Contacts of the helix formed by residues 15 - 23 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASN* 2.9 10.3 + - - +
14B LEU* 1.3 77.7 - - - +
16B SER* 1.3 54.4 + - - +
18B THR* 2.8 7.8 + - - -
19B ASN* 2.8 51.9 + - - +
317B LYS* 3.8 35.3 + - - +
320B ALA* 4.0 15.7 - - + -
321B LYS* 5.7 1.9 - - - +
355B ARG 3.5 25.5 + - - +
356B SER 3.7 14.1 - - - +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASN* 3.3 11.8 + - - -
14B LEU 3.4 0.4 - - - -
15B GLN* 1.3 77.4 - - - +
17B LEU* 1.3 64.3 + - - +
20B ALA* 2.9 26.0 + - - +
195B GLU* 3.7 27.8 - - - -
196B LYS* 3.0 32.9 + - - -
320B ALA* 4.5 18.5 + - - +
323B VAL 4.9 2.4 + - - -
324B PHE* 3.6 8.6 - - - -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.9 13.2 - - + -
13B ASN 5.4 0.9 + - - +
14B LEU* 3.6 16.5 + - + +
15B GLN 3.4 0.6 - - - -
16B SER* 1.3 79.6 - - - +
18B THR* 1.3 64.1 + - - +
20B ALA* 3.2 2.1 + - - +
21B ILE* 3.0 43.5 + - + +
46B ILE* 3.9 20.0 - - + -
48B PRO* 3.6 37.0 - - + -
82B ILE* 4.0 21.8 - - + -
195B GLU* 3.9 19.7 - - + +
205B ILE* 4.2 18.8 - - + -
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 5.0 5.4 - - + -
14B LEU* 2.9 21.0 + - + +
15B GLN* 2.8 22.5 + - - -
17B LEU* 1.3 75.4 - - + +
19B ASN* 1.3 57.9 + - - +
21B ILE* 3.3 4.4 + - - +
22B GLU* 2.9 40.1 + - - +
28B VAL* 3.7 35.9 - - + +
30B LEU* 4.2 16.4 - - + -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 2.8 39.9 + - - +
16B SER 3.8 3.1 - - - +
18B THR* 1.3 75.5 + - - +
20B ALA* 1.3 57.2 + - - +
22B GLU* 3.8 16.1 - - - +
23B HIS* 2.8 31.9 + - - +
320B ALA* 3.0 30.3 + - - +
321B LYS* 3.4 35.6 - - - +
324B PHE* 4.1 4.2 - - + -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 2.9 18.6 + - - +
17B LEU* 3.5 5.4 - - - +
19B ASN* 1.3 77.9 - - - +
21B ILE* 1.3 63.4 + - - +
23B HIS* 3.2 5.3 + - - +
24B LEU* 2.9 28.3 + - - +
195B GLU* 4.6 2.0 - - + -
202B LEU* 3.4 25.6 - - + -
205B ILE* 3.9 19.3 - - + -
324B PHE* 3.6 15.0 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.7 17.0 - - + -
6B VAL* 3.8 22.9 - - + -
17B LEU* 3.0 27.4 + - + +
18B THR* 3.7 5.4 - - - +
20B ALA* 1.3 75.7 - - - +
22B GLU* 1.3 63.0 + - - +
24B LEU* 3.0 18.8 + - - +
25B GLY 3.4 0.7 + - - -
26B TYR* 3.1 37.8 + - + +
28B VAL* 3.7 16.2 - - + -
46B ILE* 3.6 26.5 - - + -
205B ILE* 4.3 13.0 - - + -
209B LEU* 3.9 7.0 - - + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 2.9 26.7 + - - +
19B ASN* 3.8 15.2 - - - +
21B ILE* 1.3 75.1 - - - +
23B HIS* 1.3 55.3 + - - +
25B GLY* 2.6 28.4 + - - -
26B TYR 3.2 20.2 + - - +
27B GLU* 5.1 0.4 - - - -
28B VAL* 4.2 19.9 + - + +
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN 2.8 23.3 + - - +
20B ALA* 3.3 7.9 - - - +
22B GLU* 1.3 73.1 - - - +
24B LEU* 1.3 66.4 + - + +
25B GLY 3.3 3.3 + - - -
199B LYS* 6.2 1.2 - - - +
202B LEU* 4.0 30.1 - - + +
321B LYS 5.6 2.0 - - - +
324B PHE* 4.7 13.4 - + + -
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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
------------------------------------------------------------
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