Contacts of the strand formed by residues 46 - 52 (chain X) in PDB entry 1IRA
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 46 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11X GLN 3.5 0.5 - - - +
12X ALA* 3.5 0.8 - - - -
13X PHE* 2.6 42.8 + - - +
14X ARG* 5.1 0.2 - - - +
15X ILE* 3.6 32.1 - - + -
23X PHE* 4.6 13.5 - - + -
30X LEU* 5.3 1.1 - - + -
44X GLU* 5.1 2.2 - - + +
45X LYS* 1.3 72.6 - - - +
47X ASP* 1.3 63.0 + - - +
48X VAL* 3.7 7.5 + - + -
58X LEU* 3.6 35.2 - - + -
59X GLY 3.5 4.9 - - - +
60X ILE* 3.8 24.0 - - + -
67X LEU* 4.8 15.3 - - + -
148X PHE* 3.8 17.3 - - + -
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Residues in contact with ASP 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X MET* 4.0 24.4 - - - +
11X GLN 3.4 5.2 - - - +
12X ALA* 4.0 19.7 + - - +
45X LYS* 4.3 4.7 - - - +
46X ILE* 1.3 71.9 - - - +
48X VAL* 1.3 60.8 + - - +
57X PHE 3.7 0.2 - - - +
59X GLY 2.8 36.0 + - - +
60X ILE* 3.7 2.3 - - - -
61X HIS 3.7 9.2 + - - -
62X GLY* 3.2 27.1 + - - -
63X GLY* 3.4 15.8 + - - +
85X ILE* 3.5 6.8 - - + +
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Residues in contact with VAL 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X MET* 3.1 5.4 - - - -
11X GLN* 2.9 45.0 + - + +
13X PHE* 3.4 29.2 - - + -
46X ILE* 3.8 5.8 - - + +
47X ASP* 1.3 78.1 - - - +
49X VAL* 1.3 62.6 + - - +
50X PRO* 4.0 4.1 - - + +
56X LEU* 4.2 16.4 - - + -
57X PHE 3.2 8.1 - - - +
58X LEU* 3.5 27.8 - - + -
85X ILE* 4.1 0.7 - - - -
148X PHE* 3.6 23.3 - - + -
297Y THR* 5.1 0.4 - - - +
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Residues in contact with VAL 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X SER* 3.1 35.9 - - - +
8X SER* 4.7 1.1 - - - +
9X LYS 3.6 14.4 - - - +
10X MET* 3.5 26.7 - - + -
48X VAL* 1.3 72.8 - - - +
50X PRO* 1.3 75.1 - - + +
51X ILE* 3.5 1.1 + - - -
56X LEU* 3.4 2.7 - - - +
57X PHE* 3.0 42.2 + - + +
85X ILE* 3.6 30.9 - - + +
86X THR* 5.0 2.9 - - + +
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Residues in contact with PRO 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X SER* 4.8 2.8 - - - -
8X SER* 5.4 0.9 - - - +
9X LYS 4.0 11.9 - - - +
11X GLN* 5.1 9.0 - - + +
48X VAL* 4.0 9.2 - - + +
49X VAL* 1.3 91.6 - - + +
51X ILE* 1.3 63.4 + - - +
52X GLU 4.9 0.7 - - - +
55X ALA 3.8 6.1 - - - +
56X LEU* 4.1 3.8 - - + -
235Y SER* 4.5 13.0 - - - +
237Y ILE* 3.3 25.9 - - + +
296Y ASN* 4.0 18.6 - - + -
297Y THR* 3.7 32.8 - - - +
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Residues in contact with ILE 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X VAL* 5.8 0.2 - - - -
50X PRO* 1.3 76.3 - - - +
52X GLU* 1.3 80.9 + - + +
55X ALA* 3.0 15.3 + - + +
56X LEU* 4.0 16.4 - - - +
57X PHE* 3.7 35.9 - - + -
90X GLU* 3.6 41.6 - - + +
96X LYS* 5.4 3.4 - - - -
99X ALA* 3.7 29.8 - - + -
237Y ILE* 4.2 2.1 - - - +
295Y LYS* 3.5 23.2 + - - +
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Residues in contact with GLU 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X PRO 4.7 0.3 - - - -
51X ILE* 1.3 97.1 + - + +
53X PRO* 1.3 83.2 - - + +
54X HIS 3.1 0.5 + - - -
55X ALA* 2.8 30.6 + - + +
90X GLU* 5.6 0.7 - - - +
295Y LYS* 4.5 13.9 - - - +
296Y ASN 4.0 6.0 - - - +
297Y THR* 4.4 2.6 - - - -
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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