Contacts of the strand formed by residues 40 - 45 (chain U) 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 ILE 40 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35U ALA 5.7 0.2 - - - +
36U VAL* 3.2 10.5 - - - +
37U GLY 3.1 32.6 + - - +
38U ASP* 3.3 11.7 - - + +
39U GLY* 1.3 92.8 - - - +
41U ALA* 1.3 71.0 + - - +
42U ARG* 5.0 8.3 - - + +
74U GLY* 5.9 0.4 - - - -
75U ILE 3.4 3.8 - - - +
76U VAL* 3.7 14.4 - - + -
77U LEU* 4.4 3.8 - - - +
283U LEU* 4.6 2.2 - - - +
286U LEU* 3.8 29.8 - - + +
287U LEU* 3.5 38.1 - - + -
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Residues in contact with ALA 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U VAL* 5.0 4.3 - - + -
35U ALA 3.7 4.3 - - - -
36U VAL* 4.6 9.0 - - + -
40U ILE* 1.3 78.7 - - - +
42U ARG* 1.3 64.1 + - - +
43U VAL* 3.7 9.2 - - + -
57U PHE* 4.4 21.3 - - + -
73U VAL 3.0 15.4 - - - +
74U GLY* 3.8 2.6 - - - -
75U ILE* 2.9 36.8 + - + +
77U LEU* 4.8 4.5 - - + -
84U VAL* 5.2 0.2 - - + -
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Residues in contact with ARG 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U VAL* 4.5 0.6 - - - +
34U LEU* 2.6 52.4 + - + +
35U ALA* 2.9 42.0 + - - +
40U ILE* 5.2 8.5 - - + -
41U ALA* 1.3 72.6 - - - +
43U VAL* 1.3 56.2 + - - +
72U GLN* 2.8 43.4 + - - +
73U VAL 3.7 4.3 - - - +
54X LEU 4.6 5.5 + - - -
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Residues in contact with VAL 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U GLY* 3.7 14.4 - - - -
32U ARG 3.1 25.1 - - - +
33U VAL* 3.9 13.0 - - + -
34U LEU* 4.8 0.2 - - - -
41U ALA* 4.5 9.2 - - + -
42U ARG* 1.3 75.4 - - - +
44U PHE* 1.3 63.1 + - - +
46U LEU* 3.8 17.5 - - + -
57U PHE* 4.9 0.7 - - + -
72U GLN* 3.7 4.5 - - - -
73U VAL* 2.9 37.8 + - + +
75U ILE* 3.7 27.1 - - + -
90U VAL* 3.8 19.1 - - + -
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Residues in contact with PHE 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 3.9 31.3 - - + +
31U GLY* 3.2 4.2 - - - -
32U ARG* 2.6 41.9 + - + +
34U LEU* 3.9 29.8 - - + -
42U ARG 4.0 1.4 + - - -
43U VAL* 1.3 73.2 - - - +
45U GLY* 1.3 59.7 + - - +
71U GLY* 3.4 26.7 - - - -
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Residues in contact with GLY 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 3.6 22.7 - - - -
30U THR 4.3 0.2 - - - -
43U VAL 3.8 1.2 + - - -
44U PHE* 1.3 81.8 - - - +
46U LEU* 1.3 74.8 + - - +
47U ASN* 3.3 14.8 + - - +
71U GLY 5.0 2.6 + - - -
73U VAL* 3.4 13.9 - - - +
72V ARG* 3.9 5.0 + - - -
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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