Contacts of the helix formed by residues 70 - 77 (chain H) 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 70 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLU* 5.0 1.6 - - - +
27H MSE 3.9 18.2 - - - -
28H SER* 3.2 16.3 + - - +
30H GLU 2.8 17.2 + - - +
32H LEU* 4.0 13.0 - - + -
68H LEU 3.4 2.3 + - - -
69H PRO* 1.3 69.8 - - - +
71H TRP* 1.3 63.0 + - - +
73H ALA* 3.4 3.3 + - - -
74H LYS* 3.0 28.8 + - + +
119H PHE* 3.9 23.6 - - + -
122H GLN* 3.6 32.3 - - + +
123H LEU* 4.8 4.9 - - + +
126H PHE* 3.3 35.9 - - + -
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Residues in contact with TRP 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MSE 3.9 12.1 - - - -
2F PHE* 3.9 25.1 - + - -
3F CYS* 3.9 13.9 - - - -
67F CYS* 3.8 20.4 - - + -
68F SER* 4.1 4.0 - - - -
71F ARG* 3.1 65.0 - - + +
74F ARG* 5.6 1.6 - - - +
17H GLU* 5.8 0.4 - - - -
28H SER* 2.9 36.3 + - - +
29H HIS* 3.4 13.1 - - - -
69H PRO* 2.8 26.9 + - + +
70H LEU* 1.3 73.6 - - - +
72H LEU* 1.3 103.5 + - + -
74H LYS* 3.1 9.3 + - - +
75H GLY* 3.1 19.1 + - - -
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PHE* 5.1 2.5 - - + -
64F PHE* 3.8 36.6 - - + +
67F CYS* 3.7 16.8 - - + -
68H LEU* 3.2 33.7 - - + -
69H PRO* 2.8 24.3 + - + +
71H TRP* 1.3 111.5 - - + +
73H ALA* 1.3 58.9 + - - +
75H GLY* 3.2 2.1 + - - +
76H LEU* 3.2 38.9 + - + +
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Residues in contact with ALA 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 3.9 27.8 - - + -
34H VAL* 5.5 1.1 - - + -
68H LEU* 4.2 25.1 - - + -
69H PRO 3.1 10.6 + - - +
70H LEU* 3.9 6.5 - - - +
72H LEU* 1.3 74.0 - - - +
74H LYS* 1.3 62.5 + - - +
77H PHE* 3.1 31.2 + - - +
84H LEU* 4.2 10.1 - - + +
86H VAL* 4.6 2.2 - - + -
126H PHE* 3.5 3.9 - - + -
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Residues in contact with LYS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H GLU* 3.7 24.0 + - - -
17H GLU* 4.8 8.5 + - - +
70H LEU* 3.0 25.3 + - + +
71H TRP* 3.5 8.1 - - - +
73H ALA* 1.3 78.5 - - - +
75H GLY* 1.3 63.9 + - - +
77H PHE* 3.8 12.2 + - - +
122H GLN* 4.0 10.1 - - - +
125H HIS* 3.4 39.5 - - + +
126H PHE* 4.0 16.4 - - + -
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Residues in contact with GLY 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F CYS* 3.7 18.7 - - - -
71H TRP 3.1 11.9 + - - -
72H LEU 3.2 4.2 + - - -
73H ALA 3.2 0.4 - - - -
74H LYS* 1.3 79.9 - - - +
76H LEU* 1.3 64.6 + - - +
77H PHE 4.1 3.1 - - - +
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F PRO 4.7 0.4 - - - +
63F LYS* 3.9 33.2 - - + +
64F PHE* 3.8 19.5 - - + +
67F CYS* 3.9 19.3 - - - -
40H MSE 4.5 8.1 - - + -
68H LEU* 4.7 1.1 - - + -
72H LEU* 3.2 42.4 + - + +
75H GLY* 1.3 74.6 - - - +
77H PHE* 1.3 67.8 + - - +
78H ASP* 3.8 5.0 + - - +
83H ILE* 3.8 33.6 - - + +
84H LEU* 3.3 27.1 - - + +
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Residues in contact with PHE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ALA 3.1 21.8 + - - +
74H LYS 4.0 10.8 - - - +
75H GLY 3.5 3.9 - - - +
76H LEU* 1.3 81.8 - - - +
78H ASP* 1.3 87.1 + - - +
79H ASN* 3.6 17.5 - - - -
81H ARG* 3.5 32.5 - - + -
84H LEU* 3.2 22.9 - - + +
86H VAL* 4.6 15.0 - - + -
125H HIS 4.1 6.5 - - - -
126H PHE* 3.3 60.3 - + + -
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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