Contacts of the strand formed by residues 48 - 53 (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 LEU 48 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21W VAL* 3.6 39.3 - - + -
23W VAL* 4.7 9.9 - - + -
35W ASN 3.2 5.7 - - - +
36W ALA* 3.5 2.4 - - - -
37W LEU* 2.8 44.2 + - + +
39W ILE* 3.7 27.6 - - + -
46W LEU* 4.4 13.9 - - + -
47W VAL* 1.3 88.9 - - - +
49W GLU* 1.3 59.8 + - - +
50W VAL 4.2 0.2 - - - -
61W THR* 3.5 24.2 - - - +
62W ILE 3.5 13.9 - - - +
63W ALA* 3.9 9.6 - - + -
64W MET* 4.7 0.9 - - - -
70W LEU* 6.2 0.2 - - + -
76W VAL* 5.5 0.4 - - + -
83W ILE* 5.7 0.2 - - - -
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Residues in contact with GLU 49 (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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34W LEU* 3.3 29.1 - - + +
35W ASN 3.4 5.4 - - - +
48W LEU* 1.3 74.0 - - - +
50W VAL* 1.3 67.3 + - - +
51W ALA* 3.5 0.7 + - - +
61W THR* 3.0 22.0 - - - -
62W ILE* 3.1 35.6 + - + +
64W MET* 3.9 10.7 - - + +
83W ILE* 4.2 12.0 - - + +
118W HIS* 2.9 31.0 + - - -
231W ARG* 2.8 37.4 + - - -
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Residues in contact with VAL 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31W PRO* 4.1 12.3 - - + +
32W ALA 3.2 29.2 - - - +
33W ILE* 3.3 21.4 - - + +
34W LEU* 3.1 24.3 + - - +
35W ASN* 3.3 24.0 + - + +
37W LEU* 4.4 9.0 - - + -
49W GLU* 1.3 77.8 - - - +
51W ALA* 1.3 61.9 + - - +
52W GLN 4.4 1.6 - - - +
59W VAL* 4.0 28.0 - - + -
61W THR* 3.8 13.7 - - + -
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Residues in contact with ALA 51 (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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37T GLY* 4.6 5.9 - - - -
38T ASP 5.1 0.7 + - - -
81T ASP* 4.7 4.0 - - - +
33W ILE* 3.5 20.7 - - - +
49W GLU 4.4 3.8 - - - +
50W VAL* 1.3 76.2 - - - +
52W GLN* 1.3 69.2 + - + +
60W ARG 2.8 21.3 + - - +
61W THR* 4.9 1.3 - - - -
62W ILE* 5.2 6.5 - - + -
272W LEU* 4.3 24.2 - - + -
274W ARG* 5.8 3.1 + - - +
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Residues in contact with GLN 52 (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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36T VAL 3.9 7.9 - - - +
37T GLY* 4.4 12.1 - - - -
38T ASP* 3.5 28.6 + - - +
33W ILE* 4.3 1.3 - - - -
50W VAL* 4.4 0.3 - - - +
51W ALA* 1.3 89.0 - - + +
53W HIS* 1.3 68.7 + - - +
54W LEU* 3.7 10.3 - - + +
59W VAL* 3.1 9.2 - - - +
60W ARG* 2.7 56.2 + - + +
272W LEU* 3.9 32.5 + - - +
274W ARG* 4.8 4.5 - - - +
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Residues in contact with HIS 53 (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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35T ALA* 3.3 19.9 - - - +
36T VAL* 3.1 41.9 + - + +
84T VAL 4.7 4.7 + - - -
85T LYS* 4.9 3.9 - - + -
86T GLU* 4.1 22.1 - - + +
30W LEU* 3.9 24.5 - - + +
31W PRO 3.0 28.1 + - - -
32W ALA* 4.3 3.4 - - - -
33W ILE* 3.4 35.8 - - + +
50W VAL* 4.4 0.2 - - - +
52W GLN* 1.3 72.0 - - - +
54W LEU* 1.3 53.2 + - - +
55W GLY 2.7 16.7 + - - -
58W THR 3.4 4.0 - - - -
59W VAL* 3.3 21.1 - - + +
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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