Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 5ODS
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 PHE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR 4.5 0.2 - - - +
32B MET* 3.3 25.1 - - - +
33B GLU 4.5 2.1 + - - -
34B SER* 3.4 8.0 + - - +
35B ASP 3.7 0.2 - - - -
36B LYS* 1.3 97.9 - - + +
38B ILE* 1.3 65.7 + - - +
39B CYS 4.2 0.2 - - - -
52B ILE* 4.1 23.1 - - + -
53B ILE 3.4 5.4 - - - +
54B ASP* 4.2 19.7 - - + -
55B MET* 4.6 1.1 - - - -
73B MET* 3.7 30.3 - - + -
74B ASN 3.7 10.5 - - - -
76B ALA 3.2 26.9 - - - -
77B SER 3.6 15.5 - - - -
78B LYS* 4.0 34.8 - - + -
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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
----------------------------------------------------------
13B LEU* 5.2 0.9 - - + -
15B LEU* 4.5 12.8 - - + -
30B LEU* 3.9 26.9 - - + -
31B THR 3.8 2.7 - - - -
32B MET* 3.8 21.5 - - + -
37B PHE* 1.3 80.7 - - - +
39B CYS* 1.3 61.0 + - - +
40B ILE* 3.7 18.8 - - + +
51B VAL 3.7 2.4 - - - +
52B ILE* 4.8 0.2 - - - -
53B ILE* 2.9 39.2 + - + +
55B MET* 3.7 24.7 - - - -
318B VAL* 4.1 10.3 - - + -
324B VAL* 4.0 25.6 - - + -
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Residues in contact with CYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR 3.6 2.1 - - - +
30B LEU* 3.5 1.9 - - - -
31B THR* 2.9 50.5 + - - +
37B PHE 4.2 0.4 - - - -
38B ILE* 1.3 73.0 - - - +
40B ILE* 1.3 64.8 + - - +
41B ARG* 5.1 1.5 - - - +
50B VAL* 3.8 27.6 - - - -
51B VAL 3.4 3.4 - - - -
52B ILE* 4.7 0.2 - - - +
71B ALA* 3.5 28.7 - - - +
73B MET* 4.0 32.5 - - + +
80B ILE* 4.3 0.2 - - - -
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Residues in contact with ILE 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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15B LEU* 5.2 1.3 - - + -
20B ILE* 4.2 21.5 - - + -
24B ASN* 3.8 38.6 - - + +
29B THR 3.5 3.1 - - - +
30B LEU* 3.7 22.4 - - + -
38B ILE* 3.7 18.2 - - + +
39B CYS* 1.3 77.2 - - - +
41B ARG* 1.3 65.7 + - - +
42B GLU* 3.9 13.3 + - + +
50B VAL* 3.6 3.3 - - - +
51B VAL* 2.7 55.8 + - + +
53B ILE* 3.7 25.8 - - + -
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Residues in contact with ARG 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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24B ASN* 2.9 20.3 + - - -
28B SER* 3.1 27.5 + - - -
29B THR* 2.9 38.2 + - - +
31B THR* 6.3 1.7 - - + +
39B CYS* 5.1 1.8 - - - -
40B ILE* 1.3 76.4 - - - +
42B GLU* 1.3 61.7 + - - +
49B GLN 3.8 6.5 - - - +
50B VAL* 4.3 14.1 - - + -
68B ALA 2.8 32.9 + - - -
69B ASP* 3.1 26.7 + - - +
70B SER* 3.7 4.7 - - - +
71B ALA* 3.8 32.0 - - + +
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Residues in contact with GLU 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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19B GLY 4.3 0.7 - - - +
20B ILE* 3.4 18.7 - - - +
21B ASN* 2.8 32.8 + - - +
24B ASN* 3.1 26.8 - - - +
40B ILE* 3.9 10.0 + - + -
41B ARG* 1.3 75.1 - - - +
43B LYS* 1.3 63.1 + - - +
44B VAL* 4.1 4.6 - - + +
48B ALA* 4.2 0.9 - - - -
49B GLN* 3.1 36.9 + - + +
51B VAL* 4.3 9.4 - - + +
63B ARG* 2.9 37.0 + - - +
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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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24B ASN* 4.7 3.4 + - - +
42B GLU* 1.3 76.9 - - - +
44B VAL* 1.3 60.2 + - - +
45B GLY 3.8 2.0 + - - -
46B GLU* 3.3 48.5 + - - +
47B GLN 3.3 19.1 - - - +
48B ALA* 4.4 10.4 - - + +
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Residues in contact with VAL 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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42B GLU* 5.1 4.3 - - + +
43B LYS* 1.3 76.1 - - - +
45B GLY* 1.3 58.7 + - - +
46B GLU 3.3 0.2 - - - -
47B GLN* 2.8 46.1 + - - +
49B GLN* 3.4 35.6 + - + +
63B ARG* 4.5 8.3 - - - +
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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