Contacts of the helix formed by residues 17 - 25 (chain D) in PDB entry 3OX4
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 GLY 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C SER* 4.3 5.2 - - - -
16D GLU* 1.3 76.4 - - - +
18D SER* 1.3 64.0 + - - +
19D LEU 3.1 4.0 + - - -
20D GLU* 3.1 34.2 - - - +
21D LYS* 3.3 9.2 + - - +
176D ASP* 3.1 13.1 + - - -
178D LEU* 3.8 4.4 - - - +
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C SER* 3.8 8.4 + - - -
13D GLU* 3.7 12.1 + - - +
14D MET 3.5 28.9 - - - -
15D GLY 2.7 22.9 + - - -
16D GLU 3.3 1.6 + - - -
17D GLY* 1.3 77.4 - - - +
19D LEU* 1.3 61.7 + - - +
21D LYS* 3.7 6.5 - - - +
22D ALA* 2.9 26.5 + - - +
174D VAL* 4.1 3.2 - - - +
175D ASN 3.3 11.6 + - - -
176D ASP* 3.3 14.9 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D SER* 1.3 81.7 + - - +
20D GLU* 1.3 72.2 + - - +
22D ALA* 3.2 2.8 + - + +
23D ILE* 3.1 35.5 + - + +
47D VAL* 5.9 0.2 - - + -
50D GLN* 3.5 27.8 - - + +
51D VAL* 4.6 9.4 - - + -
54D LEU* 3.9 13.7 - - + -
134D MET* 6.3 0.2 - - - -
136D ILE* 4.1 32.8 - - + -
174D VAL* 3.9 9.9 - - + -
176D ASP* 2.9 23.2 + - + +
179D LEU* 3.7 25.8 - - + -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY* 3.1 29.0 - - - +
19D LEU* 1.3 90.0 - - - +
21D LYS* 1.3 55.9 + - - +
23D ILE* 3.1 3.5 + - - +
24D LYS* 2.8 49.3 + - + +
50D GLN* 5.3 1.0 - - - +
54D LEU* 4.3 26.2 - - + +
176D ASP* 3.8 3.5 - - - +
178D LEU* 4.8 8.9 - - - +
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C SER* 4.9 8.1 - - - +
5C THR* 3.5 10.4 + - - -
7C TYR* 3.9 14.3 + - - -
166C ARG* 4.0 1.6 - - - +
13D GLU* 2.8 37.1 + - - +
17D GLY 3.3 11.3 + - - +
18D SER* 3.7 12.3 - - - +
19D LEU 3.2 0.6 - - - -
20D GLU* 1.3 78.2 - - - +
22D ALA* 1.3 61.6 + - - +
24D LYS* 3.2 22.3 + - - +
25D ASP* 2.8 50.4 + - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 3.8 17.5 - - + -
18D SER 2.9 19.2 + - - +
19D LEU* 3.5 5.2 - - + +
21D LYS* 1.3 78.2 - - - +
23D ILE* 1.3 63.5 + - + +
25D ASP* 3.4 16.5 + - - +
26D LEU* 3.8 4.9 + - - +
134D MET* 3.7 22.1 - - + +
172D VAL* 4.8 2.0 - - + -
174D VAL* 3.8 27.1 - - + -
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Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.1 26.6 + - + +
20D GLU* 3.1 7.3 + - - +
22D ALA* 1.3 71.6 - - + +
24D LYS* 1.3 68.1 + - + +
25D ASP 3.1 1.6 - - - -
26D LEU* 2.9 28.7 + - + +
51D VAL* 5.0 4.7 - - + -
54D LEU* 3.4 50.0 - - + +
55D LEU* 3.3 28.0 - - + +
58D GLN* 3.5 12.6 - - + +
93D ILE* 5.0 1.6 - - + -
134D MET* 4.1 22.9 - - - -
136D ILE* 5.1 0.9 - - + -
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU* 2.8 37.7 + - + +
21D LYS* 3.2 36.0 - - - +
23D ILE* 1.3 76.3 - - + +
25D ASP* 1.3 61.5 + - - +
26D LEU 3.0 0.2 - - - -
27D ASN* 3.1 28.2 + - - +
54D LEU* 6.4 1.1 - - + -
58D GLN* 3.7 19.0 - - - +
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Residues in contact with ASP 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ARG* 3.2 29.1 + - - +
13D GLU* 3.8 3.1 - - - +
21D LYS* 2.8 48.2 + - - +
22D ALA* 3.6 11.2 - - - +
23D ILE 3.1 1.0 - - - -
24D LYS* 1.3 77.7 - - - +
26D LEU* 1.3 59.5 + - + +
27D ASN* 3.1 12.2 + - - +
29D SER* 5.0 2.4 - - - -
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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