Contacts of the strand formed by residues 58 - 62 (chain W) 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 THR 58 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T GLU* 4.5 0.2 + - - -
14W THR* 4.6 12.0 + - + +
22W ASP* 4.1 16.8 - - + -
23W VAL 3.3 13.9 - - - +
24W HIS* 4.0 10.2 - - - +
30W LEU* 4.0 2.6 - - - +
53W HIS* 3.4 5.6 + - - +
54W LEU* 2.9 38.1 + - + -
55W GLY 3.6 12.3 + - - -
56W GLU* 3.5 7.8 + - - +
57W ASN* 1.3 81.1 + - - +
59W VAL* 1.3 74.0 + - - +
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Residues in contact with VAL 59 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W VAL 3.9 0.2 - - - +
22W ASP* 3.2 28.2 - - - +
23W VAL* 3.1 23.7 + - + +
25W PHE* 4.0 17.5 - - + -
30W LEU* 4.3 11.0 - - + -
31W PRO* 4.4 7.0 - - + +
37W LEU* 4.8 2.7 - - + -
50W VAL* 4.0 15.9 - - + -
52W GLN 3.1 7.9 - - - +
53W HIS* 3.3 36.8 - - + +
54W LEU* 4.8 2.2 - - - -
58W THR* 1.3 77.2 - - - +
60W ARG* 1.3 61.3 + - - +
61W THR* 4.2 14.6 - - + -
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Residues in contact with ARG 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W ILE* 5.0 8.1 - - - +
20W ILE* 3.6 31.8 - - + +
22W ASP* 3.6 18.3 + - - +
51W ALA* 2.8 31.9 + - - +
52W GLN* 2.7 43.9 + - + +
54W LEU* 3.2 42.6 - - + +
59W VAL* 1.3 72.7 - - - +
61W THR* 1.3 60.2 + - - +
272W LEU* 4.2 23.4 + - + +
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Residues in contact with THR 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W ILE* 3.3 10.4 - - - +
21W VAL* 2.7 61.4 + - - +
23W VAL* 4.6 2.4 - - + +
37W LEU* 3.7 28.0 - - + -
48W LEU* 3.5 18.6 - - - +
49W GLU 3.0 16.8 - - - +
50W VAL* 3.8 10.5 - - - -
51W ALA* 4.9 0.2 - - - -
59W VAL* 4.2 12.6 - - + -
60W ARG* 1.3 79.0 - - - +
62W ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 62 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19W ALA 3.8 3.1 - - - +
20W ILE* 4.6 10.3 - - + -
48W LEU* 3.5 9.5 - - - -
49W GLU* 3.1 39.2 + - + +
51W ALA* 5.2 6.3 - - + -
61W THR* 1.3 79.4 - - - +
63W ALA* 1.3 69.3 + - - +
64W MET* 3.5 29.8 - - + +
227W GLY* 4.3 12.6 - - - +
231W ARG* 5.1 3.6 - - - +
268W VAL* 4.3 23.3 - - + +
271W LEU* 6.2 1.3 - - + -
272W LEU* 4.1 26.9 - - + -
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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