Contacts of the strand formed by residues 28 - 36 (chain I) in PDB entry 5FUR
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 28 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LYS* 1.3 71.8 - - - +
29I THR* 1.3 59.9 + - - +
30I HIS 5.1 0.7 - - - +
31I GLN* 3.8 13.7 - - + +
51I LEU* 3.7 39.3 - - + -
52I THR 3.4 12.8 - - - +
53I ILE* 3.4 34.3 - - + +
65I LEU* 4.6 3.1 - - + -
146I ILE* 5.3 2.9 - - + -
193I VAL* 3.3 40.8 - - + +
198I GLU* 3.4 11.4 + - + +
199I LEU 3.4 6.6 + - - +
200I CYS* 2.8 32.6 - - - -
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Residues in contact with THR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LYS* 3.5 19.5 - - + +
28I LEU* 1.3 75.5 - - - +
30I HIS* 1.3 70.0 + - - +
52I THR* 3.2 5.7 + - - +
54I PHE* 3.3 38.8 - - + -
199I LEU 4.0 6.1 - - - +
200I CYS* 3.4 6.2 - - - -
201I THR* 3.0 24.4 + - - +
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Residues in contact with HIS 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU 3.6 1.0 - - - -
29I THR* 1.3 90.8 + - - +
31I GLN* 1.3 76.2 + - - +
32I VAL* 3.3 26.5 - - + +
50I GLU 5.8 0.2 - - - -
52I THR* 3.0 41.9 + - + +
200I CYS* 4.6 1.0 - - - +
201I THR* 3.2 30.5 + - + +
202I TRP 4.4 2.5 - - - -
203I LYS* 4.1 11.2 - - + -
237I MET* 6.6 0.2 - - + -
238I LEU 5.7 1.1 - - - -
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Residues in contact with GLN 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU* 3.8 24.7 - - + +
30I HIS* 1.3 80.9 - - - +
32I VAL* 1.3 58.4 + - - +
33I VAL* 4.1 2.2 - - + +
49I VAL* 2.8 32.4 - - + +
50I GLU 3.3 7.6 - - - +
51I LEU* 3.2 21.6 - - + +
52I THR 4.8 0.2 - - - +
190I PHE* 3.1 16.7 - - + -
192I CYS* 3.7 20.2 - - - +
193I VAL 4.8 0.4 + - - +
200I CYS* 4.6 6.4 - - + -
201I THR 3.0 6.9 + - - -
202I TRP* 3.1 29.5 - - + +
203I LYS 2.7 30.7 + - - +
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I HIS* 3.3 30.3 - - + +
31I GLN* 1.3 71.2 - - - +
33I VAL* 1.3 63.1 + - - +
34I CYS* 5.5 2.9 - - + +
48I PHE 4.0 1.2 - - - +
49I VAL* 3.8 0.5 - - - +
50I GLU* 2.7 55.9 + - + +
203I LYS* 3.3 45.8 - - + +
205I GLU* 5.7 1.3 - - + +
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Residues in contact with VAL 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLN* 4.1 2.4 - - + -
32I VAL* 1.3 78.8 - - - +
34I CYS* 1.4 63.7 + - - +
35I ILE* 3.5 24.9 - - + -
48I PHE 3.7 7.6 - - - +
49I VAL* 4.2 20.6 - - + +
150I PHE* 4.4 8.7 - - + -
189I TRP* 5.4 1.6 - - + -
190I PHE* 4.9 12.3 - - + -
202I TRP* 5.7 3.6 - - + -
203I LYS 3.0 16.3 + - - +
204I LEU* 3.5 25.3 - - + -
205I GLU* 3.1 24.8 + - - +
247I ILE* 5.6 10.1 - - + -
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Residues in contact with CYS 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL* 5.5 3.8 - - + +
33I VAL* 1.4 76.8 - - - +
35I ILE* 1.3 58.3 + - - +
36I ASN* 3.7 26.9 + - - -
47I GLY* 3.6 3.5 - - - -
48I PHE* 2.8 51.0 + - + +
50I GLU* 6.5 1.6 - - - -
205I GLU* 3.4 27.4 - - + -
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Residues in contact with ILE 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 3.5 35.2 - - + -
34I CYS* 1.3 71.4 - - - +
36I ASN* 1.3 60.3 + - - +
38I ILE* 3.3 7.6 - - + +
45I VAL* 2.5 42.4 - - + -
46I VAL 3.5 9.9 - - - +
150I PHE* 4.0 8.1 - - + -
189I TRP* 3.0 51.8 - - + +
204I LEU* 4.2 4.9 - - + -
205I GLU 2.9 9.4 + - - +
206I PHE* 3.0 31.2 - - + +
207I THR 3.2 4.5 + - - -
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Residues in contact with ASN 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I CYS* 3.7 29.2 + - - -
35I ILE* 1.3 78.9 - - - +
37I ASN* 1.3 65.8 + - - +
38I ILE* 2.4 22.2 + - - +
46I VAL* 3.1 21.2 + - + +
47I GLY* 4.8 1.1 - - - -
48I PHE* 5.6 8.9 - - - -
205I GLU* 5.2 5.9 - - - +
206I PHE* 5.5 0.2 - - - -
207I THR* 4.6 12.9 + - - +
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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