Contacts of the strand formed by residues 35 - 40 (chain E) in PDB entry 3FKS
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 ASN 35 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 2.7 33.4 + - - +
85B LYS* 5.9 0.6 - - - +
31E PRO* 3.9 13.1 - - + +
32E ALA* 3.0 36.3 + - - +
33E ILE 3.1 4.4 + - - -
34E LEU* 1.3 79.2 - - - +
36E ALA* 1.3 60.3 + - - +
49E GLU* 3.5 1.3 - - - -
50E VAL* 3.0 37.8 + - + +
78E ASP* 4.1 8.0 + - - +
80E GLY 3.1 23.3 + - - -
81E GLY* 3.2 14.3 - - - +
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Residues in contact with ALA 36 (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 3.7 1.0 + - - -
35E ASN* 1.3 74.6 - - - +
37E LEU* 1.3 72.2 + - - +
38E GLU* 6.1 0.2 - - + -
47E VAL* 4.6 7.0 - - + -
48E LEU 3.3 5.8 - - - +
78E ASP* 3.5 3.3 - - - +
79E THR* 3.1 35.3 + - + +
81E GLY 2.9 7.3 + - - -
82E PRO 3.9 0.7 - - - +
83E ILE* 3.7 42.4 - - + +
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Residues in contact with LEU 37 (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 VAL* 4.1 11.4 - - + -
25E PHE* 4.4 16.4 - - + -
31E PRO* 4.5 6.3 - - + -
36E ALA* 1.3 84.6 - - - +
38E GLU* 1.3 71.3 + - - +
47E VAL* 3.3 10.7 - - - +
48E LEU* 2.6 41.5 + - + +
50E VAL* 4.4 9.6 - - + -
61E THR* 3.9 27.8 - - + -
76E VAL* 3.9 21.3 - - + -
77E LEU 3.3 15.9 - - - +
78E ASP* 3.7 19.7 - - + +
79E THR 4.9 0.2 - - - +
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Residues in contact with GLU 38 (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* 6.1 0.2 - - + -
37E LEU* 1.3 81.5 - - - +
39E ILE* 1.3 64.9 + - - +
40E LYS 4.2 1.0 + - - -
45E LYS* 3.7 38.3 + - + +
46E LEU 3.1 7.4 - - - +
47E VAL* 5.1 6.3 - - + -
75E LYS 4.1 0.9 - - - +
76E VAL* 3.8 1.4 - - - -
77E LEU* 3.0 50.0 + - + +
79E THR* 3.3 28.2 - - + +
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Residues in contact with ILE 39 (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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13E VAL* 4.7 7.9 - - + -
21E VAL* 5.2 0.4 - - + -
38E GLU* 1.3 78.3 - - - +
40E LYS* 1.3 69.1 + - + +
41E THR* 3.4 6.8 + - + +
45E LYS* 3.4 5.1 - - - -
46E LEU* 2.8 50.7 + - + +
48E LEU* 3.7 29.4 - - + -
70E LEU* 4.0 24.7 - - + -
74E GLU* 3.3 25.4 - - + +
75E LYS 4.3 9.6 - - - +
76E VAL* 3.8 25.8 - - + -
508T ALA* 6.3 0.9 - - + -
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Residues in contact with LYS 40 (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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38E GLU 4.2 1.6 + - - +
39E ILE* 1.3 75.5 - - + +
41E THR* 1.3 62.8 + - - +
44E GLY 4.1 5.2 - - - +
45E LYS* 4.7 4.0 - - - +
74E GLU* 4.9 2.9 - - - +
75E LYS* 3.4 39.5 - - - +
77E LEU* 6.2 3.2 - - - +
504T GLU 4.7 5.4 - - - +
505T SER* 4.8 12.1 - - - +
507T VAL* 3.1 48.6 - - + +
508T ALA* 3.8 25.0 - - + +
509T THR* 4.4 11.9 + - - +
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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