Contacts of the strand formed by residues 38 - 42 (chain F) in PDB entry 3SKU
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 SER 38 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E MET* 5.0 2.3 - - - +
40E TYR 4.5 13.4 + - - +
41E GLY* 5.7 2.6 - - - -
42E PHE* 5.9 5.2 - - - -
46E ASP 5.4 1.7 + - - -
47E VAL* 5.3 9.7 - - - +
36F ASN* 3.5 8.0 - - - +
37F ASP* 1.3 93.6 + - - +
39F MET* 1.3 71.3 + - - +
40F TYR* 4.6 19.6 - - - -
138F LEU* 4.0 1.4 - - - +
139F ASN* 3.9 9.2 - - - +
1L NAG 5.6 3.6 - - - -
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Residues in contact with MET 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ASN* 3.6 23.3 - - - +
38E SER 4.4 4.5 - - - +
39E MET* 3.3 39.9 - - - +
36F ASN* 3.7 20.4 - - + +
38F SER* 1.3 77.7 - - - +
40F TYR* 1.3 87.4 + - - +
47F VAL* 3.8 17.5 - - + -
48F VAL 5.7 0.9 - - - +
49F LEU* 4.1 20.2 - - + -
138F LEU* 4.7 1.3 - - + -
139F ASN 2.9 22.6 + - - +
140F LEU* 3.4 16.6 - - + +
141F THR* 3.3 15.6 + - - -
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E SER* 4.9 5.0 + - - +
40E TYR* 3.7 58.5 - + + -
42E PHE* 3.6 30.1 - - - -
143E MET* 4.1 3.3 - - + +
231E HIS* 3.7 29.7 - + - -
38F SER* 4.6 17.6 - - - -
39F MET* 1.3 96.2 - - - +
41F GLY* 1.3 59.0 + - - +
42F PHE* 5.8 1.1 - - + -
47F VAL* 4.8 0.6 - - - +
140F LEU* 5.2 0.2 - - - -
141F THR* 3.3 31.0 - - + +
143F MET* 3.9 22.9 - - - -
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Residues in contact with GLY 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F MET 4.4 0.2 - - - -
40F TYR* 1.3 75.6 - - - +
42F PHE* 1.3 67.8 + - - -
45F THR* 4.3 2.7 - - - -
47F VAL* 4.4 11.2 - - - +
114F LEU* 3.1 27.8 - - - +
140F LEU* 5.0 2.8 - - - +
141F THR 3.5 5.9 + - - -
142F VAL* 3.6 17.8 - - - +
143F MET* 4.4 3.5 - - - +
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Residues in contact with PHE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E SER* 5.7 2.9 - - - -
40E TYR* 4.2 20.2 - + - -
40F TYR 5.9 0.4 - - - -
41F GLY* 1.3 80.5 - - - +
43F ILE* 1.3 69.0 + - - +
45F THR* 2.9 34.4 + - + +
114F LEU* 3.6 6.9 - - - +
142F VAL* 4.3 0.4 - - - -
143F MET* 3.1 57.4 - - + -
145F LYS* 4.0 21.5 - - + +
230F TYR* 3.8 20.9 - + - -
231F HIS* 5.6 0.9 - - - -
233F ASP* 5.3 8.7 - - - -
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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