Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 1OX4
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 GLN 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN* 2.9 10.5 + - - +
14A LEU* 1.3 78.1 - - - +
16A SER* 1.3 58.6 + - - +
18A THR* 2.9 8.7 + - - -
19A ASN* 2.8 51.8 + - - +
317A LYS* 3.8 30.7 - - - +
320A ALA* 4.2 10.8 - - + -
321A LYS* 6.0 0.9 - - - +
355A ARG 3.3 27.5 + - - +
356A SER* 3.7 16.6 - - - +
357A GLY* 4.2 0.4 - - - -
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Residues in contact with SER 16 (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 ASN* 3.3 13.0 + - - -
14A LEU 3.4 0.2 - - - -
15A GLN* 1.3 78.9 - - - +
17A LEU* 1.3 56.7 + - - +
19A ASN* 4.5 5.2 - - - +
20A ALA* 2.9 31.5 + - - +
195A GLU* 3.7 19.2 - - - +
196A LYS* 2.8 41.1 + - - -
320A ALA* 4.6 12.4 + - - +
323A VAL 5.0 2.3 + - - -
324A PHE* 3.7 7.8 - - - -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 13.9 - - + -
13A ASN 5.4 1.5 + - - +
14A LEU* 3.6 15.4 + - + +
15A GLN 3.4 0.8 - - - -
16A SER* 1.3 77.3 - - - +
18A THR* 1.3 64.4 + - - +
20A ALA* 3.2 3.5 + - - +
21A ILE* 3.0 45.9 + - + +
46A ILE* 3.9 19.7 - - + -
48A PRO* 3.6 37.2 - - + -
82A ILE* 4.0 20.9 - - + -
195A GLU* 3.9 19.9 - - + +
205A ILE* 4.3 16.8 - - + -
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Residues in contact with THR 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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6A VAL* 5.0 5.4 - - + -
14A LEU* 2.9 21.9 + - + +
15A GLN* 2.9 21.7 + - - -
17A LEU* 1.3 76.5 - - + +
19A ASN* 1.3 59.2 + - - +
21A ILE* 3.3 3.9 + - - +
22A GLU* 2.9 40.0 + - - +
28A VAL* 3.7 36.0 - - + +
30A LEU* 4.2 17.0 - - + -
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Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 2.8 43.5 + - - +
16A SER 3.8 2.7 - - - +
18A THR* 1.3 76.5 + - - +
20A ALA* 1.3 57.9 + - - +
22A GLU* 3.8 15.3 - - - +
23A HIS* 2.8 32.1 + - - +
320A ALA* 2.9 39.3 + - - +
321A LYS* 3.5 30.5 - - - +
324A PHE* 4.0 3.8 - - + -
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Residues in contact with ALA 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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16A SER 2.9 19.7 + - - +
17A LEU* 3.2 5.6 + - - +
19A ASN* 1.3 77.0 - - - +
21A ILE* 1.3 62.7 + - - +
23A HIS* 3.2 4.5 + - - +
24A LEU* 2.9 28.7 + - - +
195A GLU* 4.5 2.2 - - + -
202A LEU* 3.6 24.6 - - + +
205A ILE* 4.0 18.4 - - + -
324A PHE* 3.5 16.3 - - + -
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Residues in contact with ILE 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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4A VAL* 3.7 17.3 - - + -
6A VAL* 3.8 22.4 - - + -
17A LEU* 3.0 28.5 + - + +
18A THR 3.7 5.6 - - - +
20A ALA* 1.3 75.5 - - - +
22A GLU* 1.3 63.3 + - - +
24A LEU* 3.0 19.4 + - - +
25A GLY 3.4 0.3 + - - -
26A TYR* 3.1 41.1 + - + +
28A VAL* 3.7 16.6 - - + -
46A ILE* 3.6 30.1 - - + -
205A ILE* 4.5 10.5 - - + +
209A LEU* 4.3 3.1 - - + -
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Residues in contact with GLU 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 THR* 2.9 25.6 + - - +
19A ASN* 3.8 16.3 - - - +
21A ILE* 1.3 75.7 - - - +
23A HIS* 1.3 54.6 + - - +
25A GLY* 2.7 27.9 + - - -
26A TYR 3.2 19.1 + - - +
27A GLU* 5.1 0.7 - - - -
28A VAL* 4.3 20.4 + - + +
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Residues in contact with HIS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN 2.8 20.4 + - - +
20A ALA* 3.4 7.9 - - - +
22A GLU* 1.3 76.4 - - - +
24A LEU* 1.3 64.6 + - + +
25A GLY 3.2 3.8 + - - -
202A LEU* 4.0 29.2 - - + +
321A LYS 5.3 3.1 + - - +
322A THR* 6.2 3.1 - - + +
324A PHE* 4.4 15.4 - + + -
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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