Contacts of the helix formed by residues 55 - 71 (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 SER 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C MET* 5.4 0.7 - - - -
53C ALA* 4.0 0.9 - - - +
54C ALA* 1.3 84.1 - - - +
56C ILE* 1.3 66.3 + - - +
57C GLU* 2.9 35.8 - - - +
58C ALA* 2.8 22.6 + - - +
59C ALA* 3.0 11.0 + - - +
61C ARG* 5.0 2.3 + - - -
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Residues in contact with ILE 56 (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* 3.6 46.4 - - + +
44C ALA* 4.8 3.1 - - + -
45C GLU* 4.2 33.7 - - + +
48C MET* 5.0 10.3 - - + -
54C ALA 4.0 0.6 + - - -
55C SER* 1.3 71.7 - - - +
57C GLU* 1.3 63.4 + - - +
59C ALA* 2.8 13.9 + - + +
60C MET* 2.8 33.5 + - + +
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Residues in contact with GLU 57 (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* 3.5 21.0 + - - -
55C SER* 2.9 29.9 - - - +
56C ILE* 1.3 81.2 + - - +
58C ALA* 1.3 54.4 + - - +
60C MET* 3.6 18.1 - - + +
61C ARG* 2.7 45.7 + - - +
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Residues in contact with ALA 58 (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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53C ALA* 4.1 6.5 - - + -
54C ALA* 5.2 0.2 - - + -
55C SER* 2.8 20.0 + - - +
57C GLU* 1.3 74.5 - - - +
59C ALA* 1.3 71.5 + - - +
60C MET 2.9 2.8 + - - -
61C ARG* 3.0 29.3 + - - +
62C MET 3.2 8.3 + - - -
30E A 3.5 32.5 - - - +
31E U 4.0 8.5 - - - +
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Residues in contact with ALA 59 (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* 3.9 14.1 - - + +
48C MET* 3.7 23.6 - - - -
51C LEU* 3.5 26.4 - - + +
53C ALA* 3.6 7.3 - - + +
55C SER 3.0 5.8 + - - +
56C ILE* 2.8 17.2 + - - +
58C ALA* 1.3 77.3 - - - +
60C MET* 1.3 61.9 + - - +
62C MET* 3.4 6.7 + - - +
63C ILE* 3.3 19.4 + - - +
30E A 4.7 0.4 - - - -
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Residues in contact with MET 60 (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* 5.8 2.7 - - + -
37C ARG* 5.4 8.5 - - + -
40C VAL* 4.2 8.3 - - + -
41C ARG* 2.8 54.7 - - - +
44C ALA* 3.7 20.6 - - + -
56C ILE* 2.8 16.4 + - + +
57C GLU* 3.6 20.4 - - + +
58C ALA 2.9 0.6 + - - -
59C ALA* 1.3 72.2 - - - +
61C ARG* 1.3 70.1 + - - +
62C MET 3.0 2.0 - - - -
63C ILE* 2.6 16.6 + - - +
64C GLU* 2.8 33.4 + - - +
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Residues in contact with ARG 61 (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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55C SER* 5.0 1.6 + - - -
57C GLU* 2.7 38.4 + - - +
58C ALA* 3.0 22.2 + - - +
60C MET* 1.3 77.4 - - - +
62C MET* 1.3 57.4 + - - +
64C GLU* 3.7 14.9 + - - +
65C GLY* 2.9 23.9 + - - -
29E C 2.9 14.1 + - - +
30E A 4.3 18.7 + - - +
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Residues in contact with MET 62 (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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51C LEU* 4.5 12.8 - - + -
58C ALA 3.2 3.9 + - - +
59C ALA 3.5 7.4 - - - +
60C MET 2.7 3.8 + - - -
61C ARG* 1.3 68.6 - - - +
63C ILE* 1.3 62.2 + - + +
65C GLY* 2.8 17.2 + - - -
66C THR* 3.0 17.0 + - - -
9E G 2.2 42.2 - - + +
29E C 2.2 55.2 + - + +
30E A 1.9 90.2 - - + +
38E A 5.4 0.2 - - - -
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Residues in contact with ILE 63 (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* 3.9 22.2 - - + -
14C LEU* 3.6 22.2 - - + +
40C VAL* 3.9 18.6 - - + -
43C ILE* 4.1 25.6 - - + -
44C ALA* 4.1 20.0 - - + +
47C LYS* 4.3 21.3 - - + -
51C LEU* 4.6 9.2 - - + -
59C ALA 3.3 13.4 + - - +
60C MET 2.6 10.8 + - - +
62C MET* 1.3 71.9 - - + +
64C GLU* 1.3 64.4 + - - +
66C THR* 2.8 18.1 + - - +
67C ALA 3.0 8.8 + - - -
9E G 5.9 1.1 - - - +
10E U 5.9 0.4 - - - +
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Residues in contact with GLU 64 (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* 4.7 20.2 - - - +
40C VAL* 3.2 32.9 - - + +
60C MET* 2.8 41.9 + - - +
61C ARG* 3.8 12.2 + - - +
63C ILE* 1.3 71.7 - - - +
65C GLY* 1.3 61.9 + - - +
67C ALA* 3.1 20.3 + - - +
68C ARG* 3.1 12.6 + - - +
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Residues in contact with GLY 65 (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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61C ARG 2.9 13.2 + - - -
62C MET* 2.8 12.1 + - - -
64C GLU* 1.3 78.2 - - - +
66C THR* 1.3 57.7 + - - -
68C ARG* 3.6 9.9 + - - +
27E A 3.0 24.6 + - - -
28E U 4.6 6.0 - - - +
29E C 4.9 11.9 - - - -
38E A 5.7 2.4 - - - +
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Residues in contact with THR 66 (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* 3.7 22.4 - - + +
11C ALA* 4.2 3.6 - - - +
14C LEU* 3.9 3.1 - - - -
62C MET 3.2 11.6 + - - -
63C ILE* 2.8 10.0 + - - +
65C GLY* 1.3 71.2 - - - +
67C ALA* 1.3 64.9 + - - +
68C ARG 3.2 0.2 - - - -
69C SER* 2.5 30.6 + - - +
70C MET* 3.2 9.2 - - - +
12E G 3.8 35.9 - - + +
13E G 4.0 9.2 - - - +
38E A 3.8 17.8 + - + +
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Residues in contact with ALA 67 (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* 3.4 30.0 - - + +
40C VAL* 5.8 2.7 - - + -
63C ILE 3.0 6.9 + - - +
64C GLU* 3.3 15.0 - - - +
66C THR* 1.3 79.5 - - - +
68C ARG* 1.3 56.3 + - - +
70C MET* 3.3 7.5 + - - +
71C GLY 2.7 23.0 + - - -
72C ILE* 3.1 31.0 + - + +
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Residues in contact with ARG 68 (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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26C GLU* 3.4 9.6 - - + +
64C GLU 3.1 10.7 + - - +
65C GLY* 3.9 11.0 - - - +
66C THR 3.2 0.6 - - - -
67C ALA* 1.3 72.9 - - - +
69C SER* 1.3 57.0 + - - +
70C MET 2.9 4.5 - - - -
71C GLY* 2.6 24.5 + - - +
72C ILE* 4.6 4.0 + - - -
27E A 4.0 16.2 + - - +
28E U 3.6 31.4 + - - -
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Residues in contact with SER 69 (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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65C GLY 3.6 1.3 + - - -
66C THR* 2.5 25.6 + - - -
68C ARG* 1.3 72.8 - - - +
70C MET* 1.3 53.5 + - - +
12E G 2.1 35.9 + - - -
26E C 1.9 47.9 + - - +
27E A 2.7 45.7 + - - -
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Residues in contact with MET 70 (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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11C ALA* 4.2 9.4 - - - +
14C LEU* 4.1 19.7 - - - -
15C LYS* 3.8 25.6 - - + +
20C ILE* 4.8 1.3 - - + -
23C GLY* 3.6 20.9 - - - +
24C SER* 3.1 20.8 - - - +
26C GLU* 3.6 6.7 - - - -
66C THR 3.2 17.7 - - - +
67C ALA* 3.3 10.1 - - - +
69C SER* 1.3 78.9 + - - +
71C GLY* 1.3 65.7 + - - +
72C ILE* 3.7 22.6 - - + +
13E G 2.6 45.1 - - + +
14E C 4.4 4.3 - - - -
26E C 3.8 0.4 - - - -
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Residues in contact with GLY 71 (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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26C GLU* 3.5 16.8 - - - +
30C ASN* 4.1 14.1 - - - -
31C LYS* 2.9 26.2 + - - +
67C ALA 2.7 3.0 + - - -
68C ARG* 2.6 16.4 + - - -
70C MET* 1.3 80.7 - - - +
72C ILE* 1.3 67.5 + - - +
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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