Contacts of the strand formed by residues 41 - 47 (chain B) in PDB entry 1D4W
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 TYR 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.5 38.4 + + - -
31B LEU* 4.0 20.2 - - + -
32B ARG 3.4 5.4 - - - +
33B ASP* 3.6 19.7 + - - -
39B GLY* 3.6 23.4 - - - -
40B VAL* 1.3 75.5 - - - +
42B CYS* 1.3 62.6 + - - +
43B LEU 4.1 0.2 - - - -
54B TYR 3.6 0.2 - - - +
55B ARG* 3.5 4.5 - - - -
56B VAL* 2.7 46.0 + - + +
64B TRP* 3.6 36.8 - + - -
80B ILE* 4.6 4.0 - - + -
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Residues in contact with CYS 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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31B LEU* 3.3 7.3 - - - -
32B ARG* 2.7 50.3 + - + +
34B SER* 3.7 17.0 - - - -
41B TYR* 1.3 78.7 - - - +
43B LEU* 1.3 62.9 - - - +
44B CYS* 3.5 4.6 + - - -
53B THR* 3.6 20.6 - - + -
54B TYR 3.5 3.1 - - - -
55B ARG* 4.3 5.2 - - - -
281D PTR 3.2 39.7 - - - -
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Residues in contact with LEU 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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6B VAL* 5.6 0.2 - - + -
29B TYR* 4.2 8.7 - - + -
30B LEU 3.7 14.8 - - - +
31B LEU* 3.7 16.2 - - + +
41B TYR 4.1 0.2 - - - -
42B CYS* 1.3 71.8 - - - +
44B CYS* 1.3 58.2 + - - +
45B VAL* 4.6 3.1 - - + -
52B TYR 3.6 2.3 - - - +
53B THR* 3.4 1.9 - - - -
54B TYR* 2.7 57.4 + - + +
56B VAL* 4.2 8.3 - - + +
83B LEU* 4.4 20.9 - - + -
84B ILE* 4.9 9.4 - - + -
87B PHE* 4.8 9.4 - - + -
94B ILE* 5.2 3.4 - - + -
98B LEU* 3.9 43.7 - - + -
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Residues in contact with CYS 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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16B GLY* 5.8 2.2 - - - +
20B LEU* 3.5 11.3 - - + +
29B TYR* 3.1 8.0 - - - +
30B LEU* 2.8 47.8 + - + +
32B ARG* 3.8 24.9 - - - -
42B CYS 3.6 14.6 - - - -
43B LEU* 1.3 72.5 - - - +
45B VAL* 1.3 63.4 + - - +
51B ILE* 3.5 18.2 - - + -
52B TYR 3.5 3.8 - - - -
53B THR* 4.0 18.6 - - - -
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Residues in contact with VAL 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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27B GLY* 4.3 5.8 - - - -
28B SER 3.4 10.5 - - - +
29B TYR* 4.2 0.9 - - + -
43B LEU* 4.5 3.8 - - + +
44B CYS* 1.3 76.6 - - - +
46B LEU* 1.3 64.9 + - - +
47B TYR 3.6 0.7 + - - -
51B ILE* 3.5 4.6 - - - +
52B TYR* 2.7 46.3 + - - +
54B TYR* 4.0 21.3 - - + -
94B ILE* 4.6 4.9 - - + -
95B VAL* 4.7 8.1 - - + -
96B ILE* 3.9 29.8 - - + +
97B PRO 4.8 0.4 - - - +
98B LEU* 3.6 32.8 - - + -
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Residues in contact with LEU 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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20B LEU* 3.7 30.9 - - + +
21B LEU* 3.8 32.8 - - + +
24B GLY* 4.1 5.6 - - - -
25B LEU 3.4 38.6 - - - +
26B ASP* 3.3 7.9 - - - +
27B GLY* 2.8 29.1 + - - -
28B SER* 3.0 16.4 + - - +
45B VAL* 1.3 68.6 - - - +
47B TYR* 1.3 64.2 + - - +
49B GLY* 4.1 13.2 - - - +
50B TYR 3.5 17.5 - - - +
51B ILE* 4.5 4.9 - - + +
96B ILE* 4.0 1.9 - - - +
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Residues in contact with TYR 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 ASP* 3.5 12.6 - - - -
45B VAL 3.6 0.8 + - - -
46B LEU* 1.3 76.7 - - - +
48B HIS* 1.3 115.2 + + + +
49B GLY 3.3 1.8 - - - -
50B TYR 3.0 18.7 + - - +
52B TYR* 3.5 23.3 - + + -
95B VAL* 3.3 51.6 - - + -
96B ILE* 4.0 26.2 - - + -
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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