Contacts of the helix formed by residues 22 - 31 (chain D) in PDB entry 2OX6
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 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.8 6.3 - - - +
20D SER 4.3 0.4 + - - -
21D LEU* 1.3 76.1 - - - +
23D ALA* 1.3 65.6 + - - +
24D ALA* 3.4 9.4 + - - +
25D GLN* 3.0 41.1 + - - +
26D VAL* 3.0 21.5 + - - +
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Residues in contact with ALA 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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16D ARG* 3.8 21.8 - - - +
22D SER* 1.3 72.7 - - - +
24D ALA* 1.3 63.2 + - - +
26D VAL* 3.2 1.9 + - - +
27D GLY* 3.0 17.3 + - - -
34D GLU* 4.1 11.7 - - + +
37D VAL* 3.5 26.7 - - + +
38D LEU* 3.7 34.5 - - + -
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Residues in contact with ALA 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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22D SER* 3.2 8.8 + - - +
23D ALA* 1.3 78.6 - - - +
25D GLN* 1.3 58.4 + - + +
27D GLY* 3.1 4.1 + - - +
28D GLN* 3.0 29.1 + - - +
34D GLU* 3.7 38.4 + - + +
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Residues in contact with GLN 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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20D SER 4.1 4.2 - - - +
21D LEU* 3.6 14.8 - - + +
22D SER* 3.0 39.8 + - - +
24D ALA* 1.3 74.8 - - + +
26D VAL* 1.3 64.5 + - - +
28D GLN* 3.2 10.4 + - + +
29D LEU* 3.0 28.3 + - - +
109D LEU* 3.8 24.1 - - + +
111D GLU* 3.2 36.0 + - - +
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Residues in contact with VAL 26 (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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16D ARG* 3.4 41.5 - - + -
21D LEU* 3.9 17.0 - - + -
22D SER 3.0 8.2 + - - +
23D ALA 3.2 7.6 + - - +
25D GLN* 1.3 74.3 - - - +
27D GLY* 1.3 54.5 + - - +
29D LEU* 3.4 6.4 + - - -
30D THR* 2.8 45.5 + - + +
37D VAL* 4.0 8.1 - - + -
40D TRP* 3.9 28.5 - - + +
55D LEU* 4.1 20.0 - - + -
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Residues in contact with GLY 27 (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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23D ALA 3.0 13.6 + - - -
24D ALA* 3.1 6.6 + - - -
26D VAL* 1.3 76.5 - - - +
28D GLN* 1.3 54.0 + - - +
30D THR* 3.2 1.3 + - - -
31D ASN* 2.8 32.9 + - - -
32D HIS 2.9 30.7 + - - +
33D SER 4.6 2.7 - - - -
37D VAL* 3.8 8.9 - - - +
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Residues in contact with GLN 28 (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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24D ALA 3.0 15.0 + - - +
25D GLN* 3.2 12.7 + - + +
27D GLY* 1.3 74.8 - - - +
29D LEU* 1.3 64.0 + - + +
31D ASN* 3.7 6.9 + - - +
109D LEU* 5.4 7.9 - - + -
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Residues in contact with LEU 29 (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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21D LEU* 3.5 39.3 - - + -
25D GLN 3.0 20.1 + - - +
26D VAL* 3.9 3.8 - - - +
27D GLY 3.2 0.2 - - - -
28D GLN* 1.3 76.1 - - + +
30D THR* 1.3 63.6 + - + +
31D ASN 3.5 0.6 + - - -
54D LYS* 3.4 33.1 + - + +
55D LEU* 4.5 4.7 - - + -
58D ILE* 3.9 18.2 - - + -
108D PRO* 3.7 42.0 - - + -
109D LEU* 4.1 13.5 - - + -
112D LEU* 4.6 2.5 - - + -
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Residues in contact with THR 30 (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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26D VAL* 2.8 38.7 + - + +
27D GLY* 3.8 2.6 + - - -
29D LEU* 1.3 78.0 - - - +
31D ASN* 1.3 70.6 + - - +
32D HIS* 3.8 12.4 + - - +
40D TRP* 3.9 15.1 - - - -
51D ALA* 3.8 42.0 - - + +
54D LYS* 4.1 13.7 - - + -
55D LEU* 4.4 7.6 - - + -
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Residues in contact with ASN 31 (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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27D GLY 2.8 10.0 + - - -
28D GLN* 3.7 5.9 + - - +
29D LEU 3.5 2.6 - - - +
30D THR* 1.3 82.8 - - - +
32D HIS* 1.3 67.5 + - - +
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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