Contacts of the strand formed by residues 31 - 36 (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 LYS 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PHE* 4.3 13.2 - - - -
4F GLU* 5.9 0.7 - - - -
29H HIS* 2.8 38.0 + - - +
30H GLU* 1.3 78.5 + - - +
32H LEU* 1.3 61.5 + - - +
33H PRO* 4.6 1.7 - - - +
67H GLU* 3.6 36.2 - - + +
68H LEU 3.1 5.2 - - - +
69H PRO* 3.6 31.2 - - - +
89H PRO* 4.9 3.6 - - - +
119H PHE* 3.9 10.9 - - - -
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Residues in contact with LEU 32 (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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31H LYS* 1.3 75.3 - - - +
33H PRO* 1.3 79.4 - - + +
34H VAL* 3.6 1.4 + - + +
67H GLU* 3.1 9.1 - - - +
68H LEU* 2.7 33.3 + - + +
70H LEU* 4.0 6.7 - - + -
73H ALA* 3.9 10.5 - - + -
86H VAL* 3.3 34.5 - - + -
87H GLU 4.0 3.1 - - - +
89H PRO* 3.9 9.4 - - + -
119H PHE* 4.0 12.3 - - + -
123H LEU* 3.4 31.2 - - + -
126H PHE* 3.5 28.3 - - + -
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Residues in contact with PRO 33 (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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31H LYS 4.6 1.1 - - - +
32H LEU* 1.3 89.1 - - + +
34H VAL* 1.3 60.3 + - - +
65H LYS* 6.3 3.4 - - - -
66H LEU 3.7 0.2 - - - +
67H GLU* 3.0 19.3 - - - +
86H VAL* 3.7 4.3 - - - +
87H GLU* 3.1 64.2 + - + +
88H LEU 5.0 0.9 - - - +
89H PRO* 4.1 19.3 - - + -
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Residues in contact with VAL 34 (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* 4.6 1.8 - - + +
33H PRO* 1.3 75.1 - - - +
35H ARG* 1.3 63.8 + - - +
36H THR* 4.7 0.7 - - + +
65H LYS* 3.3 7.6 - - - +
66H LEU* 2.6 63.5 + - + +
68H LEU* 3.2 36.3 - - + +
73H ALA* 5.5 1.3 - - + -
84H LEU* 3.3 37.2 - - + -
85H SER 2.8 22.9 - - - +
86H VAL* 4.2 6.3 - - + -
87H GLU* 6.0 0.2 - - - -
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Residues in contact with ARG 35 (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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34H VAL* 1.3 81.1 - - - +
36H THR* 1.3 67.1 + - - +
37H GLU* 2.8 41.3 + - - +
63H GLY* 3.7 22.0 - - - +
64H SER 3.1 11.0 - - - +
65H LYS* 4.5 13.2 - - + -
85H SER* 2.9 41.8 + - - +
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Residues in contact with THR 36 (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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34H VAL* 4.2 1.5 - - + -
35H ARG* 1.3 70.5 - - - +
37H GLU* 1.3 63.6 + - - +
38H THR 3.3 16.2 + - - -
40H MSE 4.4 20.4 - - - -
60H VAL* 4.5 7.1 - - + +
61H PRO 3.1 6.8 + - - -
62H GLN* 3.6 1.7 - - - +
63H GLY* 3.0 37.6 + - - -
64H SER 2.9 12.2 + - - -
66H LEU* 3.1 30.1 - - + -
68H LEU* 6.4 0.9 - - + -
83H ILE 3.5 7.4 - - - +
84H LEU* 4.3 5.2 - - + +
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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