Contacts of the strand formed by residues 75 - 81 (chain C) in PDB entry 1PKD
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 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.6 34.3 - - + +
35C ILE 3.4 8.1 - - - +
36C ARG* 4.5 9.4 - - + +
37C LEU* 4.1 5.6 - - - -
71C HIS 2.1 33.6 - - - +
72C THR* 3.2 15.4 - - + +
73C GLU 3.8 0.2 - - - -
74C ASN* 1.3 90.9 - - + +
76C LEU* 1.3 56.2 + - - +
77C TYR* 2.5 45.8 + - + -
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Residues in contact with LEU 76 (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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33C LYS 3.3 1.8 - - - +
34C LYS* 3.5 2.6 - - - -
35C ILE* 2.7 45.4 + - + +
37C LEU* 3.9 23.1 - - + +
44C VAL* 4.1 11.9 - - + -
48C ALA* 5.1 4.5 - - + -
52C ILE* 4.3 6.5 - - + -
69C VAL* 4.0 19.7 - - + -
70C ILE 3.7 1.1 - - - +
71C HIS* 3.6 47.1 - - + +
75C LYS* 1.3 75.0 - - - +
77C TYR* 1.3 62.8 + - - +
78C LEU* 4.1 6.3 - - + -
296D HIS* 4.5 5.4 - - + +
304D PHE* 4.0 20.6 - - + -
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Residues in contact with TYR 77 (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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1C MET* 3.7 52.4 - - + +
6C LYS* 4.5 18.2 + - - -
19C TYR* 5.8 0.9 - + - -
32C LEU* 4.7 13.5 - - + -
33C LYS 3.2 4.0 - - - -
34C LYS* 3.5 28.0 - - + +
68C ASP 3.8 0.3 - - - +
69C VAL* 3.4 4.2 - - - -
70C ILE* 2.9 50.7 + - + +
72C THR* 4.8 8.7 - - - -
75C LYS* 2.5 46.9 + - + -
76C LEU* 1.3 73.9 - - - +
78C LEU* 1.3 64.7 + - - +
79C VAL* 3.9 0.5 + - - +
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Residues in contact with LEU 78 (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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31C ALA 3.4 1.9 - - - +
32C LEU* 3.3 5.4 - - - -
33C LYS* 2.8 42.3 + - + +
35C ILE* 3.8 28.9 - - + -
51C GLU* 4.3 14.4 - - + +
52C ILE* 3.6 42.0 - - + -
66C LEU* 3.7 15.7 - - + -
68C ASP 3.6 4.0 - - - -
69C VAL* 3.9 11.9 - - + -
76C LEU* 4.2 7.2 - - + -
77C TYR* 1.3 78.8 - - - +
79C VAL* 1.3 61.1 + - - +
80C PHE* 3.7 26.8 + - + -
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Residues in contact with VAL 79 (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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4C PHE* 4.0 17.3 - - + -
30C VAL* 3.8 32.5 - - + -
31C ALA 3.6 2.2 - - - -
32C LEU* 3.6 17.0 - - + -
66C LEU* 3.3 6.9 - - - +
67C LEU* 2.7 42.0 + - + -
68C ASP* 2.9 28.0 + - + +
70C ILE* 3.8 25.8 - - + -
77C TYR 4.5 1.6 - - - +
78C LEU* 1.3 73.4 - - - +
80C PHE* 1.3 58.2 + - - +
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Residues in contact with PHE 80 (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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18C VAL* 5.9 0.7 - - + -
30C VAL* 3.4 9.4 - - - +
31C ALA* 2.7 39.2 + - + +
33C LYS* 4.0 13.5 - - + -
51C GLU* 3.7 19.3 - - - -
55C LEU* 3.3 28.0 - - + -
64C VAL* 3.7 14.8 - - + -
65C LYS 3.3 14.6 - - - -
66C LEU* 4.0 11.7 - - + -
67C LEU* 3.7 5.2 - - - -
78C LEU* 3.7 35.9 - - + -
79C VAL* 1.3 73.7 - - - +
81C GLU* 1.3 60.0 + - - +
411C UCN 3.5 46.4 - + + +
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Residues in contact with GLU 81 (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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28C GLU* 5.3 3.6 - - - +
29C VAL 5.3 0.2 - - - -
30C VAL* 5.2 0.4 - - - +
60C HIS 5.2 0.5 - - - +
63C ILE 3.4 9.2 - - - +
64C VAL* 3.7 10.0 - - + +
65C LYS* 2.7 54.4 + - + +
67C LEU* 3.6 16.4 - - + +
80C PHE* 1.3 70.9 - - - +
82C PHE* 1.3 62.3 + - - +
83C LEU* 3.8 8.4 - - + +
142C LYS* 3.2 32.8 + - - -
411C UCN 2.8 23.9 + - - +
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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