Contacts of the helix formed by residues 38 - 48 (chain C) in PDB entry 1C04
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 ASP 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.4 35.3 + - + +
36C LYS 2.5 7.0 + - - -
37C ARG* 1.3 84.2 - - - +
39C LYS* 1.3 62.7 + - + +
41C ARG* 4.0 1.0 - - - +
42C GLU* 3.0 33.5 + - - +
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Residues in contact with LYS 39 (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 ALA* 4.4 20.8 - - + +
34C THR* 4.2 20.2 - - + +
35C ILE* 2.6 39.1 + - + +
38C ASP* 1.3 75.8 - - + +
40C VAL* 1.3 64.7 + - - +
41C ARG 3.1 1.8 - - - -
42C GLU* 2.9 42.3 + - - +
43C ILE* 3.0 29.9 + - + +
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Residues in contact with VAL 40 (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* 5.0 10.8 - - + -
34C THR* 5.2 9.0 - - + -
35C ILE 3.4 1.5 + - - +
36C LYS* 2.6 32.3 + - + +
39C LYS* 1.3 72.7 - - - +
41C ARG* 1.3 60.8 + - - +
43C ILE* 3.3 8.1 + - + +
44C ALA* 3.0 20.4 + - - +
60C MET* 4.2 11.9 - - + -
63C ILE* 3.9 22.8 - - + +
64C GLU* 3.2 43.1 - - + +
67C ALA* 5.8 2.0 - - + -
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Residues in contact with ARG 41 (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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36C LYS 3.1 4.6 + - - -
37C ARG* 3.8 27.8 + - - +
38C ASP 4.0 2.0 - - - +
39C LYS 3.1 0.4 - - - -
40C VAL* 1.3 77.3 - - - +
42C GLU* 1.3 63.4 + - - +
44C ALA* 2.9 4.5 + - - +
45C GLU* 2.9 43.4 + - - +
56C ILE* 3.6 25.4 - - + +
57C GLU* 3.5 22.0 + - - -
60C MET* 2.8 56.7 - - - +
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Residues in contact with GLU 42 (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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38C ASP 3.0 23.5 + - - +
39C LYS* 2.9 35.1 + - - +
41C ARG* 1.3 75.6 - - + +
43C ILE* 1.3 63.1 + - - +
45C GLU* 2.9 24.1 + - - +
46C LEU* 3.1 13.6 + - - +
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Residues in contact with ILE 43 (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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10C ALA* 5.2 1.1 - - - -
13C LEU* 3.3 46.0 - - + +
14C LEU* 3.9 23.1 - - + +
17C ALA* 3.8 27.8 - - + -
39C LYS* 3.0 25.0 + - + +
40C VAL* 3.8 5.6 - - - +
42C GLU* 1.3 73.7 - - + +
44C ALA* 1.3 54.5 + - - +
45C GLU 3.1 0.3 + - - -
46C LEU* 3.1 6.6 + - - +
47C LYS* 2.8 33.7 + - + +
63C ILE* 4.1 22.2 - - + -
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Residues in contact with ALA 44 (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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40C VAL 3.0 13.1 + - - +
41C ARG 2.9 12.5 + - - +
43C ILE* 1.3 76.6 - - - +
45C GLU* 1.3 59.2 + - - +
47C LYS* 3.9 2.3 - - - -
48C MET* 3.1 23.8 + - - +
51C LEU* 4.2 0.7 - - - +
56C ILE* 4.6 6.1 - - + +
59C ALA* 3.9 25.6 - - + +
60C MET* 3.7 27.8 - - + +
63C ILE* 4.1 11.2 - - + +
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Residues in contact with GLU 45 (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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41C ARG* 2.9 44.2 + - + +
42C GLU* 2.9 13.6 + - - +
44C ALA* 1.3 77.3 - - - +
46C LEU* 1.3 62.7 + - - +
48C MET* 3.1 22.1 + - - +
49C PRO* 4.1 1.9 - - - +
56C ILE* 4.2 24.7 - - + +
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Residues in contact with LEU 46 (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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7C THR* 4.2 21.4 + - + +
8C PRO* 4.9 11.2 - - + -
13C LEU* 3.8 31.6 - - + -
42C GLU 3.1 8.3 + - - +
43C ILE* 3.8 7.2 - - - +
45C GLU* 1.3 78.8 - - - +
47C LYS* 1.3 60.6 + - - +
49C PRO* 3.3 14.6 - - - +
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Residues in contact with LYS 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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7C THR* 2.8 33.2 + - - +
8C PRO 2.8 21.2 + - - +
9C PRO* 3.5 3.4 - - - +
10C ALA* 3.9 9.4 - - - +
13C LEU* 3.9 11.2 - - + -
43C ILE 2.8 22.0 + - - +
44C ALA 4.3 1.6 - - - +
46C LEU* 1.3 72.9 - - - +
48C MET* 1.3 57.3 + - - +
49C PRO* 3.4 0.9 - - - -
50C ASP* 2.9 22.3 + - - +
51C LEU* 3.3 27.6 + - + -
63C ILE* 4.3 12.6 - - + -
9E G 3.0 10.3 - - - +
10E U 1.9 47.0 + - + -
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Residues in contact with MET 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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44C ALA 3.1 8.7 + - - +
45C GLU* 3.1 17.8 + - - +
47C LYS* 1.3 76.2 - - - +
49C PRO* 1.3 68.0 - - + +
51C LEU* 2.9 51.2 + - + +
53C ALA* 3.5 33.7 - - + +
54C ALA 4.5 8.1 - - - +
56C ILE* 5.0 12.3 - - + -
59C ALA* 3.7 24.2 - - - -
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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