Contacts of the strand formed by residues 65 - 69 (chain C) in PDB entry 1PYB
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 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.1 10.5 - - + -
20C ALA 3.4 6.7 - - - +
21C LYS* 3.0 34.6 - - + +
63C GLY 4.0 9.2 - - - +
64C LYS* 1.3 72.7 - - - +
66C ILE* 1.3 60.2 + - - +
99C VAL* 2.9 31.2 - - + +
100C PRO* 3.1 23.6 - - + +
102C ARG 4.5 1.7 + - - +
103C ASP* 3.3 26.1 + - - +
104C VAL* 3.2 38.7 + - + +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 3.4 3.8 - - - +
20C ALA 2.9 30.9 + - - +
22C VAL* 3.8 25.1 - - + -
37C LEU* 4.5 13.5 - - + -
39C LEU* 5.2 1.6 - - + -
61C LEU* 4.8 7.0 - - + -
64C LYS* 3.4 20.4 + - + +
65C LYS* 1.3 77.9 - - - +
67C VAL* 1.3 75.9 + - - +
68C ILE* 3.3 13.4 - - + +
86C ILE* 3.6 27.4 - - + -
87C LEU 4.8 1.3 - - - +
97C VAL* 3.5 28.9 - - + -
98C ILE 3.4 14.1 - - - +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.5 9.6 - - + -
18C ARG 3.9 6.7 - - - +
19C VAL* 4.0 17.9 - - + -
66C ILE* 1.3 82.3 - - - +
68C ILE* 1.3 64.4 + - - +
87C LEU* 3.6 40.2 + - + +
98C ILE* 3.4 31.9 + - + +
100C PRO* 4.8 8.3 - - + -
110C LEU* 3.6 28.9 - - + -
289D ALA* 4.9 1.6 - - + -
298D ILE* 4.5 10.1 - - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.7 0.9 - - - -
18C ARG* 2.8 38.8 + - - +
20C ALA* 4.1 13.0 - - + +
39C LEU* 3.5 37.5 - - + -
41C LEU* 5.4 7.7 - - + +
66C ILE* 3.3 27.6 - - + +
67C VAL* 1.3 77.6 - - - +
69C VAL* 1.3 66.4 + - - +
70C ALA* 3.1 5.7 + - - +
83C GLN 4.8 1.8 - - - +
84C GLY* 3.6 22.2 - - - +
85C MET 3.4 20.2 - - - +
86C ILE* 3.4 23.8 - - + +
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Residues in contact with VAL 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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15C VAL* 4.0 21.1 - - + -
16C ASP 3.5 12.3 - - - +
17C LEU* 3.2 23.8 - - + -
68C ILE* 1.3 70.4 - - - +
70C ALA* 1.3 63.4 + - - +
71C ASN* 3.9 11.9 - - - +
72C LEU* 3.3 32.7 + - + +
84C GLY* 3.1 19.1 - - - -
85C MET* 3.1 20.5 + - + +
87C LEU* 4.1 17.5 - - + -
212D PHE* 6.2 1.1 - - + -
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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