Contacts of the strand formed by residues 80 - 86 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32I LEU* 3.9 19.7 - - + -
38I TYR* 4.4 14.1 - - + -
39I THR 5.8 0.4 - - - +
40I ILE* 4.3 10.5 - - + -
41I PRO* 3.4 20.5 - - + +
73I MET* 3.5 7.8 - - - +
78I PHE* 3.4 3.4 + - - +
79I PRO* 1.3 88.7 - - + +
81I ILE* 1.3 65.6 + - - +
118I ILE* 4.1 2.6 - - - +
119I LYS* 3.1 17.0 - - + +
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Residues in contact with ILE 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU* 4.7 0.2 - - - +
40I ILE* 4.1 2.6 - - - +
41I PRO* 3.7 14.8 - - + +
43I ILE* 3.6 22.4 - - + -
69I VAL* 3.7 9.2 - - + -
70I MET* 3.8 29.6 - - + -
73I MET* 3.5 37.9 - - + -
80I ALA* 1.3 76.3 - - - +
82I ILE* 1.3 94.4 + - - +
83I LEU* 4.1 4.4 + - + -
118I ILE* 4.4 3.1 - - + -
119I LYS 3.0 6.7 + - - -
120I CYS* 3.0 37.7 - - + +
121I ALA 3.4 0.5 + - - -
330I SER* 5.2 2.2 - - - -
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Residues in contact with ILE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 3.5 32.3 - - + -
34I ILE* 4.2 12.6 - - + -
40I ILE* 3.8 9.6 - - + -
41I PRO 2.9 11.8 + - - +
42I GLU* 3.6 27.8 - - + +
43I ILE 3.0 17.7 + - - -
81I ILE* 1.3 89.7 - - - +
83I LEU* 1.3 68.4 + - - +
121I ALA* 3.3 15.0 - - + +
123I ARG* 4.6 7.2 - - + -
160I LEU* 4.7 10.5 - - + -
265I PRO* 5.4 0.2 - - + -
309I CYS* 3.8 30.5 - - + -
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ILE* 3.8 14.1 - - + -
45I TYR* 3.5 26.2 - - + +
66I THR* 3.9 33.2 - - + +
69I VAL* 4.3 12.3 - - + -
70I MET* 3.9 26.7 - - - -
81I ILE* 4.1 10.8 - - + +
82I ILE* 1.3 78.2 - - - +
84I GLU* 1.3 59.8 + - - +
105I GLN* 4.1 4.7 - - - +
109I MET* 3.9 17.9 - - + -
120I CYS* 5.5 0.7 - - + -
121I ALA 3.1 8.5 + - - +
122I LEU* 3.4 14.0 - - + +
123I ARG 2.8 24.6 + - - -
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Residues in contact with GLU 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLU* 3.5 24.9 - - + +
43I ILE 3.0 10.4 + - - +
44I ASN* 3.2 41.6 + - - +
45I TYR* 2.9 24.9 + - - -
82I ILE 4.2 0.2 - - - -
83I LEU* 1.3 72.8 - - - +
85I THR* 1.3 66.0 + - - +
86I GLU* 3.4 6.1 + - - +
123I ARG* 3.2 18.4 + - + +
125I THR* 2.6 28.8 + - - +
267I LYS* 2.7 29.2 + - - +
268I ASP* 3.6 5.7 - - - +
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Residues in contact with THR 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I TYR* 2.7 20.7 + - - -
62I TYR* 3.7 31.2 - - + +
84I GLU* 1.3 71.1 - - - +
86I GLU* 1.3 62.0 + - - +
87I HIS* 3.4 3.8 + - + -
91I MET* 3.9 15.7 - - + -
105I GLN* 2.6 24.8 + - - +
122I LEU* 4.0 1.6 - - - +
123I ARG 2.9 7.9 + - - -
124I HIS* 3.5 27.6 - - + +
125I THR 3.0 21.5 + - - -
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Residues in contact with GLU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ASN* 3.7 16.3 - - - +
45I TYR 5.0 12.1 + - - +
47I PRO* 5.8 0.7 - - - +
62I TYR* 3.9 10.6 + - - -
84I GLU* 3.4 17.8 + - - +
85I THR* 1.3 73.6 - - - +
87I HIS* 1.3 68.3 + - - +
88I VAL* 3.3 4.9 + - - +
125I THR* 3.7 12.1 - - + +
164I GLU* 3.1 3.3 - - - +
267I LYS* 2.8 21.7 + - - +
313I GLU* 3.7 14.8 - - - +
314I SER* 4.1 11.4 + - - -
515I K 2.6 28.2 - - - -
500J B13 5.3 7.6 - - - +
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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