Contacts of the strand formed by residues 32 - 38 (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 PHE 32 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M GLU* 4.9 0.9 - - - -
22N ILE* 3.4 44.2 - - + -
23N GLY 3.6 2.9 - - - -
24N LEU* 4.0 12.6 - - + -
31N ARG* 1.3 89.3 + - - +
33N HIS* 1.3 60.5 + - - +
34N HIS 4.6 5.2 - - - +
35N SER* 5.2 0.7 - - - -
56N LYS* 4.7 2.0 - - + -
58N ARG* 4.0 4.7 - - - -
113W G 2.8 82.4 + + + +
114W U 3.7 57.0 - + - +
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Residues in contact with HIS 33 (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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23N GLY 2.8 24.1 + - - -
24N LEU 4.0 5.4 - - - -
25N THR* 3.6 15.0 - - + -
31N ARG* 3.7 2.4 + - - +
32N PHE* 1.3 74.5 - - - +
34N HIS* 1.3 75.6 + - + +
51N HIS* 3.1 32.8 + - + +
52N THR* 2.3 32.6 + - - +
27O GLY 5.0 0.4 - - - -
28O ALA 4.7 14.9 + - - +
30O THR* 4.6 1.8 + - - -
101O TRP* 3.7 30.1 - + - -
114W U 6.4 1.3 - - - -
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Residues in contact with HIS 34 (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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21N VAL 3.8 0.9 - - - +
22N ILE* 3.3 5.3 - - - +
23N GLY 2.7 31.8 + - - -
32N PHE* 3.7 2.0 - - - +
33N HIS* 1.3 100.0 + - + +
35N SER* 1.3 72.6 + - - +
36N GLU* 2.6 39.0 + - + -
24O LEU* 5.8 0.2 - - + -
30O THR* 3.6 40.8 + - + +
101O TRP* 3.9 13.5 - + + -
114W U 6.5 1.6 - - - -
117W A 4.0 9.6 - + - -
118W G 3.5 14.6 + - - -
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Residues in contact with SER 35 (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* 2.7 33.8 + - - +
21N VAL 3.6 3.6 - - - -
22N ILE* 3.9 11.9 - - - +
32N PHE* 5.2 0.7 - - - -
34N HIS* 1.3 83.0 + - - +
36N GLU* 1.3 58.2 + - - +
37N LYS* 3.3 10.9 + - - +
114W U 3.2 31.3 + - - -
116W G 4.9 2.7 + - - -
117W A 3.3 18.4 - - - -
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Residues in contact with GLU 36 (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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19N VAL 3.3 3.8 - - - +
20N ASN* 3.4 1.5 - - - -
21N VAL* 2.9 43.7 + - + +
34N HIS* 2.6 37.1 + - + +
35N SER* 1.3 70.3 + - - +
37N LYS* 1.3 61.8 + - - +
38N LEU* 3.7 14.2 + - + +
44N LEU* 4.0 31.0 - - + -
24O LEU* 4.2 11.5 - - + +
56O LYS* 2.9 22.2 + - + +
101O TRP* 5.4 1.3 - - + -
117W A 3.5 5.2 - - - +
118W G 2.6 37.1 + - - +
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Residues in contact with LYS 37 (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 5.2 0.2 - - - +
19N VAL 3.2 2.7 - - - +
20N ASN* 3.2 29.8 + - - +
35N SER* 3.3 16.1 + - - +
36N GLU* 1.3 74.2 - - - +
38N LEU* 1.3 66.4 + - - +
42N GLU* 4.2 1.2 - - - +
56O LYS* 4.0 6.4 + - - -
114W U 3.1 27.5 + - - -
116W G 3.4 93.8 + - + +
117W A 2.9 31.3 + - + +
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Residues in contact with LEU 38 (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* 4.1 19.7 - - + +
14N ALA* 3.7 23.3 - - + +
16N GLU 3.9 0.7 - - - +
17N ASP 3.7 0.3 - - - -
18N GLY 2.9 22.3 + - - -
19N VAL* 2.7 26.1 + - + +
21N VAL* 3.9 22.0 - - + -
36N GLU* 4.1 22.0 - - + +
37N LYS* 1.3 81.4 - - - +
39N ASP* 1.3 65.1 + - - +
42N GLU* 3.4 20.2 - - + +
44N LEU* 4.1 20.9 - - + +
56O LYS* 4.2 13.2 - - + -
116W G 4.5 0.2 - - - -
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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