Contacts of the helix formed by residues 28 - 39 (chain A) in PDB entry 5FJH
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 GLU 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU 5.5 0.2 + - - -
25A GLU 4.6 3.1 + - - +
26A PHE 3.3 2.6 - - - +
27A ARG* 1.3 87.2 - - + +
29A PHE* 1.3 66.0 + - - +
30A ASN* 3.3 4.7 + - + +
31A LYS* 3.4 25.8 + - + +
32A TYR* 3.0 22.3 + - - +
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Residues in contact with PHE 29 (chain A).
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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27A ARG 3.6 4.8 + - - -
28A GLU* 1.3 72.4 + - - +
30A ASN* 1.3 78.4 + - - +
32A TYR* 3.1 2.1 + - - +
33A LEU* 2.8 39.5 + - + +
150A TRP* 3.6 60.6 - + + +
155A LEU* 3.9 31.6 - - + +
157A THR* 4.4 5.4 - - + -
199A ILE* 3.8 19.3 - - + -
271A ILE* 4.1 11.2 - - + -
293A PHE* 3.7 36.3 - + - -
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.3 4.8 + - + +
29A PHE* 1.3 91.3 - - - +
31A LYS* 1.3 62.5 + - - +
33A LEU* 3.4 8.2 + - - +
34A ALA* 3.2 20.8 + - - +
155A LEU 3.4 18.1 + - - -
156A ASN* 3.4 15.9 + - - +
157A THR* 3.7 19.8 - - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 5.8 4.0 - - - +
28A GLU* 3.4 25.1 + - + +
29A PHE 3.3 0.4 - - - -
30A ASN* 1.3 79.2 - - - +
32A TYR* 1.3 64.4 + - - +
34A ALA* 3.2 10.1 + - + +
35A TYR* 3.1 20.2 + - + +
1352A EDO 6.0 1.6 - - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.4 34.3 - - + +
20A ARG 4.3 1.0 + - - -
21A PRO* 3.5 38.4 - - + +
25A GLU* 3.4 33.4 + - + +
26A PHE* 5.2 0.2 - - - -
28A GLU 3.0 17.3 + - - +
29A PHE 3.8 3.6 - - - +
31A LYS* 1.3 79.1 - - + +
33A LEU* 1.3 57.2 + - - +
35A TYR* 3.1 32.0 + + + +
36A MET* 2.8 54.7 + - + +
49A VAL* 4.4 3.1 - - + -
150A TRP* 3.9 23.8 - + + -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 2.8 28.7 + - + +
30A ASN* 3.8 7.4 - - - +
32A TYR* 1.3 77.2 - - - +
34A ALA* 1.3 61.7 + - - +
36A MET* 3.2 11.7 + - - +
37A GLU* 3.1 26.8 + - + +
150A TRP* 5.6 0.4 - - - -
197A TYR* 4.2 5.8 - - + -
271A ILE* 4.2 26.5 - - + -
273A PHE* 4.1 27.1 - - + -
293A PHE* 3.5 30.1 - - + -
295A THR* 3.6 23.6 - - + -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASN 3.2 11.9 + - - +
31A LYS* 3.2 12.6 + - - +
33A LEU* 1.3 77.5 - - - +
35A TYR* 1.3 56.2 + - - +
37A GLU* 3.3 6.5 + - - +
38A SER* 2.9 28.9 + - - -
1352A EDO 6.5 0.9 - - - -
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Residues in contact with TYR 35 (chain A).
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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19A PHE* 4.1 16.6 - + - -
25A GLU* 6.4 1.6 - - - -
31A LYS* 3.1 13.4 + - + +
32A TYR* 3.3 46.2 - + + +
34A ALA* 1.3 75.9 - - - +
36A MET* 1.3 66.3 + - - +
38A SER* 2.8 27.0 + - - -
39A LYS* 3.1 44.0 + - + +
1352A EDO 5.9 10.1 - - - -
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.8 26.2 - - + -
32A TYR* 2.8 43.1 + - + +
33A LEU* 3.2 15.9 + - + +
35A TYR* 1.3 71.1 - - - +
37A GLU* 1.3 62.3 + - - +
39A LYS* 3.1 12.6 + - - +
40A GLY 3.3 0.2 + - - -
41A ALA* 3.1 23.6 + - + +
47A ALA* 3.7 28.7 - - + -
49A VAL* 3.6 34.3 - - + -
150A TRP* 4.9 1.3 - - - -
271A ILE* 4.2 20.2 - - + -
273A PHE* 4.4 8.7 - - + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.1 20.0 + - + +
34A ALA* 3.9 5.3 - - - +
36A MET* 1.3 73.2 - - - +
38A SER* 1.3 61.8 + - - +
40A GLY 2.8 15.4 + - - -
41A ALA 4.2 0.7 - - - +
42A HIS* 3.3 29.1 - - + +
197A TYR* 2.8 27.0 + - - -
273A PHE* 3.4 26.8 - - + -
295A THR* 5.1 1.0 + - - +
297A ARG* 2.9 41.3 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.5 8.7 + - - +
34A ALA 2.9 16.1 + - - -
35A TYR* 2.8 24.2 + - - -
37A GLU* 1.3 75.8 - - - +
39A LYS* 1.3 68.7 + - - +
40A GLY 3.3 0.4 + - - -
1352A EDO 4.8 17.0 + - - -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU 4.4 10.9 + - - +
11A ASN* 4.3 4.9 - - - +
17A MET* 3.5 29.0 - - + +
19A PHE* 4.3 7.4 - - + -
35A TYR* 3.1 54.9 + - + +
36A MET 3.5 7.6 - - - +
37A GLU 3.1 1.0 - - - -
38A SER* 1.3 82.9 + - - +
40A GLY* 1.3 59.2 + - - +
41A ALA 3.4 0.9 - - - -
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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