Contacts of the strand formed by residues 19 - 25 (chain T) in PDB entry 5EEY
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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T ILE* 4.7 0.4 - - + -
14T ALA* 3.7 18.2 - - + -
16T GLU* 3.5 21.1 - - + +
18T GLY* 1.3 76.7 - - - +
20T ASN* 1.3 64.5 + - - +
21T VAL* 4.2 8.5 + - + -
36T GLU 3.6 0.7 - - - +
37T LYS* 3.4 3.6 - - - -
38T LEU* 2.8 36.9 + - + +
57T VAL* 4.1 20.0 - - + -
58T ARG 3.5 11.9 - - - +
59T GLY* 4.0 1.1 - - - -
60T LYS 3.3 37.9 - - - +
61T ALA* 4.2 9.0 - - + -
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Residues in contact with ASN 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T GLY* 3.1 16.8 + - - -
19T VAL* 1.3 72.9 - - - +
21T VAL* 1.3 62.0 + - - +
22T ILE* 3.9 16.1 - - + +
35T SER* 3.9 3.1 - - - -
36T GLU 3.4 3.6 - - - +
37T LYS* 3.0 40.4 + - - +
56T LYS 3.6 1.4 - - - +
57T VAL* 3.4 5.7 - - - +
58T ARG* 2.9 46.1 + - + +
144W U 3.9 11.3 + - - +
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Residues in contact with VAL 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T ILE* 3.6 40.8 - - + -
19T VAL* 4.5 2.7 - - + -
20T ASN* 1.3 73.7 - - - +
22T ILE* 1.3 62.8 + - - +
23T GLY 4.1 0.5 + - - -
34T HIS 3.9 0.9 - - - +
35T SER* 3.4 1.0 - - - -
36T GLU* 2.8 39.1 + - - +
38T LEU* 3.9 29.2 - - + -
44T LEU* 3.8 21.8 - - + -
46T ALA* 5.2 0.9 - - + -
55T ILE* 3.7 17.5 - - + -
56T LYS 3.6 2.9 - - - +
57T VAL* 4.7 3.4 - - + +
101U TRP* 4.2 12.3 - - + -
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Residues in contact with ILE 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ASN* 4.0 19.7 - - + -
21T VAL* 1.3 76.5 - - - +
23T GLY* 1.3 62.1 + - - +
24T LEU* 3.5 6.4 - - + +
32T PHE* 3.5 51.1 - - + -
34T HIS 3.4 9.0 - - - +
35T SER* 3.6 13.2 - - - +
55T ILE* 3.4 7.1 - - - +
56T LYS* 2.8 48.9 + - + +
58T ARG* 3.9 37.2 - - + +
101U TRP* 4.1 2.7 - - - -
144W U 4.7 2.0 - - - +
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Residues in contact with GLY 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T ILE* 1.3 71.0 - - - +
24T LEU* 1.3 62.5 + - - -
32T PHE* 3.5 4.7 - - - -
33T HIS* 2.9 40.8 + - - -
34T HIS 2.8 13.9 + - - -
52T THR* 3.9 2.2 - - - -
54T ALA 3.8 5.4 - - - -
101U TRP* 3.6 25.5 - - - -
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Residues in contact with LEU 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S HIS* 5.7 0.2 - - + -
36S GLU* 3.9 26.2 - - + +
44S LEU* 3.9 24.5 - - + -
22T ILE* 3.5 30.3 - - + +
23T GLY* 1.3 75.0 - - - -
25T THR* 1.3 65.1 + - - +
30T THR* 4.0 22.9 - - + -
31T ARG 3.3 7.0 - - - +
32T PHE* 4.2 12.3 - - + -
33T HIS* 3.9 1.6 - - - -
52T THR* 3.4 5.9 - - - -
53T SER 3.3 19.9 + - - -
54T ALA* 2.9 28.3 + - + +
56T LYS* 4.0 13.2 - - + +
101T TRP* 5.2 2.0 - - + -
143W G 4.7 0.7 - - - +
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Residues in contact with THR 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T LEU* 1.3 74.2 - - - +
26T ARG* 1.3 58.7 + - - +
29T ASP 2.7 24.7 + - - +
30T THR* 4.1 1.0 - - - -
31T ARG* 2.9 66.2 + - + +
33T HIS* 3.7 26.0 - - + -
51T HIS 3.4 8.1 - - - +
53T SER* 4.1 0.9 - - - -
101T TRP* 2.8 33.6 + - - +
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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