Contacts of the strand formed by residues 42 - 50 (chain C) in PDB entry 4UQJ
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 ARG 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ASN 2.9 10.9 + - - +
11C SER* 3.7 3.7 - - - -
12C ILE* 3.0 25.3 + - - +
37C SER* 6.4 3.4 - - - +
38C THR 4.9 3.8 - - - +
41C PHE* 1.3 75.7 - - - +
43C LEU* 1.3 67.9 + - - +
44C THR* 3.8 2.4 + - - +
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Residues in contact with LEU 43 (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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12C ILE* 3.5 16.8 - - + +
14C ILE* 4.1 25.8 - - + -
33C MET* 3.3 31.3 - - + +
36C PHE 5.7 2.7 - - - +
41C PHE* 3.7 32.1 - - + +
42C ARG* 1.3 79.4 - - - +
44C THR* 1.3 62.7 + - - +
45C PRO* 3.1 11.6 - - - +
289C VAL* 4.9 4.9 - - + +
292C MET* 4.5 19.7 - - + +
293C THR* 4.2 20.6 - - - +
296C PHE* 5.6 1.8 - - + -
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Residues in contact with THR 44 (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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11C SER* 3.2 22.2 + - - +
12C ILE 2.9 13.1 + - - -
13C GLN* 3.5 13.5 - - + +
14C ILE* 3.0 24.1 + - - +
42C ARG* 4.3 3.1 + - - +
43C LEU* 1.3 73.9 - - - +
45C PRO* 1.3 68.9 - - + +
46C HIS* 3.6 2.3 + - + +
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Residues in contact with PRO 45 (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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14C ILE* 3.6 12.8 - - + +
15C GLY 5.7 0.4 - - - -
16C GLY 6.0 0.7 - - - +
29C PHE* 3.8 25.4 - - + -
33C MET* 3.6 31.4 - - + -
43C LEU 3.1 11.2 - - - +
44C THR* 1.3 89.1 - - + +
46C HIS* 1.3 60.3 + - - +
47C ILE* 3.8 14.8 + - + +
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Residues in contact with HIS 46 (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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13C GLN* 6.6 0.4 - - + -
14C ILE 3.0 16.3 + - - +
15C GLY* 4.0 3.9 - - - -
16C GLY 3.1 19.0 + - - +
44C THR* 3.6 2.2 + - + +
45C PRO* 1.3 70.5 - - - +
47C ILE* 1.3 66.6 + - - +
48C ASP* 3.6 30.8 + - - +
64C SER* 5.2 7.9 - - - -
65C GLN* 5.5 9.2 - - + +
68C ARG* 5.7 12.7 - - + +
70C VAL* 5.5 5.6 - - + -
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Residues in contact with ILE 47 (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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16C GLY* 3.5 10.5 - - - +
18C PHE* 4.1 14.8 - - + -
26C TYR* 3.5 46.0 - - + +
29C PHE* 4.0 9.6 - - + -
45C PRO* 3.8 28.4 + - + +
46C HIS* 1.3 75.3 + - - +
48C ASP* 1.3 70.2 - - - +
49C ASN* 3.5 24.5 - - - +
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Residues in contact with ASP 48 (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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16C GLY 2.8 15.0 + - - +
17C LEU* 3.7 8.4 - - + +
18C PHE 3.4 18.7 + - - -
46C HIS* 3.6 30.9 + - - +
47C ILE* 1.3 88.4 - - - +
49C ASN* 1.3 62.9 + - - +
50C LEU* 3.4 24.4 + - + +
61C ALA* 4.0 25.9 - - + +
64C SER* 4.7 7.1 + - - -
65C GLN* 4.8 5.7 - - - +
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Residues in contact with ASN 49 (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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18C PHE* 3.3 22.8 - - - +
19C PRO 5.7 0.2 - - - -
20C ARG* 5.1 16.5 - - + +
26C TYR* 5.8 0.2 - - - -
47C ILE* 3.5 23.2 + - - +
48C ASP* 1.3 67.7 - - - +
50C LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 50 (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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18C PHE 3.6 2.4 + - - -
19C PRO* 3.4 19.1 - - - +
20C ARG* 3.7 5.3 + - - -
48C ASP* 3.4 33.3 + - + +
49C ASN* 1.3 82.2 - - - +
51C GLU* 1.3 61.1 + - - +
52C VAL* 2.9 10.0 + - - -
57C ALA* 3.3 44.2 - - + +
58C VAL* 5.5 2.7 - - + +
60C ASN* 5.4 2.5 - - + -
61C ALA* 3.7 17.5 - - + +
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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