Contacts of the helix formed by residues 17 - 27 (chain A) in PDB entry 4LOU
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 ARG 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 1.3 67.8 + - - +
19A ARG 3.2 3.1 - - - +
20A GLN* 3.6 26.6 + - - +
21A LEU* 3.2 62.1 + - - +
24A GLN* 3.9 11.9 + - - -
117B GLU* 3.7 21.2 + - - -
119B GLN* 4.1 17.7 - - - +
208B PHE* 5.8 1.8 - - - +
209B ARG* 3.5 34.3 - - - +
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Residues in contact with ARG 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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17A ARG* 1.3 78.5 - - - +
19A ARG* 1.3 57.8 + - - +
21A LEU* 3.7 3.4 + - - +
22A ILE* 3.1 33.8 + - + +
119B GLN* 3.4 27.1 + - - +
453B LEU* 3.7 38.7 - - + +
456B GLN* 3.1 44.7 + - - +
457B GLU* 3.2 27.0 + - - +
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Residues in contact with ARG 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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17A ARG* 3.2 1.0 - - - +
18A ARG* 1.3 78.0 - - - +
20A GLN* 1.3 66.9 + - - +
22A ILE* 3.7 8.5 + - + +
23A ARG* 3.4 18.7 + - - +
457B GLU* 3.6 32.0 + - - +
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Residues in contact with GLN 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 ARG* 3.8 32.8 + - + +
19A ARG* 1.3 77.9 - - - +
21A LEU* 1.3 57.8 + - - +
23A ARG* 3.0 10.6 + - - +
24A GLN* 2.9 56.9 + - + +
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Residues in contact with LEU 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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17A ARG* 3.2 38.2 + - - +
18A ARG 3.9 2.9 - - - +
20A GLN* 1.3 76.7 - - - +
22A ILE* 1.3 59.8 + - - +
24A GLN* 3.2 13.2 + - - +
25A LEU* 2.8 52.1 + - + +
117B GLU* 3.8 36.1 - - + +
119B GLN* 3.6 31.6 - - + -
208B PHE* 4.4 8.5 - - + -
449B LEU* 5.4 1.3 - - + -
453B LEU* 4.0 13.2 - - + -
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Residues in contact with ILE 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 ARG 3.1 21.4 + - - +
19A ARG* 4.0 7.9 - - + +
20A GLN 3.4 0.4 - - - -
21A LEU* 1.3 75.7 - - - +
23A ARG* 1.3 62.9 + - - +
25A LEU* 3.4 8.5 + - - +
26A LEU* 3.1 45.8 + - + +
450B ALA* 4.1 16.4 - - + +
453B LEU* 3.6 47.8 - - + +
454B ALA* 4.0 8.5 - - + +
457B GLU* 3.8 20.4 - - - +
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Residues in contact with ARG 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 ARG 3.4 11.6 + - - +
20A GLN* 3.0 13.6 + - + +
22A ILE* 1.3 81.2 - - - +
24A GLN* 1.3 64.4 + - + +
26A LEU* 3.4 8.7 + - - +
27A GLU* 3.4 47.0 + - - +
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Residues in contact with GLN 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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17A ARG* 3.9 19.4 + - - -
20A GLN* 2.9 41.1 + - + +
21A LEU* 3.6 11.7 - - - +
23A ARG* 1.3 77.1 - - + +
25A LEU* 1.3 64.6 + - - +
27A GLU* 3.0 16.8 + - - +
28A ARG 3.3 3.6 + - - -
208B PHE* 3.1 60.9 + - + +
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Residues in contact with LEU 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 LEU* 2.8 37.3 + - + +
22A ILE* 3.8 4.7 - - - +
24A GLN* 1.3 73.3 - - - +
26A LEU* 1.3 60.4 + - - +
27A GLU 3.4 0.3 + - - -
28A ARG* 3.4 16.5 + - - +
117B GLU* 5.7 2.7 - - + +
207B GLN* 6.0 0.9 - - + -
208B PHE* 3.8 21.1 - - + -
442B LYS* 6.0 0.3 - - - +
443B PRO* 5.1 3.6 - - - +
446B SER* 3.9 47.7 - - - +
449B LEU* 3.6 38.6 - - + -
450B ALA* 4.1 11.0 - - + +
453B LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 26 (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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22A ILE* 3.1 37.5 + - + +
23A ARG* 3.9 9.0 - - - +
24A GLN 3.1 0.8 - - - -
25A LEU* 1.3 76.1 - - - +
27A GLU* 1.3 63.5 + - - +
28A ARG 3.4 2.8 + - - +
30A LYS* 4.7 2.8 - - - +
442B LYS* 2.7 57.4 + - + +
443B PRO* 5.9 1.0 - - - +
446B SER 5.8 0.4 - - - -
447B ALA* 5.1 9.0 - - + +
450B ALA* 4.1 18.6 - - + -
451B ARG* 6.3 1.6 - - + -
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Residues in contact with GLU 27 (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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23A ARG* 3.4 48.2 + - - +
24A GLN* 3.0 11.4 + - - +
26A LEU* 1.3 87.8 - - - +
28A ARG* 1.3 62.3 + - - +
29A ASP 3.7 1.6 + - - -
30A LYS* 2.9 50.8 + - - +
208B PHE* 5.1 1.7 - - - -
442B LYS* 4.4 5.0 + - - -
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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