Contacts of the strand formed by residues 65 - 69 (chain B) in PDB entry 4K9N
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 ALA 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 5.9 0.4 - - - -
21B PHE* 4.1 17.9 - - + -
54B ALA* 3.5 28.3 - - + +
57B TYR* 4.4 4.9 - - + -
58B ALA* 3.8 12.5 - - + +
63B LYS 3.6 0.4 + - - -
64B PRO* 1.3 75.3 - - - +
66B PHE* 1.3 60.3 + - - +
67B ILE* 4.7 1.5 - - - +
91B PRO 3.0 6.1 + - - -
92B LEU* 3.6 9.0 - - + +
93B ILE* 2.8 29.9 + - - +
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Residues in contact with PHE 66 (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* 3.8 23.1 - - + -
17B ILE* 3.8 19.0 - - + +
19B THR 3.7 15.6 + - - +
20B VAL* 3.6 26.3 - - + -
21B PHE* 2.9 31.7 + - - -
31B PHE* 3.8 35.0 - + - -
65B ALA* 1.3 73.5 - - - +
67B ILE* 1.3 68.9 + - - +
68B ASN* 4.5 0.2 - - + -
93B ILE* 3.6 21.1 - - + -
95B THR* 3.6 31.9 - - + -
139B MET* 3.7 22.0 - - + -
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Residues in contact with ILE 67 (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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21B PHE* 3.1 10.1 - - + +
50B VAL* 4.0 6.3 - - + -
51B VAL* 4.3 11.7 - - + -
54B ALA* 3.6 32.1 - - + -
65B ALA 4.7 1.3 - - - +
66B PHE* 1.3 83.2 - - - +
68B ASN* 1.3 63.8 + - - +
69B LEU* 3.6 35.9 - - + -
92B LEU* 4.0 25.4 - - + -
93B ILE 2.8 11.8 + - - +
94B VAL* 4.0 25.8 - - + -
95B THR* 2.9 30.8 + - - +
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Residues in contact with ASN 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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20B VAL* 4.0 18.8 - - + +
21B PHE 2.8 8.9 + - - -
22B GLY* 3.2 23.2 - - - -
23B ASN 3.3 8.1 + - - +
24B PRO* 5.3 1.4 - - - +
28B GLU* 3.3 35.2 - - - +
31B PHE* 4.0 22.4 - - + +
32B LEU* 3.9 17.2 - - + +
41B TYR* 4.7 2.1 + - + -
66B PHE* 4.5 0.7 - - + -
67B ILE* 1.3 74.3 - - - +
69B LEU* 1.3 65.0 + - - +
95B THR* 3.0 23.0 + - - +
96B ALA* 4.5 2.0 - - - +
97B GLY* 4.8 1.0 - - - +
163B TRP* 6.2 0.6 - - - -
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Residues in contact with LEU 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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23B ASN 4.0 5.8 - - - +
28B GLU* 3.2 10.7 - - - +
47B GLU* 3.8 18.6 - - + -
50B VAL* 3.9 17.9 - - + -
51B VAL* 4.3 2.9 - - + -
67B ILE* 3.6 22.7 - - + -
68B ASN* 1.3 80.4 - - - +
70B HIS* 1.3 60.7 + - - +
71B SER 3.8 0.2 - - - -
74B GLY 3.9 9.2 - - - +
75B THR* 4.0 21.3 - - + +
78B ALA* 3.9 26.2 - - + -
82B LEU* 6.3 0.7 - - + -
94B VAL* 3.8 21.1 - - + -
95B THR 2.8 12.4 + - - +
96B ALA* 3.2 3.0 - - + -
97B GLY 3.2 22.9 + - - -
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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