Contacts of the strand formed by residues 65 - 70 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C PHE* 4.2 12.3 - - + -
54C ALA* 3.5 34.3 - - + +
57C TYR* 4.4 4.9 - - + -
58C ALA* 3.8 12.3 - - + +
63C LYS 3.6 0.4 + - - -
64C PRO* 1.3 75.0 - - - +
66C PHE* 1.3 60.4 + - - +
67C ILE* 4.2 2.2 + - - +
91C PRO 3.0 5.9 + - - -
92C LEU* 3.5 9.6 - - + +
93C ILE* 2.8 29.7 + - - +
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.8 23.3 - - + -
17C ILE* 3.7 18.7 - - + +
19C THR 3.7 14.6 + - - +
20C VAL* 3.6 27.1 - - + -
21C PHE* 2.9 30.4 + - - -
31C PHE* 3.8 34.5 - + - -
65C ALA* 1.3 73.8 - - - +
67C ILE* 1.3 70.0 + - - +
68C ASN* 4.4 0.2 - - + -
93C ILE* 3.7 18.4 - - + -
95C THR* 3.6 33.7 - - + -
139C MET* 3.7 21.3 - - + -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.2 10.8 - - + +
50C VAL* 3.9 6.3 - - + -
51C VAL* 4.2 15.0 - - + -
54C ALA* 3.5 31.9 - - + -
65C ALA 4.7 0.7 - - - +
66C PHE* 1.3 82.5 - - - +
68C ASN* 1.3 64.4 + - - +
69C LEU* 3.6 33.4 - - + -
92C LEU* 4.0 24.9 - - + -
93C ILE 2.9 11.5 + - - +
94C VAL* 3.9 25.8 - - + -
95C THR* 2.9 29.3 + - - -
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Residues in contact with ASN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.9 20.4 - - + +
21C PHE 2.9 9.3 + - - -
22C GLY* 3.2 22.3 - - - -
23C ASN 3.3 8.7 + - - +
24C PRO* 5.5 1.2 - - - +
28C GLU* 3.4 34.3 - - - +
31C PHE* 3.8 27.7 - - + +
32C LEU* 3.9 11.5 - - + +
41C TYR* 4.7 2.1 + - + -
66C PHE* 4.4 0.2 - - + -
67C ILE* 1.3 73.6 - - - +
69C LEU* 1.3 64.4 + - - +
95C THR* 3.0 22.7 + - - +
96C ALA* 4.5 2.2 - - - +
97C GLY 4.7 1.0 - - - +
163C TRP* 6.3 0.4 - - - -
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN 4.0 5.8 - - - +
28C GLU* 3.2 15.2 - - - +
47C GLU* 3.8 21.8 - - + -
50C VAL* 3.9 16.6 - - + -
51C VAL* 4.3 4.5 - - + -
67C ILE* 3.6 22.7 - - + -
68C ASN* 1.3 76.9 - - - +
70C HIS* 1.3 61.7 + - - +
71C SER 3.8 0.2 - - - -
74C GLY* 3.9 8.3 - - - +
75C THR* 3.9 22.4 - - + +
78C ALA* 3.9 26.0 - - + -
82C LEU* 6.3 0.2 - - + -
94C VAL* 3.9 22.0 - - + -
95C THR 2.8 11.9 + - - +
96C ALA* 3.2 19.2 - - - -
97C GLY 3.2 0.7 + - - -
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Residues in contact with HIS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A TZD 3.3 55.6 + + + +
23C ASN 3.9 6.2 + - - +
25C GLY* 3.5 5.6 - - - -
26C SER 4.0 13.0 - - - -
27C ASN* 4.2 15.5 - - - -
28C GLU* 2.8 28.3 + - - +
47C GLU* 5.0 1.0 + - - +
69C LEU* 1.3 71.8 - - - +
71C SER* 1.3 68.5 + - - +
73C ALA* 3.8 4.7 + - + -
74C GLY* 2.8 34.4 + - - -
110C LEU* 3.6 41.7 - - + +
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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