Contacts of the strand formed by residues 52 - 58 (chain B) in PDB entry 1AYZ
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 THR 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B MET* 3.4 34.8 - - + -
41B ILE* 4.9 5.8 - - + -
50B ASP 3.5 7.8 + - - +
51B GLY* 1.3 71.6 - - - +
53B PHE* 1.3 61.7 + - - +
54B ARG* 3.1 23.1 + - - +
74B SER* 3.8 0.2 + - - -
148B SER* 2.9 32.0 + - - -
149B TRP* 3.8 9.1 - - + +
152B ASP* 3.1 21.3 + - - +
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Residues in contact with PHE 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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39B MET* 3.1 2.6 - - - -
40B ILE* 2.8 44.1 + - + +
42B GLY* 4.0 7.2 - - - -
48B TYR* 3.8 26.5 - + + -
51B GLY* 3.6 27.6 - - - -
52B THR* 1.3 71.3 - - - +
54B ARG* 1.3 60.9 + - - +
55B LEU* 3.6 5.0 - - - +
72B PHE* 3.8 20.6 - - + -
74B SER* 3.7 10.1 - - - -
75B GLU 4.3 2.0 - - - -
76B MET* 3.3 26.2 - - - -
113B PHE* 3.8 16.6 - + + -
144B THR* 3.8 29.4 - - - -
145B VAL* 4.0 17.7 - - + -
148B SER* 4.3 4.7 - - - -
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Residues in contact with ARG 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 ASN* 5.8 2.7 - - - +
38B ALA 3.2 10.8 - - - +
39B MET* 3.5 31.4 - - - +
52B THR* 3.1 22.6 + - - -
53B PHE* 1.3 72.4 - - - +
55B LEU* 1.3 57.6 + - - +
72B PHE* 3.5 6.9 - - - -
73B LEU* 2.7 42.4 + - + -
74B SER* 2.9 24.9 + - - +
148B SER* 4.2 1.4 + - - +
151B ASP* 5.5 8.1 - - + +
152B ASP* 2.6 41.5 + - - -
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Residues in contact with LEU 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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37B ASN* 3.7 10.9 + - - -
38B ALA* 2.8 38.4 + - + +
39B MET* 4.1 2.7 - - - +
40B ILE* 3.9 20.0 - - + -
53B PHE 3.6 18.6 - - - +
54B ARG* 1.3 74.1 - - - +
56B LEU* 1.3 62.1 + - - +
57B LEU* 4.1 10.8 - - + -
70B VAL* 3.7 24.0 - - + -
71B LYS 3.2 10.1 - - - +
72B PHE* 3.6 31.4 - - + -
73B LEU* 4.0 5.7 - - - +
87B ILE* 4.0 4.9 - - + -
106B LEU* 4.6 4.3 - - + -
109B ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 56 (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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35B VAL* 3.8 21.5 - - + -
36B TRP 3.0 20.6 - - - +
37B ASN* 4.4 11.2 - - - +
55B LEU* 1.3 73.4 - - - +
57B LEU* 1.3 63.7 + - - +
58B GLU* 3.4 39.4 - - + +
69B HIS 3.4 4.9 - - - +
70B VAL* 3.5 1.2 - - - -
71B LYS* 2.8 46.6 + - - +
73B LEU* 4.0 26.5 - - + -
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Residues in contact with LEU 57 (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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34B MET 3.8 0.5 - - - +
35B VAL* 3.5 3.6 - - - +
36B TRP* 2.8 44.6 + - + +
38B ALA* 4.0 24.7 - - + -
55B LEU* 4.1 8.1 - - + -
56B LEU* 1.3 85.3 - - - +
58B GLU* 1.3 63.5 + - - +
59B PHE* 3.9 30.2 - - + -
68B PRO* 4.8 2.5 - - + -
69B HIS 3.3 4.0 - - - +
70B VAL* 4.0 19.7 - - + -
102B VAL* 4.5 19.1 - - + -
105B ILE* 4.5 21.1 - - + -
106B LEU* 4.8 7.4 - - + -
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Residues in contact with GLU 58 (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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34B MET 3.4 5.6 - - - +
35B VAL* 4.6 14.2 - - + +
56B LEU* 3.4 30.0 - - + +
57B LEU* 1.3 77.9 - - - +
59B PHE* 1.3 62.8 + - - +
68B PRO* 3.3 3.4 - - - +
69B HIS* 2.8 66.4 + - + +
71B LYS* 4.5 6.1 + - - -
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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