Contacts of the strand formed by residues 58 - 65 (chain E) in PDB entry 5EHD
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 HIS 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E LEU* 3.6 29.7 - - + +
53E ALA* 4.1 6.0 - - + +
54E LYS 3.5 14.8 - - - -
56E GLU* 3.0 46.5 + - + -
57E LEU* 1.3 71.4 - - - +
59E ILE* 1.3 63.5 + - - +
60E VAL* 4.2 1.1 - - + -
77E ALA 3.9 0.5 - - - +
78E THR* 3.4 5.0 - - - +
79E LEU* 2.8 45.4 + - + +
102E LEU* 4.3 2.7 - - + -
104E CYS 3.2 4.9 - - - +
105E GLY* 3.5 13.5 - - - -
107E GLY* 3.1 41.2 + - - -
109E VAL* 3.8 14.6 - - + -
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 4.3 6.3 - - - +
50A GLY* 4.2 6.1 - - - -
51A ALA* 3.5 42.4 - - + +
110A HIS* 5.7 1.1 - - + -
57E LEU* 4.6 3.6 - - + -
58E HIS* 1.3 78.6 - - - +
60E VAL* 1.3 60.9 + - - +
75E THR* 4.0 23.8 - - + +
77E ALA 3.4 7.6 - - - +
78E THR* 4.0 15.3 - - + +
102E LEU* 3.4 4.8 - - - -
103E LYS* 2.7 60.5 + - + +
104E CYS* 3.0 21.0 + - - -
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 4.0 5.4 - - + -
47E VAL* 3.7 15.0 - - + -
58E HIS 5.6 0.4 - - - -
59E ILE* 1.3 73.5 - - - +
61E GLU* 1.3 61.9 + - - +
75E THR* 3.5 4.9 - - - -
76E LEU* 2.7 44.7 + - + -
77E ALA 3.1 16.4 + - - +
79E LEU* 5.0 4.7 - - + -
100E LEU* 5.3 0.9 - - + -
101E ARG 3.5 8.1 - - - +
102E LEU* 3.9 12.8 - - + -
109E VAL* 3.6 31.6 - - + -
111E ILE* 3.8 24.9 - - + -
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE 4.0 0.2 + - - -
60E VAL* 1.3 78.4 - - - +
62E ALA* 1.3 70.5 + - - +
73E LYS* 3.7 26.5 - - + +
74E VAL 3.4 13.0 - - - +
75E THR* 4.2 5.5 - - - +
76E LEU* 4.9 0.4 - - - -
99E VAL 3.7 0.3 - - - +
100E LEU* 3.3 6.5 - - - +
101E ARG* 2.7 73.9 + - + +
103E LYS* 3.3 38.2 + - + +
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.1 10.3 - - + +
61E GLU* 1.3 77.3 - - - +
63E GLU* 1.3 61.1 + - - +
72E ILE 3.7 0.5 - - - +
73E LYS* 3.3 2.6 - - - -
74E VAL* 2.8 42.7 + - + +
76E LEU* 3.8 19.5 - - + +
94E ILE* 4.6 6.5 - - + -
98E VAL* 5.8 2.0 - - + -
99E VAL 3.2 5.4 - - - +
100E LEU* 3.6 20.2 - - + -
101E ARG* 5.7 0.2 - - - -
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Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 0.2 - - - -
62E ALA* 1.3 74.7 - - - +
64E ALA* 1.3 62.3 + - - +
71E PRO* 3.7 22.8 - - + +
72E ILE 3.2 15.0 - - - +
73E LYS* 3.8 19.0 + - + +
97E PRO 4.1 0.2 - - - +
98E VAL* 3.2 7.4 - - - -
99E VAL* 2.8 43.8 + - + +
101E ARG* 3.0 37.1 + - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.5 23.1 - - + +
63E GLU* 1.3 77.8 - - - +
65E MET* 1.3 74.2 + - - +
71E PRO* 3.7 1.3 - - - +
72E ILE* 3.0 31.6 + - - +
94E ILE* 4.3 2.9 - - + -
95E THR 4.5 3.1 - - - +
97E PRO 3.7 7.4 - - - +
98E VAL* 3.5 25.6 - - + -
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Residues in contact with MET 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 4.2 10.7 - - + +
18A LEU* 3.6 21.0 + - - +
64E ALA* 1.3 78.9 - - - +
66E ASN* 1.3 64.4 + - - +
69E GLY* 3.1 31.0 - - - +
71E PRO* 3.5 35.4 - - + -
95E THR 5.7 0.2 + - - -
97E PRO* 4.6 14.4 + - + -
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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