Contacts of the strand formed by residues 80 - 86 (chain C) in PDB entry 2I2X
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 ALA 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.8 20.4 - - + -
38C TYR* 4.3 16.2 - - + -
40C ILE* 4.3 7.9 - - + -
41C PRO* 3.3 22.3 - - + +
73C MET* 3.5 7.0 - - - +
78C PHE* 3.4 3.6 + - - +
79C PRO* 1.3 89.2 - - + +
81C ILE* 1.3 66.6 + - - +
118C ILE* 4.3 1.5 - - - +
119C LYS* 3.2 14.8 - - + +
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Residues in contact with ILE 81 (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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32C LEU* 4.9 0.4 - - - +
40C ILE* 4.1 1.1 - - - +
41C PRO* 3.7 16.2 - - + +
43C ILE* 3.6 19.7 - - + -
69C VAL* 3.3 30.7 - - + -
70C MET* 4.0 24.0 - - + -
73C MET* 3.7 35.0 - - + -
80C ALA* 1.3 77.4 - - - +
82C ILE* 1.3 71.6 + - - +
83C LEU* 3.7 5.3 + - + -
118C ILE* 4.2 3.8 - - + -
119C LYS 2.9 7.5 + - - -
120C CYS* 3.0 39.3 - - + +
121C ALA 3.3 0.5 + - - -
330C SER* 5.0 2.2 - - - -
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Residues in contact with ILE 82 (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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32C LEU* 3.5 33.9 - - + -
34C ILE* 3.9 12.6 - - + -
40C ILE* 3.7 16.4 - - + -
41C PRO 2.9 11.4 + - - +
42C GLU* 3.2 30.5 - - + +
43C ILE* 2.9 30.5 + - - +
81C ILE* 1.3 74.4 - - - +
83C LEU* 1.3 71.2 + - - +
121C ALA* 3.3 15.3 - - + +
123C ARG* 4.6 0.7 - - + -
160C LEU* 4.3 15.9 - - + -
309C CYS* 3.8 26.7 - - + -
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Residues in contact with LEU 83 (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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43C ILE* 3.8 13.2 - - + -
45C TYR* 3.7 24.2 - - + +
66C THR* 3.9 38.6 - - + +
69C VAL* 3.9 12.8 - - + -
70C MET* 3.8 22.4 - - - -
81C ILE* 3.7 22.7 - - + +
82C ILE* 1.3 73.6 - - - +
84C GLU* 1.3 54.6 + - - +
105C GLN* 4.3 1.3 - - - +
109C MET* 4.2 13.7 - - + -
120C CYS* 5.4 0.9 - - + -
121C ALA 3.1 8.2 + - - +
122C LEU* 3.4 15.3 - - + +
123C ARG* 2.8 32.4 + - - +
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Residues in contact with GLU 84 (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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42C GLU* 3.5 22.5 - - + +
43C ILE 3.0 9.6 + - - +
44C ASN* 3.0 47.4 + - - +
45C TYR* 3.1 21.7 + - - -
82C ILE 4.1 0.8 + - - -
83C LEU* 1.3 71.7 - - - +
85C THR* 1.3 65.4 + - - +
86C GLU* 3.5 4.6 + - - +
123C ARG* 3.3 19.6 + - + -
125C THR* 2.6 22.5 + - - +
267C LYS* 2.6 33.6 + - - +
268C ASP* 3.7 8.5 - - - +
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Residues in contact with THR 85 (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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45C TYR* 2.5 25.9 + - - -
62C TYR* 3.9 19.3 - - + +
84C GLU* 1.3 72.5 - - - +
86C GLU* 1.3 58.8 + - - +
87C HIS* 3.5 2.4 + - - -
91C MET* 3.8 22.4 - - + -
101C VAL* 4.4 0.2 - - + -
105C GLN* 2.6 21.6 + - - +
122C LEU* 3.9 1.4 - - - +
123C ARG 2.8 7.9 + - - -
124C HIS* 3.5 32.5 - - + +
125C THR 3.0 23.2 + - - +
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Residues in contact with GLU 86 (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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44C ASN* 3.5 13.0 - - - +
45C TYR 5.0 13.3 + - - +
47C PRO* 5.6 1.4 - - - +
62C TYR* 4.0 10.1 + - - -
84C GLU* 3.5 19.6 + - - +
85C THR* 1.3 70.7 - - - +
87C HIS* 1.3 68.8 + - - +
88C VAL* 3.4 3.8 + - - +
125C THR* 3.8 11.2 - - + +
164C GLU* 2.8 13.3 - - - +
267C LYS* 2.8 10.4 + - - +
313C GLU* 3.5 16.8 - - - +
314C SER* 4.1 11.4 + - - -
512C K 2.3 30.3 - - - -
500D B13 5.5 5.8 - - - +
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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