Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 1WG8
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 ARG 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO 5.6 0.4 - - - +
23B GLY* 2.9 32.7 + - - -
24B GLY 2.9 10.3 + - - +
25B VAL* 3.4 29.1 - - + +
26B TYR* 2.8 27.7 + - - -
41B LEU* 4.2 0.4 - - - -
44B GLY 4.1 1.3 + - - +
45B GLY* 1.3 77.2 - - - +
47B VAL* 1.3 63.8 + - - +
48B ILE* 6.0 0.2 - - - -
67B GLY* 3.5 21.1 - - - +
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Residues in contact with VAL 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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26B TYR 3.3 8.5 - - - +
28B ASP* 4.0 19.7 - - + +
37B ALA* 4.0 9.4 - - + +
40B ILE* 3.5 37.2 - - + -
41B LEU* 3.6 20.6 - - + -
46B ARG* 1.3 79.0 - - - +
48B ILE* 1.3 76.0 + - - +
49B GLY 3.9 0.7 - - - +
67B GLY 2.7 12.5 + - - +
68B LEU* 3.3 19.7 - - + +
69B THR* 2.8 26.5 + - - -
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Residues in contact with ILE 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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25B VAL* 4.0 20.0 - - + -
26B TYR 2.8 10.0 + - - +
27B VAL* 3.2 13.6 - - + +
28B ASP 2.9 20.8 + - - -
47B VAL* 1.3 76.2 - - - +
49B GLY* 1.3 58.1 + - - +
50B LEU* 4.3 17.0 - - + -
69B THR* 3.4 16.2 - - - +
71B VAL* 4.5 1.1 - - + -
82B LEU* 4.0 28.7 - - + -
85B LEU* 3.7 29.8 - - + -
87B VAL* 4.0 23.6 - - + -
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Residues in contact with GLY 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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28B ASP* 3.1 13.7 - - - -
31B LEU* 3.9 21.3 - - - -
47B VAL* 3.8 5.9 - - - +
48B ILE* 1.3 73.8 - - - +
50B LEU* 1.3 62.5 + - - -
68B LEU* 4.0 2.1 - - - +
69B THR 2.9 9.3 + - - -
70B VAL* 3.5 6.8 - - - +
71B VAL* 2.8 27.4 + - - +
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Residues in contact with LEU 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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27B VAL* 4.7 6.3 - - + -
28B ASP 2.8 7.4 + - - +
29B ALA* 3.2 25.2 - - - +
30B THR* 3.6 0.2 - - - -
31B LEU* 2.8 24.3 + - - -
48B ILE* 4.3 9.6 - - + -
49B GLY* 1.3 76.0 - - - -
51B ASP* 1.3 61.3 + - - +
71B VAL* 3.3 40.2 - - + +
73B GLY 4.7 6.7 - - - +
74B ASN 4.7 3.4 - - - +
75B PHE* 4.2 25.8 - - + +
78B LEU* 4.0 31.0 - - + -
81B HIS* 4.6 15.5 - - + -
82B LEU* 5.8 1.3 - - + -
3141B SAM 4.7 0.9 - - + -
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Residues in contact with ASP 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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31B LEU* 3.8 10.5 + - + -
32B GLY* 2.7 28.4 + - - -
49B GLY 4.4 0.2 + - - -
50B LEU* 1.3 74.7 - - - +
52B GLN* 1.3 59.3 + - - +
53B ASP* 2.9 23.3 + - - +
56B ALA* 3.8 11.7 - - + -
57B VAL* 3.3 19.4 - - + +
70B VAL* 5.9 0.4 - - + +
71B VAL 3.1 5.7 + - - -
72B GLN* 3.3 10.0 - - - -
73B GLY 3.0 19.1 + - - -
3141B SAM 2.8 47.3 + - - +
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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