Contacts of the strand formed by residues 105 - 112 (chain B) in PDB entry 5MY4
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 LEU 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A HIS* 3.8 21.8 - - + +
33A ASP* 3.7 8.1 - - - +
37A TYR* 3.3 46.0 - - + +
101B TYR* 3.3 19.6 - - - +
102B ASP 4.2 1.9 + - - -
103B ASN* 3.6 2.2 + - - +
104B ILE* 1.3 83.3 - - + +
106B ASP* 1.3 71.7 + - - +
107B TYR* 3.4 11.4 + - + -
1C PCA 3.3 27.8 - - + +
2C PHE 3.2 17.9 - - - +
3C ARG* 4.3 10.5 - - - +
4C HIS* 4.3 0.2 - - - +
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Residues in contact with ASP 106 (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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33B GLY* 3.9 9.2 + - - -
50B PHE* 2.9 31.5 - - + -
52B SER* 4.7 1.6 - - - -
53B ASN* 5.1 0.2 - - - +
99B TYR* 3.6 30.8 - - + +
100B ASP 3.3 5.6 - - - +
101B TYR* 3.4 8.3 - - - +
105B LEU* 1.3 69.6 - - - +
107B TYR* 1.3 57.3 + - - +
1C PCA 2.8 25.6 + - - -
2C PHE* 2.8 17.0 + - + +
3C ARG 4.0 8.0 - - - +
4C HIS* 2.6 36.7 + - - -
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Residues in contact with TYR 107 (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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37A TYR* 3.4 41.3 - + + -
39A HIS* 3.1 6.0 + + - -
54A TYR* 4.1 20.8 - + - -
55A LYS* 3.7 21.8 - - + -
96A SER* 2.4 33.9 + - - -
99B TYR* 4.1 1.3 - - - -
100B ASP* 3.0 28.6 + - - -
101B TYR* 3.7 20.6 - - - -
102B ASP* 3.1 31.4 + - + -
105B LEU* 3.7 16.4 - - + +
106B ASP* 1.3 74.8 - - - +
108B VAL* 1.3 79.3 + - + +
1C PCA 4.3 3.4 - - - -
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Residues in contact with VAL 108 (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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39A HIS* 3.6 34.8 - - + +
41A TYR* 3.8 9.2 - - - +
51A LEU* 3.9 17.7 - - + -
54A TYR* 4.2 7.4 - - + -
96A SER* 5.1 0.7 - - - -
99B TYR* 3.3 9.5 - - - -
100B ASP* 2.8 45.3 + - + +
107B TYR* 1.3 107.3 - - + +
109B MET* 1.3 64.4 + - - +
110B ASP* 3.4 8.6 + - + -
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Residues in contact with MET 109 (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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41A TYR* 2.8 31.5 + - - +
51A LEU* 4.5 0.3 - - - +
94A SER* 5.3 1.8 - - - +
96A SER* 6.4 0.4 - - - -
101A PRO* 4.3 14.8 - - + -
103A PHE* 3.8 30.1 - - + -
35B ALA* 4.1 6.7 - - - -
37B VAL* 3.5 28.9 - - + -
47B TRP* 4.5 3.1 - - + -
97B ALA* 4.1 11.7 - - + -
98B ARG 3.1 8.3 - - - +
99B TYR* 3.4 45.7 - - + +
108B VAL* 1.3 72.0 - - - +
110B ASP* 1.3 60.6 + - - +
111B TYR 3.8 0.4 - - - -
112B TRP* 3.3 22.5 + - + +
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Residues in contact with ASP 110 (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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50A LYS* 5.8 0.2 - - - -
51A LEU* 3.9 30.3 + - + +
60A PHE* 4.0 24.0 - - + -
98B ARG* 2.8 59.6 + - - +
100B ASP* 3.3 23.6 - - + +
108B VAL* 3.4 9.3 + - + +
109B MET* 1.3 74.9 - - - +
111B TYR* 1.3 87.8 + - - -
112B TRP* 4.1 5.9 - - - -
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Residues in contact with TYR 111 (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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60A PHE* 3.5 34.5 - + - -
61A SER* 4.8 8.5 - - - -
1B GLU* 6.4 0.2 - - + -
2B VAL* 3.5 60.5 + - + -
4B LEU* 3.2 7.7 - - + +
97B ALA* 3.2 4.3 - - - +
98B ARG* 2.8 43.4 + - + -
110B ASP* 1.3 101.7 + - - +
112B TRP* 1.3 62.5 + - - +
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Residues in contact with TRP 112 (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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41A TYR* 3.5 29.9 - + - -
48A SER* 3.7 13.0 + - - +
49A PRO* 3.7 44.6 - - + +
50A LYS* 5.0 3.2 + - - -
51A LEU 5.5 0.7 - - - -
103A PHE* 3.7 32.5 - + - -
4B LEU* 4.3 4.6 + - - -
37B VAL* 3.6 31.6 - - + -
45B PRO* 4.2 3.1 - - + -
95B TYR* 3.9 20.0 - + + -
96B CYS 3.3 7.2 - - - +
97B ALA* 4.1 7.6 - - + -
109B MET* 3.3 31.2 + - + +
110B ASP 4.1 3.8 - - - -
111B TYR* 1.3 89.1 - - - +
113B GLY* 1.3 69.8 + - - +
114B GLN* 4.3 3.3 - - - +
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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