Contacts of the strand formed by residues 11 - 17 (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 GLN 11 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10X MET* 1.3 76.7 - - - +
12X ALA* 1.3 65.0 + - - +
13X PHE* 3.3 37.1 - - + -
46X ILE 3.5 0.9 - - - +
47X ASP* 3.4 3.8 - - - -
48X VAL* 2.9 42.3 + - + +
50X PRO* 5.1 9.7 - - + +
150X GLU* 4.3 13.9 + - + +
233Y GLN* 4.8 11.4 + - - +
235Y SER* 3.4 24.4 + - - +
296Y ASN* 5.7 5.3 - - - +
297Y THR* 4.4 11.7 + - - -
298Y HIS* 6.0 2.0 - - - -
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Residues in contact with ALA 12 (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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11X GLN* 1.3 73.6 - - - +
13X PHE* 1.3 62.0 + - - +
45X LYS* 4.6 13.9 - - + -
46X ILE 3.5 4.7 - - - +
47X ASP* 4.0 14.9 + - - +
150X GLU* 3.8 2.1 - - - +
151X ASP* 3.1 39.7 + - + +
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Residues in contact with PHE 13 (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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11X GLN* 3.3 44.4 - - + -
12X ALA* 1.3 75.6 - - - +
14X ARG* 1.3 58.9 + - - +
45X LYS* 3.3 9.2 - - - +
46X ILE 2.6 38.2 + - - +
48X VAL* 3.4 18.4 - - + -
56X LEU* 5.9 0.7 - - + -
102X ARG* 4.3 13.9 - - - -
148X PHE* 3.5 50.5 - + + -
149X GLN 3.5 7.4 - - - -
150X GLU* 3.4 48.5 - - + -
151X ASP* 3.7 5.4 - - - -
297Y THR* 5.4 2.7 - - - -
298Y HIS* 6.0 0.4 - - - -
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Residues in contact with ARG 14 (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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13X PHE* 1.3 74.7 - - - +
15X ILE* 1.3 64.6 + - - +
16X TRP* 4.2 15.0 - - + -
40X VAL* 6.0 1.8 - - - +
43X GLU* 2.8 36.7 + - - +
45X LYS* 3.2 24.9 - - - +
147X TYR 3.3 3.3 - - - +
148X PHE* 3.7 3.8 - - - -
149X GLN* 2.8 39.6 + - + +
151X ASP* 3.5 27.6 - - - +
111Y LYS* 3.4 33.0 - - - +
198Y LEU* 5.6 3.4 - - - +
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Residues in contact with ILE 15 (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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14X ARG* 1.3 76.7 - - - +
16X TRP* 1.3 71.1 - - - +
22X THR* 4.3 14.9 - - - +
23X PHE* 3.8 33.6 + - + -
43X GLU* 4.6 8.3 + - - +
44X GLU 4.5 9.9 + - - +
46X ILE* 3.6 24.2 - - + -
58X LEU* 6.4 1.1 - - + -
111X PHE* 4.2 10.3 - - + -
121X LEU* 5.0 5.6 - - + -
146X PHE* 4.0 35.4 - - + -
147X TYR 3.6 4.5 - - - +
148X PHE* 3.9 27.1 - - + -
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Residues in contact with TRP 16 (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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14X ARG* 4.2 18.8 - - + -
15X ILE* 1.3 88.7 - - - +
17X ASP* 1.3 82.4 + - - +
20X GLN* 3.8 21.3 + - - +
21X LYS 3.1 17.7 - - - +
22X THR* 4.0 13.9 - - + +
23X PHE* 5.7 2.0 - - - -
146X PHE* 4.1 3.8 - - - -
147X TYR* 2.9 67.5 + + + -
149X GLN* 4.0 13.5 - - + -
111Y LYS* 3.3 51.3 + - + -
113Y PRO* 4.7 1.8 - - + -
198Y LEU* 3.3 35.2 - - + -
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Residues in contact with ASP 17 (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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16X TRP* 1.3 86.5 - - - +
18X VAL* 1.3 59.2 + - - +
19X ASN* 3.0 15.8 + - - -
20X GLN 3.0 16.8 + - - -
21X LYS* 2.9 51.1 + - - +
23X PHE* 5.5 0.8 - - - -
123X THR* 2.8 25.6 + - - +
143X VAL* 3.8 10.5 - - + +
145X LYS 3.5 16.2 - - - +
146X PHE* 3.7 20.4 - - + -
147X TYR* 4.2 2.0 - - - -
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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