Contacts of the strand formed by residues 67 - 73 (chain B) in PDB entry 4KY2
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 GLY 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ARG* 4.2 8.7 - - - -
35B LYS 6.1 0.4 - - - -
65B VAL 3.5 1.4 + - - -
66B GLU* 1.3 76.9 - - - +
68B ILE* 1.3 63.1 + - - -
69B TYR* 3.5 11.0 - - - -
96B THR* 3.3 7.6 - - - +
97B ALA 2.9 29.5 + - - -
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Residues in contact with ILE 68 (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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89A GLU* 4.1 21.1 - - + +
34B ARG* 3.6 4.9 - - - +
35B LYS* 2.9 60.8 + - + +
41B TRP* 3.7 23.3 - - + -
67B GLY* 1.3 72.3 - - - -
69B TYR* 1.3 64.6 + - - +
94B VAL* 3.8 14.1 - - + -
95B PHE 3.4 9.2 - - - +
96B THR* 3.5 18.8 - - + +
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Residues in contact with TYR 69 (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 VAL* 4.3 15.3 - - + -
33B PHE 3.2 15.9 - - - +
34B ARG* 3.3 34.8 + - + -
41B TRP* 4.0 3.6 - - - -
44B PHE* 3.9 12.7 - + - -
63B GLU 4.1 1.9 + - - -
64B PHE* 3.6 37.7 - + - -
65B VAL* 2.7 40.3 + - - +
67B GLY* 3.5 21.8 - - - -
68B ILE* 1.3 73.4 - - - +
70B LYS* 1.3 59.9 + - - +
93B VAL 3.8 0.9 - - - +
94B VAL* 3.3 5.0 - - - +
95B PHE* 2.9 51.8 + + + -
97B ALA* 3.8 11.0 - - + -
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Residues in contact with LYS 70 (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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92A GLU* 4.3 3.8 - - - +
31B HIS 3.6 1.4 - - - +
32B VAL* 3.2 4.9 - - - +
33B PHE* 2.8 56.2 + - + +
41B TRP* 3.7 56.3 - - + +
69B TYR* 1.3 75.6 - - - +
71B VAL* 1.3 67.0 + - - +
72B GLU* 4.2 8.1 + - - -
92B GLU* 3.6 37.8 + - - +
93B VAL 3.3 3.8 - - - +
94B VAL* 4.0 18.6 - - + +
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Residues in contact with VAL 71 (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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12B LEU* 5.0 4.3 - - + -
14B VAL* 4.1 17.5 - - + -
30B VAL* 3.8 25.6 - - + -
31B HIS 3.5 3.1 - - - +
32B VAL* 4.2 17.5 - - + +
70B LYS* 1.3 76.4 - - - +
72B GLU* 1.3 58.7 + - - +
73B ILE* 4.0 14.9 + - + +
91B ALA 3.6 1.7 - - - +
92B GLU* 3.5 3.5 - - - -
93B VAL* 2.8 45.4 + - + +
95B PHE* 4.0 23.6 - - + -
107B ILE* 4.6 15.7 - - + -
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Residues in contact with GLU 72 (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 ALA 4.0 0.3 - - - +
30B VAL* 3.3 4.5 - - - -
31B HIS* 2.7 48.7 + - + +
33B PHE* 3.6 27.6 - - + -
70B LYS* 4.0 8.5 + - + -
71B VAL* 1.3 70.5 - - - +
73B ILE* 1.3 60.6 + - - +
74B ASP* 4.0 1.3 + - + +
90B HIS* 2.9 47.6 + - + -
91B ALA 3.5 3.1 - - - -
92B GLU* 3.0 18.6 - - - +
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Residues in contact with ILE 73 (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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14B VAL* 4.5 9.6 - - + -
16B VAL* 4.3 22.7 - - + -
28B VAL* 3.5 26.9 - - + -
29B ALA 3.7 3.1 - - - +
30B VAL* 4.5 9.9 - - + +
71B VAL* 4.2 15.9 - - + +
72B GLU* 1.3 76.1 - - - +
74B ASP* 1.3 58.0 + - - +
75B THR* 2.8 22.7 + - + +
90B HIS* 3.1 5.0 - - - +
91B ALA* 2.8 43.8 + - + +
93B VAL* 4.9 11.0 - - + -
107B ILE* 5.4 2.5 - - + -
109B ALA* 3.8 28.3 - - + -
111B LEU* 4.9 0.7 - - + -
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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