Contacts of the helix formed by residues 54 - 65 (chain C) in PDB entry 2IVB
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 PRO 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.7 29.2 - - + -
42C PHE* 4.5 3.1 - - + -
52C ALA 3.7 7.2 - - - +
53C LEU* 1.4 84.8 - - + +
55C ALA* 1.3 61.2 - - - +
56C ASP* 3.3 5.6 - - + +
57C ALA* 3.2 7.7 + - + +
58C ALA* 2.9 25.6 + - - +
155I PRO* 4.1 19.7 - - + -
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Residues in contact with ALA 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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53C LEU 3.7 1.0 + - - -
54C PRO* 1.3 72.7 - - - +
56C ASP* 1.3 65.9 + - - +
58C ALA* 3.3 2.1 + - - +
59C ARG* 2.8 52.4 + - - +
76C GLN* 3.3 31.1 - - - +
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Residues in contact with ASP 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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54C PRO* 3.3 3.2 - - + +
55C ALA* 1.3 78.0 - - - +
57C ALA* 1.3 58.8 + - - +
59C ARG* 2.9 31.5 + - - +
60C LEU* 2.8 36.5 + - + +
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Residues in contact with ALA 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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36C THR* 3.9 16.8 - - - +
38C LEU* 3.8 29.2 - - + -
53C LEU* 4.2 10.5 - - + -
54C PRO* 3.2 16.3 + - + +
56C ASP* 1.3 77.7 - - - +
58C ALA* 1.3 55.3 + - - +
60C LEU* 3.1 9.4 + - - +
61C VAL* 2.8 39.9 + - + +
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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 LEU* 3.9 19.6 - - + +
54C PRO 2.9 16.5 + - - +
55C ALA 3.5 4.5 - - - +
57C ALA* 1.3 77.3 - - - +
59C ARG* 1.3 56.9 + - - +
61C VAL* 3.7 2.8 - - - +
62C GLY* 2.9 27.0 + - - -
72C ILE* 3.7 22.1 - - + +
75C LEU* 4.4 5.9 - - + +
76C GLN* 3.6 25.8 - - + +
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Residues in contact with ARG 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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55C ALA* 2.8 40.4 + - - +
56C ASP* 2.9 33.6 + - - +
58C ALA* 1.3 73.0 - - - +
60C LEU* 1.3 63.6 + - + +
62C GLY* 3.3 1.4 + - - -
63C ALA* 2.9 24.4 + - - +
69C GLU* 5.9 2.0 - - - +
72C ILE* 4.1 22.6 - - + +
76C GLN* 5.3 4.0 + - - +
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Residues in contact with LEU 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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35C GLY 3.6 26.5 - - - +
36C THR* 3.8 22.7 - - - +
56C ASP* 2.8 22.7 + - + +
57C ALA* 3.4 10.3 - - - +
59C ARG* 1.3 71.7 - - - +
61C VAL* 1.3 64.3 + - + +
63C ALA* 3.2 8.1 + - + +
64C LYS* 3.1 33.7 + - + +
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Residues in contact with VAL 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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32C ILE* 3.9 36.1 - - + +
36C THR* 4.2 11.9 - - - +
43C VAL* 4.3 12.3 - - + -
47C LEU* 4.1 10.5 - - + -
53C LEU* 3.7 21.8 - - + -
57C ALA* 2.8 26.8 + - + +
58C ALA 3.7 5.8 - - - +
60C LEU* 1.3 73.0 - - + +
62C GLY* 1.3 57.6 + - - +
64C LYS* 3.4 8.8 + - + +
65C LEU* 3.0 35.9 + - + +
67C LEU* 4.9 0.7 - - + -
75C LEU* 3.9 13.5 - - + -
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Residues in contact with GLY 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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58C ALA 2.9 19.8 + - - -
59C ARG 3.3 2.0 + - - -
61C VAL* 1.3 73.1 - - - +
63C ALA* 1.3 59.4 + - - +
66C ASP* 3.0 9.4 + - - -
67C LEU* 2.8 40.8 + - - +
72C ILE* 3.8 23.3 - - - -
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Residues in contact with ALA 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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59C ARG 2.9 13.6 + - - +
60C LEU* 3.2 10.5 + - + +
62C GLY* 1.3 72.4 - - - +
64C LYS* 1.3 66.7 + - - +
65C LEU 3.1 1.2 + - - -
66C ASP* 3.2 21.6 + - - +
72C ILE* 5.1 0.2 - - - +
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Residues in contact with LYS 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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25C LYS* 3.4 22.5 + - - +
27C LEU* 4.1 14.2 - - + +
31C GLU* 3.1 13.7 + - - -
32C ILE* 2.8 34.1 + - + +
34C ASP 2.6 30.9 + - - -
35C GLY* 4.9 2.4 - - - -
36C THR* 5.2 1.8 + - - +
60C LEU* 3.1 22.2 + - - +
61C VAL* 3.5 13.7 - - - +
63C ALA* 1.3 78.5 - - - +
65C LEU* 1.3 64.2 + - + +
66C ASP 3.4 0.2 - - - -
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Residues in contact with LEU 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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18C ILE* 4.0 24.5 - - + +
21C SER* 2.7 27.2 + - - +
22C LYS* 3.7 41.3 - - + +
25C LYS* 3.7 1.8 - - - +
27C LEU* 4.0 15.9 - - + -
32C ILE* 4.1 26.9 - - + -
47C LEU* 4.5 10.1 - - + -
61C VAL* 3.0 21.1 + - + +
64C LYS* 1.3 78.5 - - + +
66C ASP* 1.3 71.1 + - - +
67C LEU* 3.3 21.2 + - + +
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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