Contacts of the strand formed by residues 53 - 57 (chain D) in PDB entry 1FSK
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 ILE 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ASN* 3.4 2.8 - - - -
44D ILE* 2.8 56.1 + - + -
45D GLU* 2.9 23.4 + - + +
51D GLY 2.8 30.5 - - - +
52D THR* 1.3 73.4 - - - +
54D LYS* 1.3 59.3 + - - +
68D LYS* 4.8 12.1 - - + -
69D ASP 3.7 5.8 - - - +
70D ARG* 4.0 18.8 - - + -
86D ILE* 4.6 4.7 - - + -
31F SER 4.7 6.5 - - - +
33F TRP* 3.4 24.9 - - + +
52F PHE* 4.0 20.9 - - + -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU 5.2 5.3 + - - -
27D ASP* 3.8 38.9 + - - +
41D VAL* 4.1 15.7 - - + -
42D GLU 3.2 7.9 - - - +
43D ASN* 3.8 21.4 + - - +
44D ILE* 4.3 2.7 - - - -
48D GLY* 4.4 13.1 + - - -
52D THR* 4.0 19.3 - - + +
53D ILE* 1.3 76.4 - - - +
55D LYS* 1.3 59.2 + - - +
56D ILE* 3.8 7.0 - - + +
67D VAL 3.6 0.9 - - - +
68D LYS* 3.0 27.3 - - - +
69D ASP* 3.1 20.3 + - + +
71D VAL* 4.0 19.9 - - + +
81D TYR* 5.5 2.8 + - - +
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER 3.8 0.9 - - - +
41D VAL* 3.5 2.4 - - - -
42D GLU* 2.8 50.6 + - + +
44D ILE* 3.4 31.1 - - + +
54D LYS* 1.3 71.6 - - - +
56D ILE* 1.3 61.3 + - - +
57D SER* 3.7 20.0 + - - +
66D TYR* 4.0 39.7 - - + +
67D VAL 3.7 2.5 - - - -
68D LYS* 4.0 18.5 - - + +
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASP* 4.3 16.2 - - - +
30D PHE* 6.3 0.9 - - + -
38D ILE* 4.1 27.8 - - + -
40D SER 3.7 2.7 - - - -
41D VAL* 4.0 17.9 - - + +
54D LYS* 4.7 9.0 - - + +
55D LYS* 1.3 72.3 - - - +
57D SER* 1.3 62.8 + - - +
58D PHE* 4.1 23.0 - - + -
66D TYR* 3.1 6.2 - - - -
67D VAL* 2.8 48.1 + - + +
69D ASP* 3.7 26.2 - - + +
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.7 6.6 - - - +
39D SER* 2.7 34.3 + - - -
40D SER* 2.7 37.4 + - - +
42D GLU* 5.5 1.6 + - - +
55D LYS* 3.9 19.6 + - - +
56D ILE* 1.3 73.8 - - - +
58D PHE* 1.3 58.6 + - - +
65D LYS* 3.6 8.1 - - - -
66D TYR* 4.3 2.8 - - - +
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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