Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 3UF2
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 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 5.0 0.2 - - + -
29C THR* 4.0 13.5 - - + +
30C SER* 3.8 20.0 - - - +
31C CYS* 3.8 22.2 - - + +
32D GLN* 1.3 78.7 - - - +
34D THR* 1.3 64.1 + - - +
35D PHE* 4.0 8.7 - - + -
64D THR* 3.9 15.7 - - + -
106D PHE 3.4 1.0 - - - +
107D TYR* 3.3 7.6 - - - -
108D GLU 2.7 38.6 + - - +
109D THR 4.4 0.4 - - - -
110D PRO* 3.9 27.8 - - + -
113D LEU* 3.5 31.2 - - + -
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Residues in contact with THR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER* 4.9 3.0 + - - -
33D ILE* 1.3 79.7 - - - +
35D PHE* 1.3 70.3 + - - +
36D GLU* 5.8 2.0 - - + -
64D THR* 4.3 9.5 + - - +
105D THR* 3.2 31.4 - - + -
106D PHE 3.3 4.3 - - - +
107D TYR* 3.8 16.8 - - - -
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Residues in contact with PHE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 4.0 13.0 - - + -
34D THR* 1.3 82.8 - - - +
36D GLU* 1.3 64.0 + - - +
37D PHE* 3.9 18.4 - + + -
60D ILE* 4.3 14.6 - - + -
64D THR* 4.8 5.6 - - - +
105D THR* 4.6 0.7 - - - -
106D PHE* 2.8 56.2 + + + +
108D GLU* 3.5 34.1 - - + -
113D LEU* 3.6 55.4 - - + -
116D LYS* 4.2 10.3 - - + -
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D THR* 5.8 1.6 - - + -
35D PHE* 1.3 76.4 - - - +
37D PHE* 1.3 59.2 + - - +
56D LEU* 3.9 20.3 - - + +
60D ILE* 4.1 12.1 - - - +
103D VAL* 3.7 26.5 - - + +
104D ARG 3.3 7.1 - - - +
105D THR* 4.2 19.7 + - + +
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 3.8 12.9 + + + -
36D GLU* 1.3 73.4 - - - +
38D VAL* 1.3 79.0 + - + +
49D TYR* 3.5 21.1 - + - -
53D ALA* 4.2 13.0 - - + -
56D LEU* 3.6 15.3 - - + -
57D VAL* 4.1 22.7 - - + -
60D ILE* 3.7 20.6 - - + -
103D VAL* 3.5 4.2 - - - -
104D ARG 3.1 29.8 + - - +
106D PHE* 3.6 18.8 - + + -
113D LEU* 5.8 0.4 - - + -
116D LYS* 3.9 40.6 - - + -
117D VAL* 5.5 0.9 - - + -
120D VAL* 3.7 25.1 - - + -
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 1.3 86.8 - - + +
39D ASP* 1.3 67.9 + - - +
40D GLN* 3.5 4.0 + - - +
43D LEU* 3.8 23.3 - - + -
49D TYR* 3.7 36.1 + - + +
52D LYS* 3.8 7.0 - - + -
53D ALA* 3.4 41.5 - - + +
56D LEU* 3.4 15.3 - - + -
102D CYS 3.7 11.2 - - - +
106D PHE* 3.7 13.6 - - - -
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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