Contacts of the helix formed by residues 46 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLY 3.5 4.0 + - - +
45C ILE* 1.3 78.4 - - - +
47C ARG* 1.3 68.7 + - - +
48C THR* 3.0 20.9 + - - -
49C ASP* 3.2 22.2 + - - +
50C ASP 3.9 1.9 + - - -
67C HIS* 3.5 14.4 - - + +
68C GLU* 4.1 7.0 - - + +
174C CYS* 3.7 4.0 - - - -
362C LEU* 4.3 1.8 - - - +
369C ARG* 3.5 22.8 - - - +
376C ZN 2.2 37.7 - - - -
505C ACT 3.5 0.4 - - - -
3377C NAD 4.0 9.0 - - - -
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE 4.0 1.4 + - - -
46C CYS* 1.3 74.4 - - - +
48C THR* 1.3 61.4 + - - +
50C ASP* 3.1 29.8 + - - +
51C HIS* 3.2 25.9 + - - +
54C LYS* 4.9 3.0 - - - +
269C ILE 5.3 1.3 - - - +
362C LEU* 3.4 50.0 + - + +
363C ASN* 3.2 25.6 + - - +
369C ARG* 4.1 0.8 - - - +
3377C NAD 3.2 65.1 + - - +
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C CYS* 3.0 8.7 - - - -
47C ARG* 1.3 74.8 - - - +
49C ASP* 1.3 57.8 + - - +
51C HIS* 2.8 38.0 + - - +
52C VAL* 3.5 5.9 + - - +
57C MET* 3.2 34.3 - - + -
67C HIS* 4.0 5.2 - - - -
140C PHE* 4.4 4.3 - - + -
141C LEU* 4.6 0.9 - - + -
294C VAL* 5.0 2.5 - - + -
505C ACT 2.6 39.2 + - - +
3377C NAD 2.7 23.7 + - - +
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY 4.2 2.3 - - - +
45C ILE 4.2 0.2 - - - -
46C CYS 3.2 28.0 + - - +
48C THR* 1.3 76.8 - - - +
50C ASP* 1.3 62.4 + - - +
52C VAL* 3.2 19.9 + - - +
53C ILE* 3.5 9.9 + - - +
65C VAL* 4.3 11.6 - - + +
66C GLY* 3.1 23.6 + - - -
67C HIS* 2.9 30.1 + - - -
68C GLU 5.7 0.2 + - - -
140C PHE* 3.2 11.2 - - - -
146C PHE* 3.7 12.7 - - - -
359C PHE* 4.1 18.6 - - + -
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C CYS 3.9 0.2 + - - -
47C ARG* 3.1 32.5 + - - +
48C THR 3.0 0.8 - - - -
49C ASP* 1.3 77.4 - - - +
51C HIS* 1.3 59.8 + - + +
53C ILE* 3.2 14.8 + - - +
54C LYS* 2.9 63.6 + - - +
359C PHE* 3.3 22.9 - - + +
362C LEU* 4.6 6.1 - - + -
363C ASN* 3.1 27.8 + - - +
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Residues in contact with HIS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ARG* 3.2 29.3 + - + +
48C THR* 2.8 22.3 + - - +
50C ASP* 1.3 79.5 - - - +
52C VAL* 1.3 48.6 + - - +
54C LYS* 3.1 4.2 + - + -
55C GLY 2.6 32.1 + - - -
56C THR* 2.9 30.2 + - - +
57C MET* 3.3 19.4 - - + +
269C ILE 5.2 1.6 + - - -
270C GLY* 5.8 1.3 - - - -
294C VAL* 4.2 20.0 - - + +
3377C NAD 3.0 40.1 + - - -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.5 3.1 - - + -
17C GLN* 4.7 1.4 - - - +
18C LYS 4.8 0.2 + - - -
48C THR 4.0 1.1 - - - +
49C ASP 3.2 10.7 + - - +
51C HIS* 1.3 75.5 - - - +
53C ILE* 1.3 63.4 + - - +
55C GLY* 3.2 11.6 + - - -
57C MET* 3.5 22.9 - - + +
59C SER* 3.6 27.4 - - - +
61C PHE* 4.0 28.2 - - + -
63C VAL* 4.3 1.3 - - + -
65C VAL* 3.9 17.9 - - + -
140C PHE* 3.3 37.7 - - + -
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.2 20.4 - - + -
17C GLN* 5.8 0.2 - - - +
18C LYS* 2.9 39.8 + - - +
19C GLN 3.8 21.8 - - - +
20C PRO* 5.5 1.8 - - + -
21C PHE* 3.4 32.8 - - + -
49C ASP 3.6 10.3 - - - +
50C ASP* 3.2 13.7 + - - +
51C HIS 3.2 0.4 - - - -
52C VAL* 1.3 75.4 - - - +
54C LYS* 1.3 64.5 + - + +
61C PHE* 5.9 0.7 - - - -
359C PHE* 3.5 27.4 - - + -
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.1 29.2 - - - +
47C ARG* 5.1 2.9 - - - +
50C ASP* 2.9 38.2 + - - +
51C HIS* 3.6 6.5 - - + +
53C ILE* 1.3 80.4 - - + +
55C GLY* 1.3 60.5 + - - +
56C THR* 3.4 17.0 - - + +
363C ASN* 2.8 34.9 + - - +
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Residues in contact with GLY 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLN* 3.8 27.9 + - - -
51C HIS 2.6 12.4 + - - -
52C VAL 3.2 12.3 + - - -
53C ILE 3.3 0.2 - - - -
54C LYS* 1.3 76.1 - - - +
56C THR* 1.3 56.4 + - - +
57C MET 3.2 11.2 + - - +
61C PHE* 6.3 0.2 - - - -
297C SER* 3.8 7.1 + - - -
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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