Contacts of the strand formed by residues 80 - 86 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.9 18.8 - - + -
38G TYR* 4.4 17.5 - - + -
39G THR 5.6 0.9 - - - +
40G ILE* 4.3 7.4 - - + -
41G PRO* 3.3 22.6 - - + +
73G MET* 3.7 5.8 - - - +
78G PHE* 3.5 3.8 + - - +
79G PRO* 1.3 88.6 - - + +
81G ILE* 1.3 66.8 + - - +
118G ILE* 4.0 2.1 - - - +
119G LYS* 3.0 14.1 - - + +
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Residues in contact with ILE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 4.8 0.8 - - - +
40G ILE* 4.1 2.1 - - - +
41G PRO* 3.7 13.9 - - + +
43G ILE* 3.4 23.6 - - + -
69G VAL* 3.6 11.9 - - + -
70G MET* 4.0 21.3 - - - -
73G MET* 3.5 32.8 - - + -
80G ALA* 1.3 75.7 - - - +
82G ILE* 1.3 93.0 + - - +
83G LEU* 3.8 3.8 + - + -
118G ILE* 3.9 19.7 - - + -
119G LYS 2.9 6.7 + - - -
120G CYS* 3.0 34.0 - - + +
121G ALA 3.3 0.9 + - - -
330G SER* 5.2 2.2 - - - -
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.7 29.4 - - + -
34G ILE* 4.3 9.6 - - + -
40G ILE* 3.7 18.2 - - + -
41G PRO 2.8 10.9 + - - +
42G GLU* 3.2 30.1 - - + +
43G ILE 2.8 31.4 + - - -
81G ILE* 1.3 83.4 - - - +
83G LEU* 1.3 66.4 + - - +
121G ALA* 3.4 14.8 - - + +
123G ARG* 4.6 5.4 - - + +
160G LEU* 4.7 7.9 - - + -
265G PRO* 5.4 0.9 - - + -
309G CYS* 3.8 27.1 - - + -
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Residues in contact with LEU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ILE* 3.7 12.1 - - + -
45G TYR* 3.6 22.2 - - + +
66G THR* 3.9 33.4 - - + +
69G VAL* 4.2 15.7 - - + -
70G MET* 3.9 22.2 - - - -
81G ILE* 3.8 18.6 - - + +
82G ILE* 1.3 75.2 - - - +
84G GLU* 1.3 60.3 + - - +
109G MET* 3.8 33.0 - - + -
120G CYS* 5.3 1.1 - - + -
121G ALA 3.0 7.1 + - - +
122G LEU* 3.4 4.0 - - + +
123G ARG* 2.7 28.9 + - - +
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Residues in contact with GLU 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G GLU* 3.6 19.7 - - + +
43G ILE 2.9 9.3 + - - +
44G ASN* 2.7 50.5 + - - +
45G TYR* 2.8 28.6 + - - -
82G ILE* 4.0 1.4 + - - +
83G LEU* 1.3 72.1 - - - +
85G THR* 1.3 64.9 + - - +
86G GLU* 3.6 2.7 + - - +
123G ARG* 3.4 16.6 - - - +
125G THR* 2.6 26.5 + - - +
267G LYS* 2.5 29.7 + - - +
268G ASP* 3.5 12.3 - - - +
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Residues in contact with THR 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G TYR* 2.9 17.0 + - - -
62G TYR* 3.9 21.3 - - + +
84G GLU* 1.3 71.5 - - - +
86G GLU* 1.3 61.7 + - - +
87G HIS* 3.5 3.0 + - + -
91G MET* 3.7 29.8 - - + -
101G VAL* 4.4 0.4 - - + -
105G GLN* 2.5 27.5 + - - +
122G LEU* 3.8 1.4 - - - +
123G ARG 2.9 7.9 + - - -
124G HIS* 3.4 24.0 - - + +
125G THR 2.8 25.6 + - - -
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Residues in contact with GLU 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ASN* 3.6 18.1 + - - +
45G TYR 4.9 13.4 + - - +
47G PRO* 5.6 0.7 - - - +
62G TYR* 3.8 13.3 + - - -
84G GLU* 3.6 19.2 + - - +
85G THR* 1.3 72.3 - - - +
87G HIS* 1.3 68.2 + - - +
88G VAL* 3.4 3.6 + - - +
125G THR* 3.8 12.1 - - + +
164G GLU* 2.8 12.2 - - - +
267G LYS* 2.8 9.2 + - - +
313G GLU* 3.6 13.2 - - - +
314G SER* 4.3 9.9 + - - -
514G K 2.5 29.4 - - - -
500H B13 5.4 10.0 - - - +
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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