Contacts of the strand formed by residues 60 - 65 (chain E) in PDB entry 3E2A
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 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER 4.3 3.6 - - - +
44C ASP* 5.6 1.0 - - - -
45C SER 4.6 7.1 - - - +
46C ARG* 5.7 0.7 - - - +
35E PRO* 4.5 0.8 - - - +
37E TYR* 3.5 28.5 - - + +
39E TRP* 4.2 23.6 - - + -
49E ALA* 3.6 44.2 - - + +
50E GLU* 3.8 21.8 - - + +
53E THR* 4.1 6.1 - - - +
55E LEU* 3.7 24.9 - - + -
58E GLY* 4.1 12.8 + - - +
59E GLU* 1.3 79.5 - - + +
61E PHE* 1.3 60.7 + - - +
62E VAL* 3.9 16.8 + - + +
94E ILE* 5.2 0.7 - - + -
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Residues in contact with PHE 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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43C SER* 3.2 23.3 - - - -
44C ASP* 3.4 37.0 - - + -
66C VAL* 3.9 9.0 - - + -
35E PRO* 4.3 15.9 - - + +
37E TYR 2.9 13.4 + - - +
38E LEU* 3.3 12.4 - - + +
39E TRP* 2.8 25.1 + - - -
59E GLU 4.1 0.4 + - - -
60E LEU* 1.3 72.5 - - - +
62E VAL* 1.3 58.7 + - - +
80E VAL* 3.6 32.8 - - + -
83E TYR* 3.5 39.5 - + - -
84E ALA* 4.1 11.2 - - + -
88E LEU* 4.3 13.0 - - + -
90E ILE* 5.4 2.2 - - + -
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 2.7 43.4 + - - -
64C ARG* 3.4 44.4 - - - +
38E LEU* 4.9 1.3 - - - -
39E TRP* 3.5 19.7 - - + +
49E ALA* 5.3 1.3 - - + -
50E GLU* 4.0 11.0 - - - +
60E LEU* 3.9 24.2 - - + +
61E PHE* 1.3 77.4 - - - +
63E HIS* 1.3 57.7 + - - +
64E ARG* 3.8 29.8 - - + -
80E VAL* 5.4 0.2 - - - -
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Residues in contact with HIS 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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63C HIS* 4.3 6.5 - + - -
64C ARG 3.2 22.2 + - - -
76C ASN* 3.3 16.5 + - - -
38E LEU* 4.5 1.0 - - + +
39E TRP 2.9 10.7 + - - +
40E ILE* 3.3 15.8 - - + -
41E GLY 2.9 25.5 + - - +
61E PHE 4.3 0.6 + - - -
62E VAL* 1.3 73.0 - - - +
64E ARG* 1.3 65.0 + - - +
65E ASN* 3.0 34.1 + - - +
76E ASN* 3.2 27.6 + - - -
77E CYS* 3.7 24.8 - - - +
80E VAL* 4.0 25.5 - - + +
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Residues in contact with ARG 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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50C GLU* 3.3 24.0 + - - -
60C LEU 5.1 0.8 + - - -
62C VAL* 3.4 43.9 - - - +
63C HIS* 3.0 24.6 + - - -
64C ARG* 3.6 21.9 + - - +
39E TRP* 5.6 1.8 - - + -
41E GLY* 3.2 17.0 - - - +
42E CYS 3.1 14.5 + - - -
43E SER* 3.4 15.6 + - - +
45E SER* 3.2 39.4 + - - -
46E ARG* 4.6 2.4 - - - +
47E VAL 5.8 0.6 + - - -
48E PRO* 5.2 8.9 - - - +
62E VAL* 3.8 20.6 - - + -
63E HIS* 1.3 81.6 - - - +
65E ASN* 1.3 61.1 + - - +
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Residues in contact with ASN 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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63C HIS* 4.6 1.1 - - - -
76C ASN* 3.5 28.8 - - - +
80C VAL* 5.5 0.9 - - - -
40E ILE* 4.6 0.6 - - - +
41E GLY 3.1 4.8 + - - -
42E CYS* 3.2 6.4 - - - -
43E SER* 3.0 25.8 + - - -
63E HIS* 3.0 26.9 + - - +
64E ARG* 1.3 73.6 - - - +
66E VAL* 1.3 67.1 + - - +
67E ALA 3.2 2.3 + - - -
68E ASN* 3.0 8.0 + - - +
69E GLN* 2.8 47.0 + - - +
77E CYS* 4.7 1.0 - - - +
119E TRP* 3.8 11.7 - - + -
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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