Contacts of the strand formed by residues 131 - 137 (chain C) in PDB entry 2I6A
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 ASN 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C PRO* 3.4 30.8 - - + +
36C ASN* 2.8 26.1 + - - +
127C ILE* 3.4 6.6 - - - +
128C THR* 2.7 40.2 + - - +
129C GLY* 4.7 0.9 - - - -
130C ASP* 1.3 84.4 + - - +
132C ARG* 1.3 67.5 + - - +
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Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 4.7 4.8 + - - -
35C PRO 3.0 3.8 - - - -
36C ASN* 2.7 33.5 + - - +
37C ASP 3.0 6.2 + - - +
125C ALA* 3.9 21.4 - - - +
126C CYS 3.7 5.4 - - - -
127C ILE* 3.6 28.0 - - + +
130C ASP 4.5 7.2 - - - +
131C ASN* 1.3 81.7 - - - +
133C SER* 1.3 59.7 + - - +
134C LEU* 4.0 17.7 - - + +
292C ILE* 6.0 4.0 - - - +
293C ILE 5.5 0.4 - - - -
294C ASP* 3.2 52.2 + - - +
295C THR 4.9 1.8 - - - +
296C ASN* 5.0 8.9 + - - +
332C ARG* 4.8 12.5 + - - +
334C THR* 5.2 4.4 + - - -
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 4.2 7.6 - - - -
33C LEU* 3.8 18.7 - - - +
34C LYS 3.0 24.8 + - - -
35C PRO 3.5 5.4 - - - -
37C ASP* 3.6 9.1 - - - +
39C ILE* 6.1 0.7 - - - +
124C ALA 3.4 0.2 - - - +
126C CYS* 3.0 42.4 + - - -
132C ARG* 1.3 74.4 - - - +
134C LEU* 1.3 61.2 + - - +
135C ILE* 3.3 13.0 - - - +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 2.8 18.9 + - - +
38C GLN* 3.3 21.3 + - + +
39C ILE* 2.7 35.7 + - - +
123C CYS* 3.9 12.8 - - - -
124C ALA 3.1 3.8 - - - +
125C ALA* 3.6 29.6 - - + -
132C ARG* 4.2 16.6 - - + +
133C SER* 1.3 85.4 + - - +
135C ILE* 1.3 57.4 + - - +
136C ALA 4.1 0.4 - - - -
294C ASP* 5.7 0.2 - - - +
296C ASN* 4.1 9.6 - - + +
500C 5I5 3.8 42.8 - - + -
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.0 24.2 - - + -
39C ILE* 3.3 28.5 - - + -
41C ALA* 3.6 27.6 - - + +
45C HIS* 4.5 9.2 - - + -
48C LEU* 4.1 10.3 - - + -
49C PHE* 3.3 17.1 - - + -
123C CYS* 3.5 1.5 - - - -
124C ALA* 2.9 36.0 + - + +
126C CYS* 3.9 19.5 - - - -
133C SER* 3.3 22.7 - - - +
134C LEU* 1.3 74.1 - - - +
136C ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 3.9 7.2 - - + -
39C ILE 2.8 10.7 + - - -
40C LEU* 3.8 9.2 - - + +
41C ALA* 3.1 21.7 + - - +
122C THR 3.7 3.1 - - - -
123C CYS* 3.8 12.1 - - - -
135C ILE* 1.3 73.1 - - - +
137C ASN* 1.3 59.2 + - - +
138C LEU* 3.5 24.3 + - + +
500C 5I5 3.7 29.3 - - + +
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Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 4.1 10.0 - - + +
46C LYS* 6.1 1.0 - - - +
49C PHE* 3.6 32.2 - - + -
119C PRO* 6.0 0.8 - - - +
120C THR 5.8 0.2 + - - -
121C GLY* 3.3 1.6 - - - -
122C THR* 2.7 39.9 + - - +
135C ILE 3.7 1.4 + - - -
136C ALA* 1.3 72.4 - - - +
138C LEU* 1.3 64.3 + - - +
139C ALA* 3.0 19.5 + - - +
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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