Contacts of the strand formed by residues 32 - 39 (chain B) in PDB entry 5OND
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 MET 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A MET* 3.5 40.3 - - + +
34A THR* 4.9 2.5 + - - -
47A SER* 4.4 4.1 + - - +
30B ALA* 4.0 12.1 - - - +
31B PRO* 1.3 79.7 - - - +
33B ILE* 1.3 62.0 + - - +
47B SER* 3.4 26.2 - - - +
48B GLU* 3.3 27.6 - - - +
49B PRO* 3.6 24.0 - - + -
50B LEU* 4.3 8.7 - - - +
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Residues in contact with ILE 33 (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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32B MET* 1.3 75.2 - - - +
34B THR* 1.3 74.3 + - - +
35B LEU* 3.9 19.6 + - + -
46B VAL 3.7 0.7 - - - +
47B SER* 3.4 2.8 - - - -
48B GLU* 2.9 45.5 + - + +
50B LEU* 3.7 28.5 - - + -
130B PHE* 3.9 34.1 - - + +
132B GLU 5.4 0.2 - - - +
138B ARG* 3.7 28.9 - - - +
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Residues in contact with THR 34 (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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29A LEU* 4.0 19.5 - - + -
31A PRO* 3.7 26.2 - - + +
32A MET 4.9 2.4 + - - -
96A LEU* 3.5 37.5 - - + +
97A SER* 3.4 20.4 - - - -
33B ILE* 1.3 78.4 - - - +
35B LEU* 1.3 67.0 + - - +
45B ALA* 4.5 5.6 - - + -
46B VAL 3.2 11.0 - - - +
47B SER* 4.1 5.9 + - - -
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Residues in contact with LEU 35 (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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97A SER* 3.9 8.5 - - - -
33B ILE* 4.0 25.1 - - + -
34B THR* 1.3 78.3 - - - +
36B GLU* 1.3 67.5 + - - +
37B LYS* 3.8 14.6 - - + -
45B ALA* 3.5 1.9 - - - -
46B VAL* 2.9 52.9 + - + +
48B GLU* 3.9 13.9 - - + +
130B PHE 6.0 0.2 - - - +
132B GLU 4.7 0.9 - - - +
133B PRO* 4.1 17.9 - - + +
138B ARG* 3.6 27.1 - - - +
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Residues in contact with GLU 36 (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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93A ILE* 5.5 3.6 - - - +
94A HIS* 3.3 32.4 + - + +
97A SER* 3.4 20.1 + - - +
35B LEU* 1.3 76.3 - - - +
37B LYS* 1.3 65.6 + - - +
43B ARG* 4.1 32.2 + - + +
44B THR* 3.1 21.6 - - - +
45B ALA* 4.9 6.3 - - - +
133B PRO* 5.5 4.9 - - - +
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Residues in contact with LYS 37 (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 LEU* 3.6 15.7 + - + -
36B GLU* 1.3 79.5 - - - +
38B ILE* 1.3 73.8 + - - +
39B VAL* 4.7 0.9 - - + -
43B ARG* 4.4 2.0 - - - +
44B THR* 2.9 33.4 + - - +
46B VAL* 4.1 17.3 - - + -
48B GLU* 3.3 29.3 + - - +
133B PRO* 2.9 39.4 + - + +
134B ASP* 4.2 6.5 + - - +
135B GLY 4.9 1.0 - - - +
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Residues in contact with ILE 38 (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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37B LYS* 1.3 75.5 - - - +
39B VAL* 1.3 67.4 + - - +
41B GLY* 3.8 14.6 - - - +
42B LYS 3.4 17.5 - - - +
43B ARG* 3.3 59.5 - - + +
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Residues in contact with VAL 39 (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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27A ASN* 3.2 25.6 + - - +
37B LYS* 3.6 3.3 + - + +
38B ILE* 1.3 80.5 - - - +
40B ARG* 1.3 92.7 + - + +
41B GLY 3.2 0.7 - - - -
42B LYS* 2.8 23.6 + - - +
44B THR* 3.6 24.1 - - + +
46B VAL* 4.0 19.7 - - + -
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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