Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 5U1R
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 HIS 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C TYR* 3.2 5.9 - - - -
28C VAL 3.0 30.8 + - - +
29C ASP* 3.4 0.4 - - + -
30C SER* 1.3 84.9 + - - +
32C PRO* 1.3 73.5 - - + +
33C ILE* 3.6 1.1 + - + +
49C TRP* 4.7 12.8 + + + -
175C THR* 3.5 25.4 - - + +
176C LEU* 3.4 23.1 - - + -
178C ARG* 4.8 1.6 - - - -
206C TYR* 2.6 43.2 + + - -
236C GLY* 5.6 6.5 - - - -
238C TYR* 6.0 1.3 - + - -
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Residues in contact with PRO 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 4.5 9.6 - - + -
26C GLY 3.4 8.7 - - - +
27C TYR* 3.8 19.7 - - + -
30C SER 3.7 7.6 - - - +
31C HIS* 1.3 89.0 - - + +
33C ILE* 1.3 61.1 + - - +
46C ARG* 3.7 36.3 - - + +
47C ALA* 3.8 6.2 - - - +
53F ASP* 6.5 1.1 - - + -
55F SER* 5.5 4.9 - - - +
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.2 7.9 - - + -
7C TYR* 3.6 20.6 - - - +
26C GLY* 2.8 26.8 + - - +
27C TYR 4.0 0.2 - - - +
28C VAL* 4.0 15.5 - - + +
31C HIS 3.8 9.2 - - - +
32C PRO* 1.3 78.4 - - - +
34C THR* 1.3 66.6 + - + +
45C PRO* 3.5 4.5 - - - +
46C ARG* 2.7 27.8 + - - +
47C ALA 3.8 3.3 + - - +
49C TRP* 3.5 34.3 - - + -
50C MET* 3.7 20.9 - - + +
168C PHE* 3.7 28.0 - - + -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR* 3.2 34.5 + - - +
24C SER 4.6 0.4 - - - -
25C VAL* 3.3 7.6 - - - +
26C GLY* 2.9 24.6 + - - -
33C ILE* 1.3 86.8 - - + +
35C THR* 1.3 62.1 + - - +
43C LYS* 3.5 35.7 - - - +
44C GLU 3.4 7.4 - - - -
46C ARG* 4.5 2.5 - - - -
50C MET* 3.8 20.9 - - + -
59C TRP* 3.8 9.9 - - + -
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Residues in contact with THR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 5.2 1.9 - - - +
24C SER 3.4 7.9 + - - -
25C VAL* 3.9 14.3 - - - +
34C THR* 1.3 76.8 - - - +
36C TYR* 1.3 70.3 + - - +
37C ASP* 5.6 2.1 + - - +
42C GLN 3.4 2.3 - - - +
43C LYS* 3.4 3.7 - - - -
44C GLU* 2.9 53.9 + - + +
46C ARG* 3.7 40.6 - - + +
53F ASP* 5.6 0.3 + - - -
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.5 38.6 - + - -
23C ILE* 3.4 4.5 - - - +
24C SER* 2.7 42.5 + - - +
35C THR* 1.3 81.3 + - - +
37C ASP* 1.3 68.6 + - - +
40C THR* 4.7 0.7 - - - -
41C ARG* 3.3 32.7 - - - +
42C GLN* 3.1 26.7 - - - +
43C LYS* 3.9 0.7 - - + -
44C GLU* 5.9 0.4 - - - -
63C THR 4.2 7.9 - - - -
66C LEU* 3.5 44.9 - - + -
67C ARG* 3.3 21.5 - - - +
70C GLN* 3.1 20.3 + - - -
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 4.3 16.3 - - + +
22C PHE 3.2 10.8 - - - +
23C ILE* 4.5 9.0 - - + -
35C THR* 5.6 1.8 + - - +
36C TYR* 1.3 83.2 - - - +
38C SER* 1.3 59.0 + - - +
39C VAL* 3.2 8.8 + - - +
40C THR* 2.6 57.0 + - - +
41C ARG* 3.1 22.5 + - - -
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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