Contacts of the helix formed by residues 46 - 55 (chain C) in PDB entry 2EHO
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 LEU 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ALA 3.9 4.3 - - - +
11C GLU* 3.7 13.1 + - - -
13C GLU* 2.8 19.8 + - + +
15C VAL* 4.1 12.3 - - + +
44C VAL 3.7 1.0 + - - -
45C PRO* 1.3 71.1 - - - +
47C TRP* 1.3 56.4 + - - +
49C ALA* 3.8 10.5 - - + -
50C ILE* 2.9 46.6 + - + +
95C LEU* 3.7 38.1 - - + -
98C LEU* 3.7 27.6 - - + -
99C LEU* 4.0 20.6 - - + -
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Residues in contact with TRP 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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77A ILE* 3.9 17.3 - - + -
80A MSE 3.5 39.0 - - + +
81A GLU* 3.9 25.1 - - + -
84A ARG* 3.6 37.1 - - - +
11C GLU* 2.9 46.2 + - + +
12C LYS* 4.7 1.4 - - - +
28C LEU* 4.3 17.3 - - + -
45C PRO* 2.9 24.4 + - + +
46C LEU* 1.3 75.1 - - - +
48C LEU* 1.3 103.4 + - + +
50C ILE* 3.5 4.4 + - - +
51C ASN* 2.9 22.3 + - - +
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Residues in contact with LEU 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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77A ILE* 3.3 40.4 - - + -
26C ILE* 4.4 3.4 - - + -
33C LEU* 3.2 34.1 - - + -
36C PHE* 4.8 4.7 - - + -
44C VAL* 3.3 15.5 - - + -
45C PRO* 2.9 11.2 + - + +
47C TRP* 1.3 100.9 - - + +
49C ALA* 1.3 65.6 + - - +
51C ASN* 2.9 6.4 + - - +
52C LEU* 2.8 50.1 + - + +
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Residues in contact with ALA 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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15C VAL* 3.4 32.5 - - + -
17C ILE* 3.7 10.3 - - + -
44C VAL* 3.9 8.3 - - + +
45C PRO 2.9 7.0 + - - +
46C LEU* 3.6 8.5 - - + +
48C LEU* 1.3 77.5 - - - +
50C ILE* 1.3 52.8 + - - +
52C LEU* 3.1 5.8 + - - +
53C LYS* 2.7 37.3 + - - +
58C CYS* 4.0 1.6 - - - -
60C LEU* 3.5 18.2 - - + -
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Residues in contact with ILE 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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144B LYS 5.9 2.5 - - - +
11C GLU* 5.3 2.7 - - - +
46C LEU* 2.9 44.8 + - + +
47C TRP* 3.9 5.4 - - - +
49C ALA* 1.3 75.6 - - + +
51C ASN* 1.3 60.0 + - - +
53C LYS* 3.7 7.0 - - - +
54C GLN* 2.9 44.2 + - - +
60C LEU* 4.7 2.9 - - + -
98C LEU* 3.4 41.5 - - + +
99C LEU* 5.1 3.8 - - + -
102C HIS* 3.5 28.0 - - + +
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Residues in contact with ASN 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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77A ILE* 4.2 6.5 - - - +
80A MSE 3.0 43.8 - - + +
145B SER* 4.8 5.9 + - - -
47C TRP 2.9 14.2 + - - +
48C LEU* 2.9 10.6 + - - +
50C ILE* 1.3 76.4 - - - +
52C LEU* 1.3 72.9 + - - +
54C GLN* 3.3 10.9 + - - +
55C ARG* 2.8 70.5 + - - +
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Residues in contact with LEU 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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73A LEU* 4.4 12.3 - - + -
77A ILE* 4.2 7.4 - - + -
17C ILE* 5.2 6.5 - - + -
21C PHE* 4.0 29.8 - - + -
36C PHE* 4.7 11.9 - - + -
44C VAL* 5.4 1.8 - - + -
48C LEU* 2.8 52.0 + - + +
49C ALA* 3.7 2.7 - - - +
51C ASN* 1.3 85.7 - - - +
53C LYS* 1.3 63.6 + - - +
55C ARG* 3.1 14.3 + - - -
57C LYS* 3.0 29.0 + - + +
58C CYS* 3.6 21.1 - - + -
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Residues in contact with LYS 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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49C ALA 2.7 21.2 + - - +
50C ILE* 3.7 7.0 - - - +
51C ASN 3.2 0.2 - - - -
52C LEU* 1.3 72.4 - - - +
54C GLN* 1.3 58.2 + - - +
56C GLN* 3.0 19.6 + - - -
58C CYS* 3.4 25.1 + - - +
59C ARG* 4.6 2.0 - - - +
60C LEU* 3.5 28.3 - - + +
102C HIS* 3.6 23.1 - - + +
103C ALA* 3.6 16.4 - - + +
105C ASP* 4.1 13.9 + - - +
106C ASN* 2.8 38.4 + - - +
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Residues in contact with GLN 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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144B LYS 4.9 4.9 + - - +
145B SER* 3.9 22.0 + - - +
50C ILE* 2.9 29.3 - - - +
51C ASN* 3.3 13.5 + - - +
53C LYS* 1.3 75.9 - - + +
55C ARG* 1.3 58.5 + - + +
56C GLN* 2.7 15.0 + - - +
102C HIS* 3.0 39.2 + - + +
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Residues in contact with ARG 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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73A LEU* 4.0 19.7 - - - +
76A SER* 2.9 32.2 + - - -
80A MSE 5.6 0.2 - - - -
51C ASN* 2.8 58.1 + - - +
52C LEU* 3.1 9.8 + - - +
54C GLN* 1.3 75.1 - - + +
56C GLN* 1.3 61.3 + - - +
57C LYS* 2.9 36.9 + - + +
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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