Contacts of the strand formed by residues 97 - 104 (chain R) in PDB entry 1ILL
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 GLY 97 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R ALA 3.3 6.2 + - - -
96R PRO* 1.4 76.7 - - - +
98R ASN* 1.4 68.0 + - - +
99R LEU* 2.9 15.2 + - - +
113R TRP* 3.5 4.7 - - - -
114R SER* 2.7 32.9 + - - -
116R PRO* 4.8 3.6 - - - +
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Residues in contact with ASN 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97R GLY* 1.4 68.1 - - - +
99R LEU* 1.3 59.8 + - - +
100R THR* 3.1 31.6 + - - +
112R THR* 2.9 20.2 - - + +
113R TRP* 3.3 4.0 - - - -
114R SER* 3.4 18.3 + - - +
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ALA* 6.2 0.2 - - + -
96R PRO 3.2 28.5 - - - +
97R GLY* 2.9 15.3 + - - +
98R ASN* 1.3 70.1 + - - +
100R THR* 1.4 53.2 + - - +
113R TRP* 4.0 12.8 - - + -
171R VAL* 4.0 24.5 - - + -
186R SER* 3.6 23.8 - - - +
188R SER 4.8 4.9 - - - +
189R THR* 2.7 52.9 + - + +
191R TRP* 2.7 14.7 + - - -
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Residues in contact with THR 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R ASN* 3.1 44.8 + - - +
99R LEU* 1.4 73.4 - - - +
101R VAL* 1.3 73.9 + - - +
111R LEU* 3.8 0.7 - - - +
112R THR* 3.0 47.0 + - + +
191R TRP* 3.7 6.1 - - - +
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Residues in contact with VAL 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R THR* 1.3 87.3 + - - +
102R HIS* 1.3 61.0 + - - +
103R THR* 2.9 30.6 + - + +
109R LEU* 3.8 32.8 - - + -
110R LEU 3.5 4.3 - - - +
111R LEU* 3.6 19.3 - - + -
191R TRP* 3.5 56.0 - - + +
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Residues in contact with HIS 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R THR* 5.7 0.2 - - - +
101R VAL* 1.3 70.1 - - - +
103R THR* 1.3 73.6 + - - +
104R ASN* 4.2 16.8 + - + -
108R THR 3.4 1.4 - - - +
109R LEU* 3.4 6.4 - - - -
110R LEU* 3.3 52.3 + - + +
112R THR* 5.6 1.8 - - - +
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Residues in contact with THR 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R VAL* 2.9 24.6 + - - +
102R HIS* 1.3 80.8 + - - +
104R ASN* 1.4 66.9 + - - +
108R THR 4.2 1.1 - - - -
109R LEU* 4.4 7.2 - - + -
161R LEU* 4.4 16.4 - - + -
191R TRP* 5.5 0.9 - - + +
192R HIS 4.1 19.9 + - - +
193R ASN* 5.0 5.8 - - - +
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Residues in contact with ASN 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R HIS* 3.9 15.4 + - + -
103R THR* 1.4 81.8 - - - +
105R VAL* 1.4 82.8 + - - +
106R SER* 2.9 31.1 + - - -
107R ASP* 3.6 8.5 + - - -
108R THR* 3.2 31.0 + - - +
109R LEU* 4.6 1.7 - - - +
110R LEU* 5.5 0.9 - - + -
193R ASN* 4.5 5.5 - - - +
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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