Contacts of the strand formed by residues 29 - 34 (chain B) in PDB entry 5Y1Z
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 TRP 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 3.6 8.7 - - - +
27B ALA* 5.1 0.3 - - - +
28B ASP* 1.3 88.3 - - - +
30B ALA* 1.3 65.4 + - - +
31B LEU* 3.7 14.4 - - + -
45B ALA* 3.6 14.1 - - + -
46B SER* 3.1 33.1 - - - -
47B GLY* 2.9 65.9 + - - +
49B GLY 3.5 2.6 - - - +
50B GLY 3.6 17.0 - - - -
53B GLU* 3.4 24.6 - - + +
54B LEU* 3.5 33.0 - - + -
57B HIS* 3.6 36.6 - + - -
67B PHE 3.0 14.6 - - - +
68B CYS* 4.2 7.6 - - + -
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Residues in contact with ALA 30 (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 ALA* 4.1 9.9 - - + +
17B TYR* 4.9 0.9 - - + +
20B VAL* 3.9 14.3 - - + +
29B TRP* 1.3 78.1 - - - +
31B LEU* 1.3 60.8 + - - +
32B TYR* 3.7 30.4 - - + +
43B LEU* 4.5 0.2 - - + -
45B ALA 3.6 6.5 - - - +
46B SER* 4.1 9.6 - - - -
66B GLY* 3.6 0.5 - - - -
67B PHE* 2.8 36.5 + - + +
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Residues in contact with LEU 31 (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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29B TRP* 3.7 16.4 - - + -
30B ALA* 1.3 73.9 - - - +
32B TYR* 1.3 56.7 - - - +
43B LEU* 3.7 1.8 - - - +
44B ALA* 2.6 41.4 + - + +
45B ALA* 2.8 17.0 + - + +
54B LEU* 4.1 6.3 - - + -
57B HIS* 3.5 43.7 - - + +
58B PHE* 3.5 28.0 - - + +
64B MET* 3.9 23.6 - - + -
65B TYR 3.4 20.0 - - - +
66B GLY* 3.8 3.1 - - - -
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Residues in contact with TYR 32 (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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13B LEU* 2.9 55.1 + - + -
16B ALA* 3.8 1.0 - - - +
17B TYR* 3.3 16.8 + - - +
30B ALA* 3.7 25.4 - - + +
31B LEU* 1.3 74.3 - - - +
33B THR* 1.3 64.6 + - - +
41B LEU* 4.0 18.4 - - + -
42B LYS 3.3 7.6 - - - +
43B LEU* 3.9 17.7 - - + -
64B MET* 3.3 5.9 - - - +
65B TYR* 2.9 44.3 + - + +
67B PHE* 3.8 23.3 - + + -
109B PHE* 3.4 34.6 - + - -
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Residues in contact with THR 33 (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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32B TYR* 1.3 77.6 - - - +
34B TYR* 1.3 74.7 + - - +
41B LEU* 3.5 12.4 - - - +
42B LYS* 2.8 55.3 + - + +
44B ALA* 4.1 8.7 - - + -
62B LYS* 3.7 22.8 - - - +
63B VAL 2.9 20.9 + - - -
64B MET* 3.7 23.7 - - + +
65B TYR* 5.2 0.2 - - - -
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Residues in contact with TYR 34 (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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4B VAL* 3.9 17.3 - - + -
33B THR* 1.3 87.4 + - - +
35B GLU* 1.3 64.3 + - - +
36B ASP* 3.9 2.9 + - - +
38B SER 3.7 12.3 - - - +
39B ASP* 3.7 20.0 - - - -
40B ASP 3.5 3.4 - - - +
41B LEU* 4.3 5.4 - - + -
42B LYS* 3.5 14.5 + - - -
62B LYS* 4.9 4.7 - - - +
63B VAL* 3.7 28.5 - - + -
65B TYR* 2.5 37.1 + + - -
94B ARG* 3.7 20.0 - - - +
98B CYS* 3.6 18.9 - - - -
101B HIS* 2.8 34.2 + + - +
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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