Contacts of the helix formed by residues 17 - 25 (chain A) in PDB entry 3ELP
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 HIS 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE 3.7 0.4 + - - -
16A GLN* 1.3 103.8 + - + +
18A PHE* 1.3 64.0 + - - +
20A THR* 2.9 5.4 + - + -
21A GLN* 2.7 46.0 + - + +
382B ASP* 2.9 23.5 + - - +
384B GLU* 4.0 4.9 + - - -
385B ASP* 3.0 41.7 + - - +
388B GLU* 5.5 2.0 + - - -
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Residues in contact with PHE 18 (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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15A PHE* 3.6 19.3 + - + +
16A GLN 2.9 7.5 + - - +
17A HIS* 1.3 74.3 - - - +
19A ALA* 1.3 60.7 + - - +
21A GLN* 3.9 8.1 - - - -
22A ALA* 2.8 30.9 + - + +
78A LEU* 3.2 53.4 - - + +
193A PRO* 3.5 24.0 - - + -
194A TYR* 3.4 50.3 - + + -
197A ARG* 4.1 9.6 - - - +
262A LEU* 3.9 28.0 - - + -
263A HIS* 4.3 7.2 - - + -
382B ASP* 3.1 2.5 + - - +
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Residues in contact with ALA 19 (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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18A PHE* 1.3 78.6 - - - +
20A THR* 1.3 63.4 + - - +
22A ALA* 3.4 2.9 + - - +
23A ILE* 3.1 31.3 + - - +
194A TYR* 6.3 0.2 - - + -
263A HIS* 3.7 31.0 - - + +
380B LEU 3.6 21.1 - - - +
381B GLU* 4.0 2.7 - - - +
382B ASP* 3.0 21.0 + - - +
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Residues in contact with THR 20 (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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17A HIS* 2.9 11.1 + - + -
19A ALA* 1.3 77.6 - - - +
21A GLN* 1.3 60.8 + - + +
23A ILE 3.2 1.4 + - - -
24A HIS* 2.8 38.1 + - + +
334B LEU* 3.6 30.7 - - + -
381B GLU* 3.5 13.5 - - + +
382B ASP* 3.1 18.0 + - - +
385B ASP* 2.8 28.5 + - + +
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Residues in contact with GLN 21 (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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16A GLN 4.2 4.0 + - - +
17A HIS* 2.7 40.3 + - + +
18A PHE* 3.7 12.4 + - - +
20A THR* 1.3 69.4 - - + +
22A ALA* 1.3 64.5 + - - +
23A ILE 3.0 2.0 - - - -
24A HIS* 5.2 0.4 - - - -
25A VAL* 2.8 53.4 + - + +
74A ALA* 4.7 2.2 - - - +
77A ALA* 3.4 39.3 + - + +
78A LEU* 4.1 7.9 + - + +
197A ARG* 4.9 2.4 + - - -
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Residues in contact with ALA 22 (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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18A PHE* 2.8 26.5 + - + +
19A ALA* 3.7 9.0 - - - +
20A THR 3.4 0.2 - - - -
21A GLN* 1.3 72.4 - - - +
23A ILE* 1.3 59.9 + - + +
25A VAL 5.3 1.6 - - - +
27A GLN* 5.4 0.2 - - - +
74A ALA* 5.4 5.8 - - - +
78A LEU* 3.8 25.7 - - + +
256A ASN* 4.6 7.1 + - - -
259A LEU* 3.9 22.6 - - - +
260A LYS* 3.1 25.9 + - - +
263A HIS* 5.2 1.3 - - + -
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Residues in contact with ILE 23 (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 ALA 3.1 17.6 + - - +
20A THR 3.8 2.5 - - - +
21A GLN 3.0 0.4 - - - -
22A ALA* 1.3 83.0 - - - +
24A HIS* 1.3 79.6 + - + +
27A GLN* 3.0 23.5 - - - +
260A LYS* 3.4 38.8 + - + +
263A HIS* 4.3 0.9 - - - +
344B PHE* 3.7 35.7 - - + +
345B GLU* 4.6 6.8 - - + +
380B LEU* 3.6 36.8 - - + +
381B GLU* 4.0 3.8 - - + +
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Residues in contact with HIS 24 (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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20A THR* 2.8 40.2 + - + +
21A GLN* 5.2 0.2 - - - -
23A ILE* 1.3 82.8 + - + +
25A VAL* 1.3 67.6 + - + +
26A GLY 3.1 0.5 + - - -
27A GLN* 2.9 21.8 + - - +
334B LEU* 4.1 24.5 - - + +
336B THR* 5.0 0.9 - - - -
345B GLU* 3.4 40.6 + - + -
381B GLU* 2.9 35.6 + - + +
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Residues in contact with VAL 25 (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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21A GLN* 2.8 52.6 + - + +
22A ALA 5.3 0.9 - - - +
23A ILE 5.1 0.2 - - - -
24A HIS* 1.3 72.5 - - + +
26A GLY* 1.3 62.9 + - - +
27A GLN* 3.4 10.7 + - - +
70A CYS 4.6 0.3 - - - +
73A LYS* 3.9 13.9 - - + +
74A ALA* 3.5 43.2 - - - +
77A ALA* 4.4 8.5 - - + -
256A ASN* 5.2 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