Contacts of the strand formed by residues 54 - 61 (chain B) in PDB entry 1O92
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 LYS 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ASN* 3.2 28.4 + - - +
53B ALA* 1.3 70.8 - - - +
55B VAL* 1.3 62.1 + - - +
56B ALA* 5.6 0.2 - - - -
71B GLU 4.1 0.7 - - - +
72B ILE* 3.1 7.3 - - - +
73B THR* 2.7 57.5 + - + +
74B SER* 5.2 0.2 - - - -
287B ASP* 3.1 9.9 - - - +
288B TYR* 4.5 10.0 + - + +
289B THR* 4.3 25.2 - - - +
290B LYS* 5.2 6.1 - - - +
1397B ADP 5.6 4.5 - - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL 5.0 0.9 - - - -
43B LEU* 3.5 43.7 - - + +
46B HIS* 4.1 27.8 - - + -
53B ALA* 3.6 8.2 + - + +
54B LYS* 1.3 75.7 - - - +
56B ALA* 1.3 64.7 + - - +
57B CYS* 3.9 15.9 - - - -
72B ILE* 3.4 18.4 - - + -
285B GLY 3.4 13.5 - - - +
286B LYS* 3.7 0.7 - - - -
287B ASP* 2.8 37.8 + - + -
290B LYS* 3.7 4.2 + - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 1.3 77.3 - - - +
57B CYS* 1.3 60.1 + - - +
70B GLY* 3.3 1.7 - - - -
71B GLU* 2.8 28.5 + - - +
72B ILE* 3.3 5.6 - - - +
285B GLY 3.4 4.7 - - - -
286B LYS* 4.9 0.2 - - - +
290B LYS* 4.3 0.9 - - - +
1397B ADP 2.6 66.9 - - + +
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Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 3.6 29.7 - - - -
42B VAL* 4.1 17.9 - - - -
55B VAL* 3.9 15.9 - - - -
56B ALA* 1.3 75.0 - - - +
58B GLU* 1.3 64.1 + - - +
68B LEU* 4.2 6.1 - - + -
69B CYS 3.2 16.2 - - - +
70B GLY* 3.8 4.5 - - - -
72B ILE* 4.4 4.0 - - + -
111B LEU* 4.1 11.2 - - + -
284B SER 4.4 1.2 - - - +
285B GLY* 3.0 32.0 + - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLY 4.0 3.8 - - - +
259A ASP* 2.6 29.0 - - + +
260A ALA* 3.0 27.3 - - + +
262A VAL* 4.3 5.0 - - - +
265A ARG* 3.3 28.5 + - - +
39B SER* 3.5 6.7 - - - -
57B CYS* 1.3 76.8 - - - +
59B THR* 1.3 66.0 + - - +
60B VAL* 4.8 5.2 - - + +
68B LEU* 3.9 2.4 - - - +
69B CYS* 2.9 35.3 + - + +
262B VAL* 5.1 1.4 - - - +
263B THR* 3.9 15.3 - - + -
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B CYS* 3.4 19.5 + - - -
38B ILE* 3.6 27.5 - - + +
39B SER* 2.9 18.0 + - - -
58B GLU* 1.3 76.1 + - - +
60B VAL* 1.3 74.9 + - - +
61B CYS* 5.3 0.2 - - + -
66B VAL* 3.5 27.1 - - + -
67B LEU 3.3 12.3 - - - +
68B LEU* 4.6 6.3 - - - +
262B VAL* 3.7 0.5 - - - +
263B THR* 2.8 32.5 + - - -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.5 35.2 - - + -
67A LEU* 5.9 5.6 - - + -
260A ALA* 4.9 8.7 - - + -
262A VAL* 4.9 2.0 - - + -
35B CYS* 3.9 1.1 - - - -
58B GLU* 4.8 11.9 - - - +
59B THR* 1.3 81.8 - - - +
61B CYS* 1.3 67.7 + - - +
62B LYS* 5.9 0.7 - - + -
65B MET* 3.9 5.9 - - + +
66B VAL* 3.4 1.9 - - - -
67B LEU* 2.7 55.4 + - + +
69B CYS* 5.3 3.6 - - - -
260B ALA* 5.1 4.0 - - + -
261B GLY 3.4 12.8 - - - +
262B VAL* 4.6 9.0 - - + -
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Residues in contact with CYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 3.7 32.3 - - - -
34B ILE* 4.8 8.1 - - + -
35B CYS* 3.7 10.1 - - - -
38B ILE* 6.0 0.2 - - + -
59B THR* 5.3 0.4 - - + -
60B VAL* 1.3 77.1 - - - +
62B LYS* 1.3 65.7 + - - +
65B MET* 3.1 11.0 - - - +
66B VAL* 4.2 15.9 - - + -
100B PHE* 4.2 16.2 - - + -
256B PRO* 4.6 4.7 - - - -
257B GLN 4.7 0.2 - - - +
260B ALA* 3.3 3.3 - - - +
261B GLY* 2.8 40.1 + - - +
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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