Contacts of the strand formed by residues 64 - 68 (chain U) in PDB entry 4ZKO
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 64 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U ILE* 4.2 8.7 - - + -
34U TYR 3.3 13.9 - - - +
35U ARG* 4.0 23.0 - - + -
36U ARG* 5.4 0.5 - - - -
41U VAL* 4.1 9.4 - - + -
58U CYS 4.3 1.9 + - - -
59U PHE* 3.5 40.9 - + - -
60U TYR* 2.6 41.3 + - - +
61U LYS 3.3 20.0 - - - -
62U GLU* 3.2 10.1 + - - +
63U ASP* 1.3 82.1 - - + +
65U ILE* 1.3 69.1 + - - +
84U GLU* 3.9 15.4 - - - +
85U VAL* 3.6 33.6 + - + -
88U LEU* 3.7 17.7 - - + -
106U LEU* 5.4 0.9 - - + -
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Residues in contact with ILE 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U ALA 3.8 0.9 - - - +
33U ILE* 3.5 3.1 - - - +
34U TYR* 2.8 40.7 + - + +
36U ARG* 3.6 37.0 - - + +
38U VAL* 4.1 20.9 - - + -
64U TYR* 1.3 79.2 - - - +
66U VAL* 1.3 65.5 + - - +
67U TYR* 3.6 27.4 - - + +
82U LYS* 3.7 38.1 - - + +
83U PHE 3.6 7.0 - - - +
84U GLU* 5.0 6.3 - - - +
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Residues in contact with VAL 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31U ALA* 4.1 18.6 - - + -
32U ALA 3.5 4.9 - - - +
33U ILE* 4.2 10.1 - - + -
52U VAL* 4.3 7.2 - - + -
65U ILE* 1.3 78.0 - - - +
67U TYR* 1.3 73.8 + - - +
68U LEU* 4.9 2.9 - - + -
82U LYS* 3.6 2.4 - - - -
83U PHE* 2.8 45.2 + - + +
85U VAL* 3.7 25.8 - - + -
106U LEU* 4.0 17.3 - - + -
108U ILE* 4.0 26.0 - - + -
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Residues in contact with TYR 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U PHE 4.2 0.3 - - - +
31U ALA* 3.4 7.4 - - - +
32U ALA* 2.9 34.8 + - + +
34U TYR* 3.5 35.4 - + - -
38U VAL* 6.2 0.7 - - + -
65U ILE* 3.6 19.2 - - + +
66U VAL* 1.3 75.5 - - - +
68U LEU* 1.3 64.6 + - - +
70U ARG* 3.7 35.5 + - + +
76U ASN* 4.8 2.6 + - - -
80U GLU* 3.4 31.0 - - - -
81U MET 3.3 13.7 - - - +
82U LYS* 3.6 44.6 + - + +
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Residues in contact with LEU 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28U PRO 5.5 1.8 - - - +
29U TRP 4.6 1.3 - - - +
30U PHE 4.0 7.2 - - - +
31U ALA* 3.7 31.4 - - + -
46U LEU* 3.8 30.1 - - + -
52U VAL* 4.5 3.4 - - + -
66U VAL* 4.9 1.6 - - + -
67U TYR* 1.3 73.8 - - - +
69U GLY* 1.3 64.4 + - - +
70U ARG 3.3 2.2 - - - +
80U GLU* 3.3 4.5 - - - +
81U MET* 2.9 28.6 + - + -
83U PHE* 3.6 22.4 - - + -
108U ILE* 3.9 4.7 - - + -
112U ALA* 3.5 32.1 - - + -
118U ILE* 3.9 24.5 - - + -
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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