Contacts of the helix formed by residues 37 - 48 (chain B) in PDB entry 5OED
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 GLY 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLY 3.5 0.4 - - - -
36B VAL* 1.3 75.0 - - - +
38B LYS* 1.3 68.5 + - - +
39B THR 3.3 2.5 - - - -
40B SER* 3.3 2.4 + - - -
41B ILE* 3.0 31.5 + - - +
143B ASN* 3.5 10.3 + - - -
900B GDP 2.8 36.8 + - - -
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Residues in contact with LYS 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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30B VAL* 3.7 23.0 - - + +
31B ILE 3.5 5.2 - - - -
32B GLY* 3.2 28.7 + - - +
33B GLU 2.7 25.3 + - - -
36B VAL* 3.6 11.8 - - + +
37B GLY* 1.3 78.6 - - - +
39B THR* 1.3 63.5 + - - +
41B ILE* 3.4 7.6 + - - +
42B ILE* 3.3 25.2 + - - +
81B ASP* 4.2 9.9 - - - +
82B ILE* 3.4 24.5 - - + -
86B GLU* 2.7 23.3 + - - -
105B VAL* 4.0 8.1 - - + -
900B GDP 2.3 30.7 + - - +
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Residues in contact with THR 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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148A GLU* 2.7 27.2 + - + +
901A MG 2.1 33.2 - - - -
38B LYS* 1.3 77.1 - - - +
40B SER* 1.3 51.4 + - - +
42B ILE* 3.2 5.6 + - + +
43B LYS* 2.7 42.1 + - + +
81B ASP* 2.8 18.6 + - - +
900B GDP 2.7 10.6 + - - -
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Residues in contact with SER 40 (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 GLY 3.3 2.2 + - - -
39B THR* 1.3 75.7 - - - +
41B ILE* 1.3 57.9 + - - +
43B LYS* 3.8 8.5 - - - +
44B ARG* 2.8 32.2 + - - +
49B LEU 4.8 0.5 - - - +
50B PHE* 4.0 14.8 - - - -
51B SER 5.4 2.6 + - - -
175B ALA* 3.6 21.3 - - - +
900B GDP 3.0 45.0 + - - -
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Residues in contact with ILE 41 (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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30B VAL* 5.6 4.3 - - + -
37B GLY 3.0 21.9 + - - +
38B LYS* 3.6 5.2 - - - +
40B SER* 1.3 77.6 - - - +
42B ILE* 1.3 61.3 + - + +
44B ARG* 3.8 1.6 - - - +
45B TYR* 2.9 28.9 + - + +
79B LEU* 6.5 0.4 - - + -
103B PHE* 5.7 6.1 - - + -
105B VAL* 3.7 30.3 - - + -
141B LEU* 4.0 25.6 - - + -
143B ASN* 3.8 24.9 - - + +
173B THR* 4.4 4.0 - - - +
175B ALA* 4.5 1.3 - - + -
181B ILE* 3.8 38.1 - - + +
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Residues in contact with ILE 42 (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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146A GLY 5.5 0.2 - - - +
30B VAL* 3.8 29.8 - - + -
38B LYS 3.3 15.5 + - - +
39B THR* 3.2 6.8 + - + +
41B ILE* 1.3 76.8 - - + +
43B LYS* 1.3 65.3 + - - +
46B VAL* 2.9 26.2 + - + +
47B HIS* 5.5 1.8 - - + -
63B ALA* 3.7 30.1 - - + -
79B LEU* 3.8 26.0 - - + +
81B ASP* 3.6 39.7 - - + +
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Residues in contact with LYS 43 (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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78A LEU* 5.0 10.8 - - - -
39B THR* 2.7 28.6 + - + +
40B SER* 3.8 8.7 - - - +
42B ILE* 1.3 73.1 - - - +
44B ARG* 1.3 62.5 + - - +
47B HIS* 3.1 41.8 + - + +
49B LEU* 3.2 37.6 + - + +
50B PHE* 5.1 1.1 - - - -
51B SER* 3.9 32.0 + - - +
53B HIS* 3.9 23.0 + - - -
54B TYR* 5.8 0.2 - - - +
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Residues in contact with ARG 44 (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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40B SER 2.8 18.6 + - - +
41B ILE 3.8 2.9 - - - +
43B LYS* 1.3 78.2 - - - +
45B TYR* 1.3 63.2 + - - +
48B GLN* 3.2 37.2 + - - +
49B LEU 3.2 13.2 + - - +
50B PHE* 3.4 24.1 - - + +
175B ALA 2.9 21.5 + - - +
176B LYS 3.0 25.6 + - - -
177B ASP* 4.9 0.6 - - - +
178B ASN* 3.8 42.7 - - - +
181B ILE* 4.0 15.3 - - + -
182B GLU* 5.5 0.2 - - - +
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Residues in contact with TYR 45 (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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41B ILE* 2.9 19.1 + - + +
42B ILE* 4.0 3.4 - - - +
44B ARG* 1.3 81.9 - - - +
46B VAL* 1.3 59.2 + - + +
48B GLN* 4.7 1.2 + - - +
65B MLY 3.3 56.9 - - + +
67B LEU* 3.5 32.6 - - + +
77B LEU* 4.0 12.1 - - + -
79B LEU* 3.8 20.2 - - + -
103B PHE* 6.5 0.9 - + - -
178B ASN* 6.0 0.2 - - - -
181B ILE* 3.9 21.5 - - + -
182B GLU* 3.0 39.5 + - - +
185B ALA* 3.4 32.4 - - + +
186B ARG* 5.0 1.7 + - - +
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Residues in contact with VAL 46 (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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77A ILE* 5.7 3.3 - - + +
42B ILE* 2.9 22.2 + - + +
45B TYR* 1.3 80.8 - - - +
47B HIS* 1.3 86.3 + - + +
48B GLN* 3.6 1.9 - - - +
63B ALA* 4.3 6.3 - - + -
64B LEU 3.2 32.8 - - - +
65B MLY 3.7 27.5 - - + -
79B LEU* 3.6 27.8 - - + -
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Residues in contact with HIS 47 (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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77A ILE* 3.0 43.1 + - + +
78A LEU* 3.8 36.0 + - + +
42B ILE* 5.5 1.6 - - + -
43B LYS* 3.1 28.5 + - + +
46B VAL* 1.3 101.6 + - + +
48B GLN* 1.3 74.4 + - - +
49B LEU* 3.0 15.4 + - + +
63B ALA* 5.4 5.1 - - - +
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Residues in contact with GLN 48 (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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44B ARG* 3.2 34.6 + - - +
45B TYR 5.3 0.2 - - - +
46B VAL 3.6 1.0 - - - +
47B HIS* 1.3 79.1 - - - +
49B LEU* 1.3 57.2 + - - +
65B MLY 4.1 30.5 + - - -
178B ASN* 5.5 4.7 + - - -
182B GLU* 6.0 1.2 - - - -
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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