Contacts of the helix formed by residues 46 - 55 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K ALA* 4.2 5.8 - - + +
11K GLU* 3.2 20.8 + - - +
13K GLU 2.7 20.7 + - - +
15K VAL* 4.4 7.9 - - + -
44K VAL 3.4 1.8 + - - -
45K PRO* 1.3 70.7 - - - +
47K TRP* 1.3 63.5 + - - +
49K ALA* 3.3 9.0 + - + +
50K ILE* 3.0 41.0 + - + +
95K LEU* 3.8 34.5 - - + +
98K LEU* 3.4 31.6 - - + -
99K LEU* 4.6 17.0 - - + -
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Residues in contact with TRP 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ILE* 4.6 7.4 - - + -
80I MSE 3.7 41.5 - - + +
81I GLU* 4.0 22.9 - - + -
84I ARG* 3.4 49.4 - - - +
11K GLU* 3.1 44.7 + - + +
12K LYS* 4.6 3.0 - - - +
28K LEU* 4.0 28.3 - - + -
45K PRO* 3.4 23.1 - - + +
46K LEU* 1.3 78.1 - - - +
48K LEU* 1.3 94.3 + - + +
50K ILE* 3.4 7.9 + - - +
51K ASN* 3.1 21.3 + - - +
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Residues in contact with LEU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ILE* 3.8 30.5 - - + -
80I MSE 5.5 0.2 - - - -
26K ILE* 4.7 1.8 - - + -
33K LEU* 3.5 31.6 - - + -
36K PHE* 4.7 9.2 - - + -
44K VAL* 3.7 13.0 - - + -
45K PRO* 3.0 11.5 + - + +
47K TRP* 1.3 99.9 - - + +
49K ALA* 1.3 64.5 + - - +
51K ASN* 3.0 6.3 + - + +
52K LEU* 2.9 59.4 + - + +
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Residues in contact with ALA 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 4.7 7.0 - - + -
17K ILE* 3.6 29.4 - - + -
44K VAL* 3.6 8.4 - - + +
45K PRO 3.1 9.8 + - - +
46K LEU* 3.6 14.6 - - + +
48K LEU* 1.3 79.9 - - - +
50K ILE* 1.3 63.2 + - - +
52K LEU* 3.9 5.4 - - - +
53K LYS* 2.9 25.4 + - - +
58K CYS* 4.2 2.9 - - - -
60K LEU* 3.7 13.3 - - + +
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Residues in contact with ILE 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K GLU* 5.0 4.7 - - - +
46K LEU* 3.0 40.5 + - + +
47K TRP* 3.8 6.5 - - - +
48K LEU 3.3 0.2 - - - -
49K ALA* 1.3 75.9 - - + +
51K ASN* 1.3 62.3 + - - +
53K LYS* 3.4 6.3 + - - +
54K GLN* 3.0 34.3 + - - +
60K LEU* 5.8 1.3 - - + -
98K LEU* 3.5 39.3 - - + +
99K LEU* 5.6 3.8 - - + -
102K HIS* 3.2 37.5 - - + -
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Residues in contact with ASN 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I ILE* 4.8 4.2 - - - +
80I MSE 3.3 38.1 - - + +
145J SER 4.3 11.1 - - - +
47K TRP 3.1 12.6 + - - +
48K LEU* 3.0 9.7 + - - +
50K ILE* 1.3 74.2 - - - +
52K LEU* 1.3 76.4 + - - +
54K GLN* 2.8 26.1 + - - +
55K ARG* 2.8 50.7 + - - +
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Residues in contact with LEU 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I LEU* 5.1 8.3 - - + -
77I ILE* 4.2 13.7 - - + -
17K ILE* 3.9 24.5 - - + -
21K PHE* 4.2 26.9 - - + -
36K PHE* 4.4 9.0 - - + -
44K VAL* 5.6 1.3 - - + -
48K LEU* 2.9 46.9 + - + +
49K ALA* 3.9 2.2 - - - +
51K ASN* 1.3 80.0 - - - +
53K LYS* 1.3 60.8 + - - +
55K ARG* 3.2 13.4 + - - +
56K GLN 2.9 4.0 + - - -
57K LYS* 2.8 32.9 + - + -
58K CYS* 3.6 15.3 - - - -
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Residues in contact with LYS 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ALA 2.9 19.8 + - - +
50K ILE* 3.5 7.9 - - - +
52K LEU* 1.3 77.6 - - - +
54K GLN* 1.3 58.9 + - + +
56K GLN* 2.8 25.0 + - - +
58K CYS* 3.7 19.0 - - - +
60K LEU* 3.2 24.7 - - + -
102K HIS* 3.2 22.5 + - + +
103K ALA* 3.9 7.0 - - + -
105K ASP* 2.8 33.6 + - - -
106K ASN* 3.1 27.1 - - - +
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Residues in contact with GLN 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J LYS* 4.4 14.8 + - - +
145J SER 4.1 24.4 + - - -
50K ILE* 3.0 42.4 + - + +
51K ASN* 2.8 16.5 + - - +
53K LYS* 1.3 73.2 - - - +
55K ARG* 1.3 62.5 + - + +
56K GLN* 3.3 13.0 + - - +
102K HIS* 4.7 21.5 + - + +
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Residues in contact with ARG 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ASP* 6.1 0.6 - - - +
73I LEU* 3.6 32.7 - - - +
76I SER* 3.4 25.8 + - - -
77I ILE* 5.9 1.1 - - - +
80I MSE 5.1 3.2 - - - +
51K ASN* 2.8 48.1 + - - +
52K LEU* 3.5 14.7 - - - +
53K LYS 3.0 0.2 - - - -
54K GLN* 1.3 74.6 - - + +
56K GLN* 1.3 74.1 + - - +
57K LYS* 3.4 22.8 + - + +
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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