Contacts of the strand formed by residues 18 - 22 (chain Z) in PDB entry 6P59
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 TYR 18 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14W ILE* 5.0 1.1 - - + -
15W PHE 4.2 10.8 - - - -
16W THR* 3.4 19.8 + - - -
30W ILE* 4.6 11.4 - - + +
34W ILE* 3.8 40.8 - - + +
17Z MET* 1.3 90.6 - - - +
19Z VAL* 1.3 65.2 + - - +
30Z ILE* 3.7 20.0 - - + -
31Z VAL* 3.5 19.7 - - - -
32Z LYS* 3.5 34.4 - - + -
58Z ASN* 4.2 8.5 - - - +
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Residues in contact with VAL 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Z TYR* 1.3 75.6 - - - +
20Z LYS* 1.3 61.1 + - - +
21Z LEU* 4.6 10.8 - - + -
29Z PHE 3.9 0.3 - - - +
30Z ILE* 3.3 7.3 - - - +
31Z VAL* 2.9 43.3 + - + +
33Z ARG* 3.6 45.3 - - + +
36Z ALA* 3.7 27.6 - - + -
46Z LEU* 4.0 15.5 - - + -
58Z ASN* 3.7 18.2 - - - +
60Z VAL* 6.1 1.1 - - + -
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Residues in contact with LYS 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z VAL* 1.3 76.3 - - - +
21Z LEU* 1.3 66.8 + - - +
22Z ILE* 4.1 9.2 - - + -
28Z GLU* 3.9 36.3 + - + +
29Z PHE 3.6 2.2 - - - +
30Z ILE* 3.8 26.2 - - + +
58Z ASN 3.1 13.6 + - - +
59Z GLU* 3.3 35.8 + - - +
60Z VAL 2.8 26.5 + - - +
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Residues in contact with LEU 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z VAL* 4.6 13.7 - - + -
20Z LYS* 1.3 83.4 - - - +
22Z ILE* 1.3 64.9 + - - +
27Z HIS 3.5 1.6 - - - +
28Z GLU* 4.6 0.2 - - - -
29Z PHE* 2.6 52.9 + - + +
31Z VAL* 4.5 11.7 - - + -
36Z ALA* 4.8 1.6 - - + -
42Z ILE* 4.1 23.8 - - + -
60Z VAL* 3.4 27.1 - - + +
62Z PHE* 4.0 13.7 - - + -
70Z LEU* 4.3 14.8 - - + -
74Z CYS* 4.2 20.9 - - - -
77Z PHE* 4.3 10.5 - - + -
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Residues in contact with ILE 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Z LYS* 4.4 9.0 - - + +
21Z LEU* 1.3 75.0 - - - +
23Z SER* 1.3 69.8 + - - +
26Z GLY* 4.0 18.2 - - - +
27Z HIS 3.3 9.2 - - - +
28Z GLU* 4.3 19.1 - - + +
59Z GLU* 3.5 36.1 - - + +
60Z VAL 2.8 16.2 + - - +
61Z ASN* 3.3 29.4 - - + +
62Z PHE* 2.8 34.8 + - - +
70Z LEU* 4.1 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