Contacts of the helix formed by residues 36 - 46 (chain C) in PDB entry 2E52
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 ARG 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LEU 3.9 0.4 + - - -
35C ASN* 1.3 73.2 - - - +
37C ASN* 1.3 63.4 + - + +
39C VAL* 3.2 9.1 + - - +
40C ILE* 3.1 34.0 + - + +
73C LYS* 6.4 0.4 - - - +
77C LEU* 4.1 46.0 + - + +
176C LEU* 2.8 46.1 + - - +
179C ASP* 3.6 32.5 + - - +
180C LEU 4.7 1.8 + - - +
181C GLU* 4.9 7.5 + - - +
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Residues in contact with ASN 37 (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 ASN* 3.2 22.5 + - - +
36C ARG* 1.3 76.1 - - - +
38C GLU* 1.3 70.2 + - - +
40C ILE* 3.5 13.5 + - + +
41C GLU* 3.1 34.7 + - - +
177C GLN* 6.0 1.3 - - - +
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Residues in contact with GLU 38 (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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4C ALA* 3.9 8.0 + - + +
7C LYS* 3.2 25.6 + - - -
34C LEU* 3.6 25.8 - - + +
35C ASN* 2.8 46.4 + - - +
37C ASN* 1.3 91.2 + - - +
39C VAL* 1.3 64.8 + - - +
41C GLU* 3.3 20.0 + - - +
42C LEU* 2.9 25.6 + - - +
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Residues in contact with VAL 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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31C ILE* 4.4 4.5 - - + +
34C LEU* 3.9 19.3 - - + +
35C ASN 3.0 18.7 + - - +
36C ARG 3.2 7.8 + - - +
38C GLU* 1.3 75.7 - - - +
40C ILE* 1.3 51.9 + - - +
42C LEU* 3.0 9.8 + - - +
43C VAL* 2.8 44.1 + - + +
70C VAL* 4.9 4.7 - - + +
73C LYS* 3.8 39.3 - - + -
74C ALA* 4.6 7.9 - - - +
77C LEU* 3.7 22.7 - - + -
176C LEU* 4.8 2.5 - - + -
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Residues in contact with ILE 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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36C ARG* 3.1 30.7 + - + +
37C ASN* 3.6 11.9 - - + +
39C VAL* 1.3 72.6 - - + +
41C GLU* 1.3 65.2 + - - +
43C VAL* 3.2 9.6 + - - +
44C ARG* 3.0 56.8 + - + +
77C LEU* 5.8 0.2 - - + -
173C ALA* 4.6 8.1 - - + +
176C LEU* 3.7 45.3 - - + +
177C GLN* 4.0 22.7 - - + +
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Residues in contact with GLU 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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3C SER* 4.4 8.3 - - - -
4C ALA* 3.5 27.4 + - + +
5C LEU 5.0 1.2 + - - +
37C ASN* 3.1 22.8 + - - +
38C GLU* 3.4 21.9 - - - +
40C ILE* 1.3 75.2 - - - +
42C LEU* 1.3 62.0 + - - +
44C ARG* 3.3 20.6 + - - +
45C SER* 2.8 29.3 + - - +
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Residues in contact with LEU 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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4C ALA* 3.9 10.1 - - + +
5C LEU* 3.9 33.2 - - + +
8C LEU* 4.2 17.9 - - + -
30C PHE* 4.3 8.7 - - + -
31C ILE* 4.0 11.9 - - + -
34C LEU* 3.5 26.0 - - + -
38C GLU 2.9 14.4 + - - +
39C VAL* 3.0 9.4 + - - +
41C GLU* 1.3 74.3 - - - +
43C VAL* 1.3 59.0 + - - +
45C SER* 3.0 4.0 + - - +
46C ILE* 2.8 37.6 + - + +
70C VAL* 3.8 29.8 - - + -
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Residues in contact with VAL 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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39C VAL* 2.8 22.1 + - + +
40C ILE* 3.2 10.1 + - - +
42C LEU* 1.3 73.8 - - - +
44C ARG* 1.3 61.6 + - - +
45C SER 3.4 0.3 + - - -
46C ILE* 3.9 6.2 + - - +
47C GLY 4.4 0.2 + - - -
70C VAL* 3.6 22.6 - - + +
74C ALA* 4.1 12.8 - - + -
169C TRP* 3.2 52.1 - - + +
172C LEU* 4.1 10.8 - - + -
173C ALA* 3.8 17.3 - - + +
176C LEU* 4.0 20.0 - - + -
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Residues in contact with ARG 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 ILE* 3.0 31.1 + - - +
41C GLU* 3.6 24.1 - - - +
43C VAL* 1.3 75.7 - - - +
45C SER* 1.3 61.2 + - - +
47C GLY* 4.8 2.1 + - - -
48C ILE* 4.4 12.8 - - - +
169C TRP* 5.3 4.9 - - - +
170C GLU* 5.7 1.0 - - - +
173C ALA* 4.0 12.0 - - + +
177C GLN* 3.4 39.6 + - - +
237C GLU* 3.0 38.7 + - - +
240C PHE* 3.4 46.7 - - + -
241C ILE* 5.8 2.4 - - - +
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Residues in contact with SER 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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5C LEU* 4.1 29.8 - - - +
41C GLU* 2.8 17.8 + - - +
42C LEU* 3.0 8.1 + - - -
44C ARG* 1.3 78.4 - - - +
46C ILE* 1.3 64.9 + - - +
47C GLY 3.2 2.9 - - - -
48C ILE* 3.1 14.5 + - - +
63C PHE* 4.3 1.7 - - - -
244C ARG* 3.1 33.3 + - - +
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Residues in contact with ILE 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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5C LEU* 5.7 0.4 - - + -
8C LEU* 3.5 32.5 - - + -
42C LEU* 2.8 21.6 + - + +
43C VAL 3.9 1.3 - - - +
45C SER* 1.3 76.8 - - - +
47C GLY* 1.3 53.8 + - - +
48C ILE 3.2 0.4 - - - -
63C PHE* 3.2 33.6 - - + +
66C ALA* 4.0 17.3 - - + +
67C GLY* 3.6 20.9 - - - +
70C VAL* 4.2 15.3 - - + -
111C SER* 2.6 24.9 + - - +
169C TRP* 3.6 38.4 - - + -
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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