Contacts of the helix formed by residues 19 - 30 (chain A) in PDB entry 3OJE
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 SER 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 4.4 0.4 - - - -
14A VAL* 3.9 1.9 - - - +
15A ALA 3.1 40.3 + - - -
16A ASN 2.3 25.7 + - - -
17A GLN 2.5 18.8 + - - +
18A ARG* 1.3 69.1 - - - +
20A ILE* 1.3 63.9 + - - +
21A ALA 3.2 3.9 + - - -
22A TRP* 3.3 22.7 + - - +
23A GLY 3.5 5.4 + - - -
96A PHE* 3.8 15.5 - - - -
196A LEU* 4.3 4.9 - - - -
223A GLN* 3.7 2.9 - - - +
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Residues in contact with ILE 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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13A GLY 5.1 3.6 - - - +
18A ARG 3.5 1.4 + - - -
19A SER* 1.3 72.9 - - - +
21A ALA* 1.3 61.3 + - + +
22A TRP 3.4 0.2 - - - -
23A GLY* 3.4 3.6 + - - -
24A ILE* 3.1 27.8 + - + +
93A CYS* 4.2 9.4 - - + +
95A ALA* 3.9 28.9 - - + +
96A PHE* 5.9 1.6 - - + -
145A LEU* 3.5 26.5 - - + -
147A TYR* 5.6 7.4 - - + -
190A ALA* 5.4 2.2 - - + -
193A ILE* 4.7 8.5 - - + -
196A LEU* 4.1 13.3 - - + +
223A GLN* 3.8 20.3 - - + +
226A VAL* 3.5 36.3 - - + -
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Residues in contact with ALA 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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11A VAL* 3.5 12.9 - - + +
12A MET 3.6 24.2 - - - +
13A GLY 3.9 3.6 - - - +
14A VAL* 3.7 22.9 - - + +
19A SER* 3.2 1.2 - - - -
20A ILE* 1.3 77.6 - - + +
22A TRP* 1.3 61.2 + - - +
23A GLY 3.2 0.2 - - - -
24A ILE* 3.8 9.1 - - - +
25A ALA* 2.8 26.7 + - - +
93A CYS* 3.8 13.5 - - + -
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Residues in contact with TRP 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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14A VAL* 4.2 7.3 - - + +
17A GLN* 3.8 38.1 - - + +
19A SER* 3.3 20.5 + - - +
21A ALA* 1.3 74.6 - - - +
23A GLY* 1.3 61.0 + - - +
25A ALA* 2.9 15.3 + - + +
26A ARG* 2.8 85.7 + - + +
37A PHE* 4.2 16.3 - + - -
51A LEU* 3.8 41.5 + - + +
52A ALA* 5.5 0.2 - - - +
54A THR* 3.4 27.6 - - + -
55A LEU* 4.5 13.9 - - + +
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Residues in contact with GLY 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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17A GLN 4.8 0.6 + - - -
19A SER 3.5 5.9 + - - -
20A ILE 3.4 8.5 + - - -
21A ALA 3.2 0.6 - - - -
22A TRP* 1.3 78.5 - - - +
24A ILE* 1.3 60.0 + - - +
26A ARG* 3.7 15.8 + - - +
27A SER* 2.9 25.1 + - - -
223A GLN* 3.6 32.0 - - - +
224A GLU* 6.0 0.3 - - - +
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Residues in contact with ILE 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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11A VAL* 5.1 2.2 - - + -
20A ILE* 3.1 27.9 + - + +
21A ALA* 3.8 8.7 - - - +
22A TRP 3.3 0.2 - - - -
23A GLY* 1.3 75.1 - - - +
25A ALA* 1.3 64.3 + - - +
27A SER* 3.2 5.0 + - - -
28A LEU* 3.0 38.8 + - + +
91A ALA* 5.1 8.1 - - + -
93A CYS* 3.3 34.3 - - - -
143A LEU* 4.9 8.7 - - + -
145A LEU* 4.9 4.3 - - + -
226A VAL* 4.0 21.5 - - + +
227A GLY* 3.9 9.0 - - - -
230A ALA* 3.8 23.8 - - + -
234A PHE* 5.2 0.4 - - + -
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Residues in contact with ALA 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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11A VAL* 4.4 4.5 - - + -
21A ALA 2.8 16.8 + - - +
22A TRP* 2.9 20.2 + - + +
24A ILE* 1.3 74.7 - - - +
26A ARG* 1.3 64.4 + - - +
28A LEU* 3.0 9.4 + - - +
29A HIS* 2.9 20.3 + - - +
35A LEU* 3.7 14.5 - - + +
37A PHE* 3.7 32.5 - - + -
55A LEU* 5.2 2.2 - - + -
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Residues in contact with ARG 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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17A GLN* 5.8 0.8 - - - +
22A TRP* 2.8 72.5 + - + +
23A GLY* 4.1 18.1 + - - +
25A ALA* 1.3 71.7 - - - +
27A SER* 1.3 60.4 + - - +
29A HIS* 3.0 8.5 + - - +
30A ASN* 2.9 46.2 + - - +
55A LEU* 4.7 14.1 - - + +
223A GLN* 4.4 4.0 - - - +
224A GLU* 2.6 34.3 + - - +
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Residues in contact with SER 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 GLY 2.9 12.7 + - - -
24A ILE 3.2 10.2 + - - -
26A ARG* 1.3 78.2 - - - +
28A LEU* 1.3 59.3 + - - +
30A ASN* 4.2 7.5 + - - +
31A ALA* 3.7 12.6 + - - +
224A GLU* 4.2 10.4 + - - +
227A GLY* 3.5 31.2 - - - -
228A ASP* 3.4 18.1 + - - +
231A VAL* 3.3 16.3 - - - +
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Residues in contact with LEU 28 (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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4A LEU* 3.4 26.7 - - + -
9A PHE* 4.8 13.7 - - + -
11A VAL* 4.5 20.2 - - + -
24A ILE* 3.0 36.3 + - + +
25A ALA* 3.0 6.4 + - - +
27A SER* 1.3 76.7 - - - +
29A HIS* 1.3 65.2 + - - +
30A ASN 3.3 0.2 - - - -
31A ALA* 3.0 14.4 + - - +
33A ALA* 3.3 23.0 + - + +
35A LEU* 4.7 5.8 - - + -
91A ALA* 5.3 2.2 - - + -
230A ALA* 4.5 1.3 - - + -
231A VAL* 4.1 16.4 - - + +
234A PHE* 3.7 31.4 - - + -
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Residues in contact with HIS 29 (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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1A MET* 4.6 11.5 - - + +
25A ALA 2.9 8.5 + - - +
26A ARG* 3.6 6.7 - - - +
28A LEU* 1.3 76.5 - - - +
30A ASN* 1.3 66.2 + - - +
32A GLY* 2.6 29.6 + - - -
33A ALA 3.5 17.7 + - - +
35A LEU* 4.1 11.3 - - + +
55A LEU* 3.7 36.9 - - + +
56A GLU* 3.2 53.9 + - + -
57A GLY* 4.9 3.0 - - - -
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Residues in contact with ASN 30 (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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1A MET* 3.7 19.2 + - - +
26A ARG* 2.9 31.2 + - - +
27A SER* 4.5 7.1 - - - +
29A HIS* 1.3 83.5 + - - +
31A ALA* 1.3 57.1 + - - +
32A GLY 3.0 7.4 + - - -
55A LEU* 5.4 3.7 - - - +
56A GLU* 5.1 1.7 - - - +
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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