Contacts of the strand formed by residues 19 - 25 (chain N) in PDB entry 5EF3
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14N ALA* 3.5 24.0 - - + -
16N GLU* 3.6 10.1 - - + +
17N ASP 3.4 0.6 - - - -
18N GLY* 1.3 73.8 - - - +
20N ASN* 1.3 71.0 + - - +
21N VAL* 4.3 10.1 - - + -
36N GLU 3.3 1.2 - - - +
37N LYS* 3.2 6.4 - - - -
38N LEU* 2.7 40.0 + - + -
57N VAL* 4.1 15.5 - - + -
58N ARG 3.5 12.3 - - - +
59N GLY* 4.2 1.3 - - - -
60N LYS 3.2 39.0 - - - +
61N ALA* 4.3 7.4 - - + -
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Residues in contact with ASN 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N GLY 3.2 16.2 + - - -
19N VAL* 1.3 75.4 + - - +
21N VAL* 1.3 62.2 + - - +
22N ILE* 3.8 13.7 - - + +
35N SER* 2.7 25.3 + - - +
36N GLU 3.4 2.7 - - - -
37N LYS* 3.2 27.2 + - - +
56N LYS 3.6 1.7 - - - +
57N VAL* 3.5 6.1 - - - +
58N ARG* 3.0 44.9 + - + +
114W U 3.8 6.9 + - - +
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Residues in contact with VAL 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N ILE* 3.5 50.3 - - + -
19N VAL* 4.3 3.1 - - + -
20N ASN* 1.3 74.8 - - - +
22N ILE* 1.3 62.7 + - - +
23N GLY 3.9 0.3 + - - -
34N HIS 3.8 1.4 - - - +
35N SER* 3.6 0.5 - - - -
36N GLU* 2.9 36.9 + - - +
38N LEU* 3.9 18.6 - - + -
44N LEU* 3.8 21.8 - - + -
46N ALA* 5.4 0.9 - - + -
55N ILE* 3.6 17.9 - - + -
56N LYS 3.7 2.5 - - - +
57N VAL* 4.6 3.6 - - + +
101O TRP* 4.3 12.8 - - + -
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Residues in contact with ILE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N ASN* 3.9 20.2 - - + +
21N VAL* 1.3 77.0 - - - +
23N GLY* 1.3 63.4 + - - +
24N LEU* 3.6 7.6 - - + +
32N PHE* 3.4 60.1 - - + -
34N HIS 3.3 9.6 - - - +
35N SER* 3.9 10.1 - - - +
55N ILE* 3.3 7.1 - - - +
56N LYS* 2.9 43.4 + - + +
58N ARG* 3.8 34.8 - - + +
101O TRP* 4.1 2.7 - - - -
114W U 5.1 0.7 - - - +
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Residues in contact with GLY 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N ILE* 1.3 72.5 - - - +
24N LEU* 1.3 58.4 + - - -
32N PHE* 3.6 4.0 - - - -
33N HIS* 2.8 38.9 + - - -
34N HIS 2.7 15.8 + - - +
52N THR* 4.0 6.7 - - - -
54N ALA 3.8 4.7 - - - -
101O TRP* 3.5 25.4 - - - -
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Residues in contact with LEU 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M HIS* 5.9 0.2 - - + -
36M GLU* 4.1 19.3 - - + +
44M LEU* 3.9 25.6 - - + -
22N ILE* 3.6 30.1 - - + +
23N GLY* 1.3 74.9 - - - -
25N THR* 1.3 67.1 + - - +
30N THR* 4.1 24.7 - - + -
31N ARG 3.3 9.2 - - - +
32N PHE* 4.0 13.5 - - + -
33N HIS* 4.0 1.6 - - - -
52N THR* 3.4 5.9 - - - -
53N SER 3.3 20.1 + - - -
54N ALA* 2.8 25.9 + - + +
56N LYS* 4.0 14.4 - - + +
101N TRP* 6.3 0.4 - - + -
113W G 4.6 1.1 - - - +
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Residues in contact with THR 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N LEU* 1.3 73.6 - - - +
26N ARG* 1.3 64.4 + - - +
29N ASP 2.8 25.3 + - - +
30N THR* 4.3 1.0 - - - -
31N ARG* 2.9 67.9 + - + +
33N HIS* 3.6 24.2 - - + -
51N HIS 3.4 7.6 - - - +
53N SER* 4.1 0.7 - - - -
101N TRP* 2.9 27.5 + - - +
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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