Contacts of the helix formed by residues 17 - 25 (chain F) in PDB entry 5EIG
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F PHE 3.8 0.4 + - - -
16F GLN* 1.3 108.3 + - + +
18F PHE* 1.3 63.8 + - - +
20F THR* 3.4 3.2 + - + +
21F GLN* 3.0 42.0 + - + +
382G ASP* 3.3 17.0 + - - -
384G GLU* 3.8 8.7 + - - -
385G ASP* 2.8 40.9 + - - +
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 3.6 22.3 + - + +
16F GLN 3.1 3.8 - - - -
17F HIS* 1.3 77.9 - - - +
19F ALA* 1.3 60.9 + - - +
21F GLN* 4.9 2.5 - - - -
22F ALA* 2.9 35.9 + - + +
78F LEU* 3.7 50.8 - - + +
193F PRO* 3.5 27.8 - - + -
194F TYR* 3.5 50.7 - + + -
197F ARG* 4.0 17.9 - - - +
262F LEU* 4.1 13.0 - - + -
263F HIS* 4.4 8.3 - - + -
382G ASP* 3.5 3.0 + - - +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 1.3 80.1 - - - +
20F THR* 1.3 63.1 + - - +
22F ALA* 3.5 3.1 + - - +
23F ILE* 3.1 31.9 + - - +
263F HIS* 3.6 39.2 - - + +
380G LEU 3.6 13.9 - - - +
381G GLU* 4.1 0.7 - - - -
382G ASP* 3.2 20.6 + - - +
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Residues in contact with THR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F HIS* 3.8 9.0 - - + +
18F PHE 3.3 0.2 - - - -
19F ALA* 1.3 77.6 - - - +
21F GLN* 1.3 59.7 + - + +
23F ILE 3.3 1.0 + - - -
24F HIS* 2.9 34.7 + - + +
334G LEU* 3.7 36.1 - - + -
381G GLU* 3.8 10.3 - - + +
382G ASP* 3.1 21.4 + - - +
385G ASP* 2.7 29.2 + - + +
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Residues in contact with GLN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN 4.6 3.5 - - - +
17F HIS* 3.0 36.9 + - + +
18F PHE* 4.0 3.0 - - - +
20F THR* 1.3 76.2 - - + +
22F ALA* 1.3 64.8 + - - +
23F ILE 3.0 1.8 - - - -
24F HIS* 5.0 0.4 - - - -
25F VAL* 2.9 54.0 + - + +
74F ALA* 5.0 1.8 - - - +
77F ALA* 4.0 30.0 + - + +
78F LEU* 4.4 5.0 - - + +
197F ARG* 4.8 5.7 + - - -
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 2.9 24.8 + - + +
19F ALA* 3.8 7.0 - - - +
21F GLN* 1.3 76.0 - - - +
23F ILE* 1.3 61.1 + - + +
27F GLN* 4.9 4.3 + - - -
74F ALA* 5.1 7.0 - - - +
78F LEU* 3.6 27.3 - - + +
256F ASN* 5.0 0.7 + - - -
259F LEU* 3.9 24.8 - - - +
260F LYS* 3.5 20.8 + - - +
263F HIS* 5.5 3.1 - - - +
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Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA 3.1 18.1 + - - +
20F THR 3.8 3.1 - - - +
21F GLN 3.0 0.6 - - - -
22F ALA* 1.3 83.1 - - + +
24F HIS* 1.3 77.1 + - + +
27F GLN* 3.2 18.4 - - - +
260F LYS* 3.7 34.2 + - + +
263F HIS* 4.5 1.6 - - + -
344G PHE* 3.5 45.0 - - + +
345G GLU* 4.2 7.9 - - + -
380G LEU* 3.7 31.0 - - + +
381G GLU* 3.7 4.9 - - + +
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Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F THR* 2.9 25.4 + - + +
21F GLN* 5.0 0.7 - - - -
23F ILE* 1.3 89.4 + - + +
25F VAL* 1.3 69.0 + - + +
26F GLY 3.2 0.9 + - - -
27F GLN* 3.0 20.1 + - - +
28F ASP* 3.8 7.1 + - - +
333G LYS 5.8 0.4 - - - -
334G LEU* 3.5 44.3 + - + +
336G THR* 4.9 6.5 - - - -
345G GLU* 4.4 11.7 - - + -
381G GLU* 2.8 36.6 + - + +
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLN* 2.9 55.4 + - + +
22F ALA 5.3 0.2 - - - +
24F HIS* 1.3 69.8 - - + +
26F GLY* 1.3 60.7 + - - +
27F GLN* 3.1 19.6 + - - -
73F LYS* 3.4 43.7 - - + +
74F ALA* 3.5 13.1 - - - +
77F ALA* 4.0 13.5 - - + -
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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