Contacts of the strand formed by residues 11 - 17 (chain 2) in PDB entry 1ILR
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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92 LYS* 3.5 15.0 + - + +
102 MET* 1.3 75.6 - - - +
122 ALA* 1.3 60.3 + - - +
132 PHE* 3.6 30.9 - - + -
462 ILE 3.7 0.2 - - - +
472 ASP* 3.5 2.6 - - - -
482 VAL* 2.7 47.3 + - + +
502 PRO* 3.5 28.3 - - - +
1502 GLU* 4.0 17.4 + - - +
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Residues in contact with ALA 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102 MET 4.4 0.2 + - - -
112 GLN* 1.3 70.8 - - - +
132 PHE* 1.3 71.9 + - - +
452 LYS* 5.2 10.5 - - + +
462 ILE 3.6 5.4 - - - +
472 ASP* 4.7 10.3 - - - +
1502 GLU* 3.7 3.7 - - - +
1512 ASP* 2.8 41.4 + - + +
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Residues in contact with PHE 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112 GLN* 3.6 39.3 - - + -
122 ALA* 1.3 80.1 - - - +
142 ARG* 1.3 64.6 + - - +
452 LYS* 3.1 8.8 - - - +
462 ILE 2.8 32.2 + - - +
482 VAL* 3.7 26.2 - - + -
562 LEU* 6.5 0.2 - - + -
1022 ARG* 4.2 15.0 - - - -
1482 PHE* 3.4 49.8 - + + -
1492 GLN 3.2 7.9 - - - -
1502 GLU* 3.5 39.5 - - + -
1512 ASP* 4.0 1.6 - - - +
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Residues in contact with ARG 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 PHE* 1.3 75.0 - - - +
152 ILE* 1.3 61.5 + - - +
162 TRP* 4.1 15.9 - - + -
222 THR* 5.8 1.2 - - - +
432 GLU* 2.9 37.8 + - - +
452 LYS* 3.9 23.8 - - + +
1472 TYR 3.8 0.3 - - - +
1482 PHE* 3.5 5.4 - - - -
1492 GLN* 2.8 48.4 + - + +
1512 ASP* 3.3 26.2 - - - +
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Residues in contact with ILE 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 PHE 4.3 0.2 + - - -
142 ARG* 1.3 76.2 - - - +
162 TRP* 1.3 71.3 + - - +
222 THR* 3.8 16.5 - - - +
232 PHE* 3.9 37.2 - - + -
432 GLU* 4.2 6.6 + - - +
442 GLU 4.3 9.7 + - - +
462 ILE* 3.6 24.9 - - + -
1112 PHE* 4.2 11.0 - - + -
1212 LEU* 4.8 4.3 - - + -
1462 PHE* 3.8 33.2 - - + -
1472 TYR 3.4 11.7 - - - +
1482 PHE* 4.0 21.1 - - + -
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Residues in contact with TRP 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142 ARG* 4.1 11.4 - - + -
152 ILE* 1.3 88.0 - - - +
172 ASP* 1.3 66.1 + - - +
202 GLN* 3.5 31.4 + - - +
212 LYS 3.0 18.2 - - - +
222 THR* 3.9 12.6 - - + +
232 PHE* 5.8 0.9 - - - -
432 GLU* 5.9 0.2 - - - -
1462 PHE* 3.7 4.9 - - - -
1472 TYR* 2.8 79.2 + + + +
1492 GLN* 3.7 45.1 - - + -
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Residues in contact with ASP 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162 TRP* 1.3 82.1 - - - +
182 VAL* 1.3 56.3 + - - +
192 ASN* 2.8 19.4 + - - +
202 GLN* 2.7 26.5 + - - -
212 LYS* 2.9 48.0 + - - +
232 PHE* 5.6 0.6 - - + -
1232 THR* 2.7 29.5 + - + +
1432 VAL* 4.1 8.4 - - + +
1452 LYS 3.6 14.4 - - - +
1462 PHE* 3.7 20.6 - - + -
1472 TYR* 3.9 3.6 - - - -
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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