Contacts of the strand formed by residues 45 - 53 (chain E) in PDB entry 6CP3
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 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E GLU* 3.6 36.0 + - + +
39E ILE 3.5 8.7 - - - +
40E LYS* 5.2 5.4 - - + -
41E THR* 4.6 1.1 - - - -
44E GLY* 1.3 75.3 - - - +
46E LEU* 1.3 62.3 + - - +
47E VAL* 4.3 10.7 + - + +
65E ASP* 5.1 7.4 - - - +
99E ILE* 3.8 29.7 + - + +
101E GLU* 3.3 31.4 + - - +
114E ARG* 5.3 8.7 - - - +
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Residues in contact with LEU 46 (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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37E LEU 3.8 0.3 - - - +
38E GLU* 3.6 1.2 - - - -
39E ILE* 2.9 52.3 + - + +
41E THR* 4.0 15.0 - - + -
45E LYS* 1.3 73.2 - - - +
47E VAL* 1.3 66.2 + - - +
48E LEU* 4.0 5.9 + - + +
64E MET 5.3 0.4 - - - +
65E ASP* 3.7 33.7 - - + +
66E GLY 3.4 26.5 - - - +
67E THR* 4.7 6.1 - - + -
68E GLU 5.9 0.7 - - - +
70E LEU* 3.7 41.3 - - + -
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Residues in contact with VAL 47 (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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36E ALA* 4.7 13.0 - - + -
37E LEU 3.4 10.8 - - - +
38E GLU* 5.0 6.5 - - + -
45E LYS* 4.3 16.4 + - + -
46E LEU* 1.3 78.0 - - - +
48E LEU* 1.3 75.7 + - - +
64E MET* 3.2 37.4 + - + +
65E ASP* 4.6 1.7 + - - +
83E ILE* 4.8 15.5 - - + -
99E ILE* 3.7 45.4 - - + +
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Residues in contact with LEU 48 (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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21E VAL* 3.7 31.2 - - + -
23E VAL* 4.3 11.7 - - + -
35E ASN 3.6 0.2 - - - +
36E ALA* 3.5 4.7 - - - -
37E LEU* 2.9 43.4 + - + +
39E ILE* 3.7 26.0 - - + -
46E LEU* 4.6 11.0 - - + +
47E VAL* 1.3 88.1 - - - +
49E GLU* 1.3 61.5 + - - +
50E VAL 4.2 0.4 - - - -
61E THR* 3.5 29.8 - - + +
62E ILE 3.7 11.4 - - - +
63E ALA* 3.8 13.2 - - + -
64E MET* 4.4 1.1 - - - +
67E THR* 5.3 0.7 - - + -
76E VAL* 5.6 0.4 - - + -
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Residues in contact with GLU 49 (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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34E LEU* 3.3 28.8 - - + +
35E ASN 3.7 4.7 - - - +
48E LEU* 1.3 74.3 - - - +
50E VAL* 1.3 65.2 + - - +
51E ALA* 3.2 5.0 + - + +
61E THR* 3.3 15.7 - - - -
62E ILE* 3.4 23.8 + - + +
64E MET* 4.5 6.8 - - - +
83E ILE* 3.9 19.0 - - + +
118E HIS* 2.4 38.5 + - - -
231E ARG* 2.5 41.8 + - - +
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Residues in contact with VAL 50 (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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31E PRO* 4.7 5.4 - - + +
32E ALA 3.7 14.4 - - - +
33E ILE* 3.4 1.7 - - - +
34E LEU* 2.5 35.1 + - - +
35E ASN 3.3 10.3 + - - +
37E LEU* 3.7 26.0 - - + -
49E GLU* 1.3 69.4 - - - +
51E ALA* 1.3 60.3 + - - +
52E GLN 4.4 1.6 - - - +
53E HIS* 3.4 36.8 - - + +
59E VAL* 3.8 22.9 - - + -
60E ARG 4.6 0.2 - - - +
61E THR* 3.7 21.1 - - + -
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Residues in contact with ALA 51 (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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37B GLY* 5.6 1.0 - - - -
38B ASP 5.7 0.5 + - - -
81B ASP* 5.0 2.6 - - - +
33E ILE* 3.4 25.2 - - - +
34E LEU* 5.0 7.0 - - + -
49E GLU* 3.2 7.7 + - + +
50E VAL* 1.3 75.3 - - - +
52E GLN* 1.3 61.6 + - + +
60E ARG 3.1 9.8 + - - +
62E ILE* 4.8 15.5 - - + -
231E ARG* 5.6 2.9 - - - +
272E LEU* 4.4 22.7 - - + -
274E ARG* 4.5 10.4 + - - +
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Residues in contact with GLN 52 (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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36B VAL 4.2 1.8 - - - -
37B GLY* 3.7 23.5 - - - -
38B ASP* 3.8 26.0 + - - +
33E ILE* 5.3 0.9 - - - -
50E VAL* 3.9 1.0 - - - +
51E ALA* 1.3 81.9 - - + +
53E HIS* 1.3 73.7 + - - +
54E LEU* 3.9 21.7 - - + +
59E VAL* 3.5 2.9 - - - +
60E ARG* 2.8 54.0 + - + +
272E LEU* 4.1 27.0 + - + +
274E ARG* 5.2 4.4 + - - +
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Residues in contact with HIS 53 (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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35B ALA* 3.3 12.1 - - - +
36B VAL* 2.8 46.5 + - + +
37B GLY* 4.6 0.3 - - - -
85B LYS* 4.7 0.4 - - - -
86B GLU* 3.4 35.6 - - + +
30E LEU* 5.0 2.5 - - + -
31E PRO 3.1 28.2 + - - -
32E ALA* 3.6 18.4 - - + -
33E ILE* 3.8 10.4 + - + +
50E VAL* 3.4 17.1 - - + +
52E GLN* 1.3 80.6 - - - +
54E LEU* 1.3 58.9 + - - +
55E GLY 3.1 10.5 + - - +
58E THR 3.9 4.7 - - - +
59E VAL* 3.5 21.9 - - + +
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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