Contacts of the strand formed by residues 42 - 50 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASN 2.9 11.4 + - - +
11A SER* 3.7 4.0 - - - -
12A ILE* 3.0 24.4 + - - +
37A SER* 6.4 2.7 - - - +
38A THR 4.7 4.3 - - - +
41A PHE* 1.3 75.0 - - - +
43A LEU* 1.3 67.3 + - - +
44A THR* 3.8 3.2 + - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.5 16.2 - - + +
14A ILE* 4.1 26.2 - - + -
33A MET* 3.3 31.1 - - + +
36A PHE 5.7 3.1 - - - +
41A PHE* 3.7 31.2 - - + +
42A ARG* 1.3 81.7 - - - +
44A THR* 1.3 60.7 + - - +
45A PRO* 3.1 11.9 - - - +
289A VAL* 4.9 5.6 - - + +
292A MET* 4.5 19.3 - - + +
293A THR* 4.2 20.4 - - + +
296A PHE* 5.6 1.8 - - + -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 3.2 22.1 + - - +
12A ILE 2.9 13.0 + - - -
13A GLN* 3.5 12.9 - - + +
14A ILE* 3.0 24.0 + - - +
42A ARG* 4.3 3.5 + - - +
43A LEU* 1.3 73.2 - - - +
45A PRO* 1.3 66.7 - - + +
46A HIS* 3.6 2.1 + - + +
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.6 12.8 - - + +
15A GLY 5.7 0.4 - - - -
16A GLY 6.0 0.7 - - - +
29A PHE* 3.8 26.7 - - + -
33A MET* 3.6 31.4 - - + -
43A LEU 3.1 11.0 - - - +
44A THR* 1.3 88.8 - - + +
46A HIS* 1.3 60.2 + - - +
47A ILE* 3.8 14.3 + - + +
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Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN* 6.6 0.4 - - + -
14A ILE 3.0 16.3 + - - +
15A GLY* 4.0 4.0 - - - -
16A GLY 3.1 18.4 + - - +
44A THR* 4.9 2.5 - - + +
45A PRO* 1.3 70.5 - - - +
47A ILE* 1.3 66.6 + - - +
48A ASP* 3.6 30.4 + - - +
64A SER* 5.2 7.9 - - - -
65A GLN* 5.5 9.1 - - + +
68A ARG* 5.7 12.9 - - + +
70A VAL* 5.5 5.4 - - + -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.5 11.2 - - - +
18A PHE* 4.2 15.0 - - + -
26A TYR* 3.5 46.2 - - + +
29A PHE* 4.0 9.4 - - + -
45A PRO* 3.8 28.0 + - + +
46A HIS* 1.3 76.1 + - - +
48A ASP* 1.3 71.7 - - - +
49A ASN* 3.5 24.9 - - - +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 2.8 14.9 + - - +
17A LEU* 3.7 8.5 - - + +
18A PHE 3.4 18.2 + - - -
46A HIS* 3.6 29.6 + - - +
47A ILE* 1.3 88.0 - - - +
49A ASN* 1.3 63.1 + - - +
50A LEU* 3.4 23.1 + - + +
61A ALA* 4.0 25.8 - - + +
64A SER* 4.7 7.1 + - - -
65A GLN* 4.8 6.2 + - - +
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.3 23.6 - - - +
19A PRO 5.6 0.4 - - - -
20A ARG* 5.1 16.5 - - + +
26A TYR* 5.8 0.3 - - - -
47A ILE* 3.5 23.6 + - - +
48A ASP* 1.3 68.6 - - - +
50A LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE 3.6 2.4 + - - -
19A PRO* 3.4 18.5 - - - +
20A ARG* 3.7 6.5 + - - -
48A ASP* 3.4 32.6 + - + +
49A ASN* 1.3 83.0 - - - +
51A GLU* 1.3 60.6 + - - +
52A VAL* 2.9 11.2 + - - +
57A ALA* 3.3 44.9 - - + +
58A VAL* 5.5 2.7 - - + +
60A ASN* 5.4 2.2 - - + -
61A ALA* 3.7 16.4 - - + +
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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