Contacts of the strand formed by residues 48 - 55 (chain B) in PDB entry 4OWW
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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.6 9.8 - - - +
44B ALA* 3.4 0.9 - - - -
45B ASP* 3.1 28.8 + - - +
46B LYS 3.4 0.8 - - - -
47B THR* 1.3 81.7 + - - +
49B SER* 1.3 59.0 + - - -
103B SER* 3.3 21.7 + - - -
106B PRO 3.4 13.5 - - - -
108B PHE* 4.1 3.1 - - - -
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Residues in contact with SER 49 (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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7B VAL* 3.8 2.0 - - - -
24B LEU* 4.5 0.9 - - - -
42B LYS* 3.4 27.7 + - - -
43B VAL 3.2 14.8 - - - -
44B ALA* 3.8 10.1 - - - -
48B GLY* 1.3 73.7 - - - -
50B ILE* 1.3 64.2 + - - +
103B SER 3.7 0.6 + - - -
104B GLU 2.7 26.3 + - - -
106B PRO 3.0 4.9 + - - -
107B ASN* 3.6 9.2 - - - +
108B PHE* 2.9 30.1 + - - -
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Residues in contact with ILE 50 (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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7B VAL* 3.7 19.1 - - + -
10B ILE* 3.8 37.0 - - + -
42B LYS* 3.8 1.5 - - - -
43B VAL* 2.9 49.2 + - + +
49B SER* 1.3 76.8 - - - +
51B ASN* 1.3 71.4 + - - +
82B LEU* 4.0 20.9 - - + +
84B LEU* 4.1 25.8 - - + +
107B ASN* 4.5 3.1 - - - -
108B PHE* 4.5 9.4 - - + -
109B SER* 3.3 15.5 - - - +
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Residues in contact with ASN 51 (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 THR* 4.1 23.7 - - + +
41B CYS 3.4 7.9 - - - +
42B LYS* 4.4 15.5 + - - +
50B ILE* 1.3 76.3 - - - +
52B ILE* 1.3 53.6 + - - +
81B CYS* 5.0 8.3 - - - +
82B LEU 4.7 0.2 - - - +
83B THR* 3.6 11.1 + - + +
84B LEU* 2.7 34.7 + - - +
107B ASN* 4.5 6.2 + - - +
109B SER* 2.7 36.3 + - - +
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Residues in contact with ILE 52 (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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21B PHE* 4.0 21.8 - - + -
40B THR* 3.4 3.1 - - - -
41B CYS* 2.8 49.9 + - + +
43B VAL* 3.7 24.0 - - + -
50B ILE 3.8 0.6 + - - -
51B ASN* 1.3 74.1 - - - +
53B SER* 1.3 69.4 + - - +
54B VAL* 3.8 7.6 + - + -
62B ILE* 5.9 1.6 - - + -
70B LEU* 4.6 5.2 - - + -
84B LEU* 3.3 37.7 - - + +
85B TYR* 4.2 1.8 - - - +
86B THR* 4.6 6.3 - - - +
92B LEU* 4.1 26.5 - - + -
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Residues in contact with SER 53 (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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38B VAL* 4.3 7.2 - - - +
39B ARG 3.6 4.9 - - - -
40B THR* 3.4 13.5 - - - +
52B ILE* 1.3 77.5 - - - +
54B VAL* 1.3 63.0 + - - +
55B TRP* 3.4 30.2 - - - -
78B PHE* 5.4 1.6 - - - -
83B THR* 3.3 14.4 - - - +
84B LEU 3.0 9.2 + - - +
85B TYR* 3.6 16.5 - - - -
86B THR* 4.9 3.8 + - - -
6L T 5.2 0.2 - - - +
7L T 3.3 16.6 + - - -
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Residues in contact with VAL 54 (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 GLU 3.8 0.2 - - - +
38B VAL* 3.4 4.0 - - - +
39B ARG* 2.9 34.1 + - + +
41B CYS* 4.3 9.6 - - - -
52B ILE* 4.2 22.4 - - + +
53B SER* 1.3 78.5 - - - +
55B TRP* 1.3 68.0 + - - +
56B ASP 3.9 0.5 + - - -
58B VAL* 3.7 21.5 - - + -
59B GLY* 3.3 33.7 - - - +
62B ILE* 4.3 9.9 - - + -
92B LEU* 4.0 21.1 - - + -
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Residues in contact with TRP 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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36B HIS* 4.0 25.1 - + + +
37B GLU 3.4 5.8 - - - -
38B VAL* 4.1 16.9 - - + +
53B SER* 3.4 32.5 - - - -
54B VAL* 1.3 79.7 - - - +
56B ASP* 1.3 68.7 + - - +
57B ASP 3.1 3.8 + - - -
58B VAL* 3.9 9.0 + - - +
59B GLY 4.0 2.1 + - - -
85B TYR* 3.6 28.9 - + - -
3L T 3.3 33.1 - - + +
6L T 3.4 57.7 + + + +
7L T 3.7 38.1 + + - -
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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