Contacts of the strand formed by residues 105 - 111 (chain B) in PDB entry 5AJQ
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 LYS 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.0 18.2 - - + -
100B TYR 3.9 0.7 - - - +
101B TYR* 3.2 6.7 - - - -
102B HIS 3.2 30.2 + - - +
103B ASP* 5.7 0.9 - - + -
104B GLY* 1.3 80.0 - - - +
106B LEU* 1.3 60.3 + - - +
107B TRP* 3.8 24.3 - - + +
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Residues in contact with LEU 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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26B VAL* 4.1 20.9 - - + -
65B LYS 3.6 0.7 - - - +
66B VAL* 3.4 35.8 - - - +
75B LEU* 4.4 31.2 - - + +
78B TYR* 3.7 29.8 - - + -
82B ILE* 4.2 17.9 - - + -
99B ALA* 5.3 0.2 - - + -
100B TYR 3.5 14.8 - - - +
101B TYR* 4.2 3.3 - - + -
104B GLY 4.1 1.2 + - - -
105B LYS* 1.3 72.5 - - - +
107B TRP* 1.3 63.8 + - - +
108B ILE* 4.3 15.2 - - + +
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Residues in contact with TRP 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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32B PRO* 3.6 37.9 - - + +
33B ASN* 3.9 26.9 - - - -
36B TRP* 5.1 5.6 - - + -
38B ILE* 3.9 30.1 - - + -
64B ALA* 5.3 3.8 - - + -
65B LYS 3.7 3.8 - - - -
66B VAL* 4.4 12.9 - - + +
98B GLY 3.9 0.3 - - - +
99B ALA* 3.2 6.1 - - - +
100B TYR* 2.8 47.8 + - + +
102B HIS* 4.9 7.0 + + - +
105B LYS* 3.8 26.6 - - + +
106B LEU* 1.3 79.9 - - - +
108B ILE* 1.3 62.5 + - - +
109B MET* 4.0 25.4 - - + -
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Residues in contact with ILE 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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63B ALA 3.6 1.7 - - - +
64B ALA* 3.3 5.9 - - - -
65B LYS* 3.1 37.7 + - + +
66B VAL* 6.0 3.1 - - - +
78B TYR* 5.1 5.2 - - + -
81B GLU* 5.6 6.1 - - + +
82B ILE* 4.1 31.6 - - + -
85B LEU* 5.0 4.3 - - + -
96B LEU* 3.8 12.6 - - + -
98B GLY 3.7 2.2 - - - -
99B ALA* 4.7 0.7 - - + +
106B LEU* 4.3 16.6 - - + +
107B TRP* 1.3 76.9 - - - +
109B MET* 1.3 62.0 + - - +
110B ILE* 3.7 27.8 - - + -
800B DB8 3.6 19.0 - - + +
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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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36B TRP* 3.7 52.3 - - + +
53B ALA* 3.8 15.5 - - + -
62B ALA* 4.3 5.2 - - + -
63B ALA 3.6 4.3 - - - -
64B ALA* 3.3 28.3 - - + -
96B LEU* 3.5 5.7 - - - +
97B LEU* 2.8 30.2 + - - -
98B GLY* 2.7 29.3 + - - +
100B TYR* 3.7 10.5 - - + -
107B TRP* 4.0 30.7 - - + -
108B ILE* 1.3 79.2 - - - +
110B ILE* 1.3 56.8 + - - +
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Residues in contact with ILE 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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62B ALA* 3.2 3.7 - - - +
63B ALA 2.7 42.5 + - - +
85B LEU* 3.7 29.8 - - + -
94B VAL* 3.5 23.8 - - + -
95B LYS 3.5 3.1 - - - +
96B LEU* 3.8 13.5 - - + +
97B LEU* 4.2 3.6 - - - -
108B ILE* 3.7 17.0 - - + -
109B MET* 1.3 78.2 - - - +
111B GLU* 1.3 71.0 + - - +
112B PHE 3.1 0.9 + - - -
800B DB8 3.2 54.3 - - + +
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Residues in contact with GLU 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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61B LEU 4.4 0.2 - - - -
94B VAL* 5.0 2.2 - - - +
95B LYS* 2.9 39.2 + - + +
97B LEU* 3.7 19.8 - - + +
110B ILE* 1.3 73.6 - - + +
112B PHE* 1.3 65.2 + - - +
113B CYS* 3.4 11.0 + - - -
172B ARG* 5.8 5.8 - - - +
800B DB8 3.5 12.6 - - - -
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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