Contacts of the helix formed by residues 17 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU* 1.3 73.0 - - - +
18C SER* 1.3 63.7 + - - +
19C LEU 3.2 2.7 - - - -
20C GLU* 3.3 18.2 + - - +
21C LYS* 3.2 21.0 + - - +
176C ASP* 2.9 14.1 + - - -
178C LEU* 3.9 8.6 - - - +
3D SER* 3.9 3.1 - - - -
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 3.8 11.7 + - - +
14C MET 3.6 27.9 - - - -
15C GLY 3.0 17.5 + - - -
16C GLU 3.4 1.0 - - - -
17C GLY* 1.3 75.8 - - - +
19C LEU* 1.3 61.0 + - - +
21C LYS* 3.8 8.6 - - - +
22C ALA* 2.9 31.2 + - - +
174C VAL* 3.6 7.5 - - - +
175C ASN 3.7 4.0 - - - -
176C ASP* 3.3 17.5 + - - +
3D SER* 3.6 5.5 + - - -
4D SER 5.1 0.2 - - - -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY 3.2 0.6 - - - -
18C SER* 1.3 82.3 + - - +
20C GLU* 1.3 63.2 + - + +
22C ALA* 3.5 1.4 - - - +
23C ILE* 3.1 42.6 + - + +
47C VAL* 5.9 0.2 - - + -
50C GLN* 4.1 22.4 - - - +
51C VAL* 4.5 15.9 - - + -
54C LEU* 4.3 11.9 - - + -
136C ILE* 3.6 38.4 - - + -
174C VAL* 3.7 7.4 - - + +
176C ASP* 3.4 20.2 + - + +
179C LEU* 3.9 22.7 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY* 3.3 16.8 + - - +
18C SER 3.3 0.2 - - - -
19C LEU* 1.3 78.6 - - + +
21C LYS* 1.3 60.7 + - - +
23C ILE* 3.3 3.1 + - - +
24C LYS* 2.8 57.5 + - - +
50C GLN* 5.8 2.6 + - - +
54C LEU* 4.1 28.9 - - + +
176C ASP* 5.8 0.2 - - - +
178C LEU* 5.8 3.3 - - - +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 2.7 36.1 + - - +
17C GLY 3.2 13.7 + - - +
18C SER* 3.9 7.9 - - - +
19C LEU 3.4 0.2 - - - -
20C GLU* 1.3 77.2 - - - +
22C ALA* 1.3 62.9 + - - +
24C LYS* 3.3 9.4 + - + +
25C ASP* 2.9 50.9 + - - +
3D SER* 5.7 9.2 - - - +
4D SER 5.8 0.7 - - - +
5D THR* 3.7 14.6 + - - +
7D TYR* 4.2 6.9 + - - -
166D ARG* 4.2 7.5 - - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 4.2 12.5 - - + +
18C SER 2.9 19.5 + - - +
19C LEU 3.5 4.7 - - - +
20C GLU 3.2 0.2 - - - -
21C LYS* 1.3 79.3 - - - +
23C ILE* 1.3 62.6 + - - +
25C ASP* 3.3 20.0 + - - +
26C LEU* 3.6 3.8 + - - +
134C MET* 4.0 22.4 - - + +
136C ILE* 5.2 0.2 - - + -
172C VAL* 5.0 2.2 - - + -
174C VAL* 3.5 28.7 - - + -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.1 32.7 + - + +
20C GLU* 3.9 3.8 - - - +
22C ALA* 1.3 73.6 - - - +
24C LYS* 1.3 62.4 + - + +
26C LEU* 2.9 33.0 + - + +
51C VAL* 4.3 21.1 - - + +
54C LEU* 3.6 53.6 - - + +
55C LEU* 3.6 26.5 - - + -
58C GLN* 3.8 11.6 - - + +
93C ILE* 5.9 0.4 - - + -
134C MET* 4.8 11.2 - - - -
136C ILE* 5.9 0.2 - - + -
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLU* 2.8 50.6 + - - +
21C LYS* 3.7 8.1 - - - +
23C ILE* 1.3 72.7 - - + +
25C ASP* 1.3 64.0 + - - +
27C ASN* 3.0 22.7 + - - +
54C LEU* 5.4 6.9 - - - +
58C GLN* 3.9 28.2 - - - +
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Residues in contact with ASP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 3.5 7.6 - - - +
21C LYS* 2.9 48.9 + - - +
22C ALA* 3.4 11.2 - - - +
23C ILE 3.1 0.6 - - - -
24C LYS* 1.3 77.5 - - - +
26C LEU* 1.3 61.1 + - - +
27C ASN* 3.2 5.2 + - - +
28C GLY 5.5 0.9 - - - -
29C SER* 5.1 2.4 + - - -
166D ARG* 3.6 27.4 + - - +
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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