46B CYS* 1.3 71.2 - - - +
48B THR* 1.3 65.8 + - - +
49B ASP 3.2 0.2 - - - -
50B ASP* 3.0 30.9 + - - +
51B HIS* 3.1 40.7 + - - +
54B LYS* 4.9 2.0 - - - +
269B ILE 5.1 2.0 - - - +
362B LEU* 3.9 37.3 + - + +
363B ASN* 3.0 18.8 + - - +
369B ARG* 4.6 0.4 - - - +
2377B NAD 2.9 78.7 + - - +
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B CYS* 3.1 7.2 + - - -
47B ARG* 1.3 77.1 - - - +
49B ASP* 1.3 57.8 + - - +
51B HIS* 2.8 29.1 + - - +
52B VAL* 3.4 7.6 + - - +
57B MET* 3.5 27.4 - - + -
67B HIS* 4.1 5.6 - - + -
140B PHE* 4.2 12.3 - - + -
141B LEU* 4.6 1.3 - - + -
294B VAL* 5.1 1.6 - - + -
506B ACT 2.6 43.2 + - - +
2377B NAD 2.7 24.0 + - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY 4.3 1.6 - - - +
45B ILE* 4.0 0.3 - - - -
46B CYS* 2.8 40.6 + - - +
48B THR* 1.3 75.2 - - - +
50B ASP* 1.3 62.7 - - - +
52B VAL* 3.4 23.2 + - - +
53B ILE* 3.7 9.4 + - - +
65B VAL* 4.2 12.8 - - + +
66B GLY* 3.1 25.3 + - - -
67B HIS* 3.0 24.7 + - - -
68B GLU* 5.7 0.3 + - - +
140B PHE* 3.8 5.5 - - - -
146B PHE* 4.1 6.8 - - - -
359B PHE* 3.8 19.1 - - + -
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B CYS 3.6 1.4 + - - +
47B ARG* 3.0 40.8 + - - +
48B THR 3.1 0.6 - - - -
49B ASP* 1.3 78.8 - - - +
51B HIS* 1.3 60.5 + - - +
53B ILE* 3.1 16.3 + - - +
54B LYS* 2.8 56.6 + - - +
359B PHE* 3.3 27.5 - - + +
362B LEU* 4.7 2.9 - - + -
363B ASN* 3.1 16.2 + - - +
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 3.1 31.6 + - + +
48B THR* 2.8 18.3 + - - +
50B ASP* 1.3 75.0 - - - +
52B VAL* 1.3 65.3 + - - +
54B LYS* 3.1 7.0 + - + -
55B GLY 2.8 19.4 + - - -
56B THR* 3.1 29.7 + - - +
57B MET* 3.4 18.3 - - + +
269B ILE 4.8 3.0 + - - -
270B GLY* 5.5 3.0 + - - -
294B VAL* 4.2 21.6 + - + +
2377B NAD 3.1 43.4 + - - -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.2 4.9 - - + -
17B GLN* 4.2 8.5 - - - +
48B THR 3.9 4.9 - - - +
49B ASP 3.6 8.5 - - - +
50B ASP 3.2 0.6 - - - -
51B HIS* 1.3 75.3 - - - +
53B ILE* 1.3 64.4 + - - +
55B GLY* 3.0 14.0 + - - -
57B MET* 3.5 20.2 - - + +
59B SER* 4.0 15.3 - - - +
61B PHE* 3.8 28.2 - - + -
63B VAL* 4.5 0.4 - - + -
65B VAL* 4.0 18.6 - - + -
140B PHE* 3.5 39.5 - - + -
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.9 27.4 - - + -
16B GLU 6.0 0.2 - - - -
17B GLN* 5.2 1.3 - - - +
18B LYS* 2.8 33.9 + - - +
19B GLN 4.1 18.8 - - - +
20B PRO* 6.0 0.4 - - + -
21B PHE* 3.7 30.3 - - + -
49B ASP 3.7 5.4 + - - +
50B ASP* 3.1 28.7 + - - +
52B VAL* 1.3 78.8 - - - +
54B LYS* 1.3 71.9 + - + +
55B GLY 3.1 1.6 + - - -
359B PHE* 3.7 15.3 - - + -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LYS* 3.7 23.3 - - - -
47B ARG* 5.3 1.1 - - - +
50B ASP* 2.8 54.5 + - - +
51B HIS* 3.1 8.7 + - + +
53B ILE* 1.3 82.6 - - + +
55B GLY* 1.3 58.8 + - - +
56B THR* 3.4 20.3 + - + +
363B ASN* 3.5 17.9 + - - +
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 3.5 32.3 + - - -
18B LYS* 5.3 0.2 - - - -
51B HIS 2.8 4.4 + - - -
52B VAL 3.0 11.8 + - - -
53B ILE 3.1 1.0 + - - -
54B LYS* 1.3 77.9 - - - +
56B THR* 1.3 57.6 + - - +
57B MET 3.3 13.2 + - - +
297B SER* 3.8 6.8 + - - -
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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