Contacts of the strand formed by residues 29 - 34 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.6 7.4 - - - +
27A ALA* 4.7 1.0 - - - +
28A ASP* 1.3 91.0 - - - +
30A ALA* 1.3 67.2 + - - +
31A LEU* 3.6 14.8 - - + -
45A ALA* 3.6 14.6 - - + -
46A SER* 3.4 33.3 - - - -
47A GLY* 3.0 55.0 + - - +
48A GLU 3.0 21.2 + - - -
50A GLY 3.7 14.8 - - - -
53A GLU* 3.5 11.3 - - + +
54A LEU* 3.6 28.5 - - + -
57A HIS* 3.5 38.8 - + - -
67A PHE 3.3 9.6 - - - +
68A CYS* 4.0 15.5 - - + -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.8 19.5 - - + +
17A TYR* 4.8 0.4 - - - +
20A VAL* 4.0 12.3 - - + -
29A TRP* 1.3 80.6 - - - +
31A LEU* 1.3 60.4 + - - +
32A TYR* 3.8 29.2 - - + +
43A LEU* 4.7 0.2 - - + -
45A ALA 3.7 3.8 - - - +
46A SER* 4.1 3.8 - - - -
54A LEU* 4.5 0.7 - - - +
65A TYR 4.0 0.3 - - - +
66A GLY* 3.6 2.3 - - - -
67A PHE* 2.8 36.6 + - + +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 3.6 16.6 - - + -
30A ALA* 1.3 75.1 - - - +
32A TYR* 1.3 55.7 + - - +
43A LEU* 3.6 2.1 - - - +
44A ALA* 2.7 45.6 + - + +
45A ALA* 2.8 17.8 + - + +
54A LEU* 4.0 8.3 - - + -
57A HIS* 3.5 32.1 - - + +
58A PHE* 3.6 20.0 - - + -
59A GLU* 5.9 0.2 - - - +
64A MET* 3.4 42.0 - - + -
65A TYR 3.6 13.5 - - - +
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.8 54.2 + - + -
16A ALA* 3.5 3.4 - - + +
17A TYR* 3.2 17.5 + - - +
30A ALA* 3.8 19.3 - - + +
31A LEU* 1.3 74.3 - - - +
33A THR* 1.3 64.1 + - - +
41A LEU* 4.0 16.8 - - + -
42A LYS 3.2 10.5 - - - +
43A LEU* 3.9 17.9 - - + -
44A ALA* 4.1 1.1 - - - +
64A MET* 3.2 8.0 - - - +
65A TYR* 2.8 46.7 + - + +
67A PHE* 4.4 12.8 - - + -
82A LEU* 6.1 0.7 - - + -
109A PHE* 3.3 42.1 - + - -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 1.3 76.8 - - - +
34A TYR* 1.3 75.9 + - - +
41A LEU* 3.5 10.5 - - - -
42A LYS* 2.8 48.2 + - + +
44A ALA* 4.0 18.8 - - + -
62A LYS* 3.1 23.6 + - + +
63A VAL 2.9 20.7 + - - -
64A MET* 3.5 16.8 - - - +
65A TYR* 5.0 0.4 - - - +
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.0 10.2 - - + +
33A THR* 1.3 89.4 + - - +
35A GLU* 1.3 63.7 + - - +
36A ASP* 3.8 1.4 + - - +
38A SER 3.7 11.0 - - - +
39A ASP 3.8 27.6 - - - -
40A ASP 3.7 2.9 - - - -
41A LEU* 4.2 6.1 - - + -
42A LYS* 4.4 3.3 + - - +
62A LYS* 3.0 26.3 + - - +
63A VAL* 3.6 37.2 - - + -
65A TYR* 2.6 37.1 + + - -
94A ARG* 3.2 23.1 - - - +
98A CYS* 3.6 9.5 - - - -
101A HIS* 2.8 33.9 + + - +
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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