Contacts of the strand formed by residues 26 - 32 (chain B) in PDB entry 1OXC
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 GLN 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 4.1 13.0 - - + -
22B SER* 3.5 6.8 - - - -
24B GLY 3.0 22.0 + - - +
25B THR* 1.3 73.4 - - - +
27B THR* 1.3 58.0 + - - +
28B VAL* 5.0 0.2 - - + -
41B SER* 2.8 36.7 + - - -
42B GLY 2.8 10.8 + - - +
50B ILE* 4.4 12.8 - - + -
67B VAL* 3.7 6.2 - - - +
68B SER 3.9 1.3 - - - -
69B VAL* 3.5 19.5 - - - +
74B SER* 4.6 0.7 + - - -
94B SER* 4.4 0.5 + - - -
96B ASP* 2.9 25.1 + - - -
104B ASP* 3.3 28.3 - - - +
105B ALA* 3.2 27.3 - - + +
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Residues in contact with THR 27 (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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25B THR* 4.7 4.2 + - - +
26B GLN* 1.3 76.2 + - - +
28B VAL* 1.3 63.5 + - - +
29B ASN* 3.8 17.7 + - - +
39B THR* 4.1 18.2 - - + -
40B PHE 3.4 4.7 - - - +
41B SER* 3.6 11.1 + - - -
66B GLN 3.8 0.5 - - - +
67B VAL* 3.4 4.5 - - - +
68B SER* 2.9 49.5 + - - +
70B ASN 5.6 2.4 + - - -
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Residues in contact with VAL 28 (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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18B ALA* 4.0 21.1 - - + -
26B GLN* 5.0 0.4 - - + -
27B THR* 1.3 78.1 - - - +
29B ASN* 1.3 66.7 + - - +
30B VAL* 4.3 12.1 - - + -
38B ALA 3.9 0.5 - - - +
39B THR* 3.1 6.9 - - - +
40B PHE* 2.8 51.8 + - + +
50B ILE* 4.5 7.9 - - + -
65B VAL* 4.1 10.3 - - + -
66B GLN 3.5 6.7 - - - +
67B VAL* 4.2 13.5 - - + -
105B ALA* 4.3 13.5 - - + -
107B VAL* 3.7 25.1 - - + -
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Residues in contact with ASN 29 (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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27B THR* 3.8 17.8 - - - +
28B VAL* 1.3 74.2 - - - +
30B VAL* 1.3 63.8 + - - +
31B LEU* 3.8 14.4 - - + +
36B THR* 3.9 14.1 + - + +
38B ALA 3.5 2.0 - - - +
39B THR* 2.9 34.3 + - - +
64B GLN 3.7 1.0 - - - +
65B VAL* 3.4 4.9 - - - +
66B GLN* 2.8 48.3 + - + +
68B SER* 4.7 4.9 + - - -
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Residues in contact with VAL 30 (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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14B PHE* 4.7 0.7 - - + -
16B VAL* 3.7 35.2 - - + -
28B VAL* 4.3 14.1 - - + -
29B ASN* 1.3 76.7 - - - +
31B LEU* 1.3 56.5 + - - +
32B VAL* 5.1 0.2 - - + -
36B THR* 3.6 1.0 - - - -
37B ALA* 2.8 32.4 + - - +
38B ALA* 2.8 27.8 + - + +
40B PHE* 4.5 5.4 - - + -
55B LEU* 3.9 20.2 - - + -
63B VAL* 4.0 24.5 - - + -
64B GLN 3.4 4.0 - - - +
65B VAL* 4.8 7.2 - - + -
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Residues in contact with LEU 31 (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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29B ASN* 3.8 18.6 - - + +
30B VAL* 1.3 76.6 - - - +
32B VAL* 1.3 62.8 + - - +
33B ASN 4.1 0.7 - - - -
34B ASN* 3.8 25.4 - - - +
35B GLU 3.3 11.9 - - - +
36B THR* 3.9 18.4 - - - +
62B LYS 3.7 0.3 - - - +
63B VAL* 3.2 7.6 - - - +
64B GLN* 2.7 62.5 + - + +
66B GLN* 4.0 36.1 - - + +
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Residues in contact with VAL 32 (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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14B PHE* 4.2 25.1 - - + -
30B VAL* 4.1 0.4 + - + -
31B LEU* 1.3 76.0 - - - +
33B ASN* 1.3 78.1 + - + +
34B ASN 3.1 0.4 - - - -
35B GLU* 2.9 20.4 + - - +
37B ALA* 3.8 23.1 - - + -
55B LEU* 4.3 6.5 - - + -
56B ASN 3.6 15.5 - - - +
57B SER* 3.5 27.6 - - - +
58B GLY* 4.6 1.8 - - - +
62B LYS 3.3 6.3 - - - +
63B VAL* 4.6 3.4 - - + -
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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