Contacts of the strand formed by residues 34 - 38 (chain C) in PDB entry 2PK9
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 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.3 7.4 - - + -
21C VAL* 4.6 9.6 - - + -
22C TYR 4.0 12.3 - - - +
23C LYS* 4.6 0.9 - - - +
33C VAL* 1.3 70.7 - - - +
35C LEU* 1.3 64.1 + - - +
36C LYS 3.9 0.2 + - - -
80C LEU 3.7 1.6 - - - +
81C VAL* 3.9 0.7 - - - -
82C PHE* 2.9 45.0 + - + +
83C GLU 4.5 3.4 - - - +
84C PHE* 4.0 23.8 - - + +
85C MET 5.3 0.4 - - - +
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Residues in contact with LEU 35 (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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7C PHE* 4.0 27.6 - - + -
8C LYS 5.5 4.0 - - - +
9C GLN* 5.2 14.4 - - + +
20C THR 4.2 0.2 - - - +
21C VAL* 3.2 3.5 - - - +
22C TYR* 2.6 46.5 + - + +
23C LYS 5.1 10.3 - - - +
24C GLY* 5.2 0.4 - - - +
33C VAL* 3.8 19.2 + - + +
34C ALA* 1.3 72.1 - - - +
36C LYS* 1.3 59.8 + - - +
37C GLU* 4.0 7.5 + - + +
72C ILE* 6.0 1.1 - - + -
79C THR* 5.2 14.4 - - + +
80C LEU 3.5 3.1 - - - +
81C VAL* 3.8 38.1 - - + -
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Residues in contact with LYS 36 (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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19C ALA* 4.3 22.4 - - + +
21C VAL* 4.1 20.6 - - + +
34C ALA 3.9 0.2 + - - -
35C LEU* 1.3 72.5 - - - +
37C GLU* 1.3 59.5 + - - +
38C VAL* 3.2 15.7 + - + +
53C GLU* 2.8 38.8 + - - +
79C THR* 3.5 1.0 - - - -
80C LEU* 2.9 39.3 + - + +
82C PHE* 3.6 30.4 - - + -
151C ASP* 4.4 16.6 + - - +
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Residues in contact with GLU 37 (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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9C GLN* 3.8 21.5 + - - +
19C ALA* 3.4 14.4 - - - +
20C THR* 3.3 38.3 + - + +
22C TYR* 3.8 25.1 + - + -
35C LEU* 5.0 8.6 - - + +
36C LYS* 1.3 69.3 - - - +
38C VAL* 1.3 64.2 + - - +
39C LYS 4.2 0.2 + - - -
77C LYS* 4.6 23.0 + - + +
79C THR* 3.8 27.2 - - + +
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Residues in contact with VAL 38 (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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19C ALA* 3.8 17.5 - - + -
36C LYS* 3.2 14.6 + - + +
37C GLU* 1.3 76.9 - - - +
39C LYS* 1.3 68.7 + - - +
47C PRO* 3.6 29.6 - - + -
49C THR* 5.9 0.7 - - - +
50C ALA* 4.1 17.3 - - + -
53C GLU* 6.0 0.4 - - - +
76C ASN 4.1 2.9 - - - +
77C LYS* 4.4 1.7 - - - -
78C LEU* 3.4 43.1 + - + +
79C THR* 5.6 0.3 - - - +
80C LEU* 4.2 19.5 - - + -
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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