Contacts of the strand formed by residues 19 - 25 (chain R) in PDB entry 5EEZ
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 VAL 19 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14R ALA* 3.9 13.7 - - + -
16R GLU* 3.8 19.1 - - + +
17R ASP 3.4 0.4 - - - -
18R GLY* 1.3 77.5 - - - +
20R ASN* 1.3 64.5 + - - +
21R VAL* 4.6 1.6 - - + -
36R GLU 3.6 0.2 - - - +
37R LYS* 3.4 3.8 - - - -
38R LEU* 2.7 49.1 + - + +
57R VAL* 4.1 18.8 - - + -
58R ARG 3.4 11.7 - - - +
59R GLY* 4.0 1.6 - - - -
60R LYS 3.1 40.8 - - - +
61R ALA* 4.3 8.1 - - + -
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Residues in contact with ASN 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R GLY 3.1 25.5 + - - -
19R VAL* 1.3 73.4 + - - +
21R VAL* 1.3 62.4 + - - +
22R ILE* 4.0 18.8 - - + +
35R SER* 2.9 20.2 + - - +
36R GLU 3.4 3.4 - - - -
37R LYS* 3.2 26.5 + - - +
56R LYS 3.7 1.2 - - - +
57R VAL* 3.4 6.8 - - - +
58R ARG* 3.0 44.1 + - + +
134W U 3.8 5.9 + - - +
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Residues in contact with VAL 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ILE* 3.6 40.6 - - + -
19R VAL* 4.6 3.1 - - + -
20R ASN* 1.3 76.2 - - - +
22R ILE* 1.3 62.8 + - - +
23R GLY 4.0 0.7 + - - -
34R HIS 3.8 1.4 - - - +
35R SER* 3.6 0.3 - - - -
36R GLU* 2.8 38.2 + - + +
38R LEU* 3.7 30.5 - - + -
44R LEU* 3.8 21.3 - - + -
46R ALA* 5.3 0.7 - - + -
55R ILE* 3.7 15.9 - - + -
56R LYS 3.7 2.7 - - - -
57R VAL* 4.7 2.7 - - + +
101S TRP* 4.3 12.2 - - + -
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Residues in contact with ILE 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ASN* 4.0 18.8 - - + +
21R VAL* 1.3 77.9 - - - +
23R GLY* 1.3 64.9 + - - +
24R LEU* 3.5 2.8 - - + +
32R PHE* 3.4 62.6 - - + -
34R HIS 3.4 9.0 - - - +
35R SER* 3.7 17.7 - - - +
55R ILE* 3.4 4.6 - - - -
56R LYS* 2.8 46.0 + - + +
58R ARG* 4.2 26.7 - - + +
101S TRP* 4.1 2.7 - - - -
134W U 4.9 2.2 - - - +
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Residues in contact with GLY 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R ILE* 1.3 72.0 - - - +
24R LEU* 1.3 62.3 + - - -
32R PHE* 3.6 4.3 - - - -
33R HIS* 3.0 38.2 + - - -
34R HIS 2.8 15.2 + - - -
52R THR* 3.9 7.2 - - - -
54R ALA 4.0 0.2 - - - -
55R ILE* 4.8 0.2 - - - -
101S TRP* 3.4 28.3 - - - -
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Residues in contact with LEU 24 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34Q HIS* 5.2 0.2 - - - +
36Q GLU* 3.9 25.6 - - + +
44Q LEU* 4.1 17.3 - - + -
22R ILE* 3.5 16.2 - - + +
23R GLY* 1.3 74.7 - - - -
25R THR* 1.3 65.6 + - - +
30R THR* 3.8 27.4 - - + -
31R ARG 3.3 5.8 - - - +
32R PHE* 3.9 26.2 - - + -
33R HIS* 3.9 1.6 - - - -
52R THR* 3.4 6.9 - - - -
53R SER 3.4 19.2 + - - -
54R ALA* 2.9 27.3 + - + +
56R LYS* 3.9 17.5 - - + +
101R TRP* 5.3 1.8 - - + -
133W G 4.2 1.3 - - - +
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Residues in contact with THR 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R LEU* 1.3 72.9 - - - +
26R ARG* 1.3 63.8 + - - +
29R ASP 2.6 27.1 + - - +
30R THR* 4.2 0.9 - - - -
31R ARG* 2.9 68.2 + - + +
33R HIS* 3.8 23.8 - - + -
51R HIS 3.4 7.0 - - - +
53R SER* 4.1 1.1 - - - -
101R TRP* 3.0 24.8 + - - +
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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