Contacts of the helix formed by residues 24 - 31 (chain D) in PDB entry 2I6A
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 ASP 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D VAL* 1.3 79.5 - - - +
25D LYS* 1.3 66.2 + - - +
26D ASP* 3.1 29.8 - - - +
27D PHE* 3.0 32.7 + - - +
28D LEU* 3.4 5.2 + - - +
56D PHE* 3.9 14.0 - - + -
128D THR* 4.2 7.0 - - - -
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Residues in contact with LYS 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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24D ASP* 1.3 73.2 - - - +
26D ASP* 1.3 65.2 + - - +
28D LEU* 3.1 15.9 + - + -
29D ASP* 2.9 51.0 + - - +
35D PRO* 5.1 18.2 - - + +
128D THR* 4.6 2.9 - - + +
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Residues in contact with ASP 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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24D ASP* 3.1 21.7 + - - +
25D LYS* 1.3 80.4 - - - +
27D PHE* 1.3 55.3 + - - +
29D ASP* 4.1 7.0 - - - +
30D LYS* 3.0 45.3 + - + +
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Residues in contact with PHE 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 VAL* 4.0 23.8 - - + -
24D ASP* 3.0 24.2 + - - +
26D ASP* 1.3 80.0 - - - +
28D LEU* 1.3 65.1 + - + +
30D LYS* 3.3 8.6 - - + +
31D TYR* 3.3 47.8 - + - -
33D LEU* 4.9 1.1 - - + -
48D LEU* 3.8 28.3 - - + -
51D GLU* 3.5 33.9 - - + -
52D LEU* 4.0 13.2 - - + -
56D PHE* 3.8 20.9 - + + -
126D CYS* 3.7 25.8 - - - -
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Residues in contact with LEU 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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23D VAL* 4.3 6.5 - - + -
24D ASP 3.8 8.5 - - - +
25D LYS* 3.1 15.6 + - + +
27D PHE* 1.3 77.2 - - + +
29D ASP* 1.3 52.2 - - - +
31D TYR 3.3 2.4 + - - -
32D SER 2.8 11.3 + - - -
33D LEU* 2.6 56.0 + - + +
34D LYS 4.5 0.2 - - - +
35D PRO* 4.1 22.4 - - + -
126D CYS* 4.1 19.3 - - + +
128D THR* 3.7 30.7 - - + +
133D SER* 4.0 29.4 - - - +
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Residues in contact with ASP 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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25D LYS* 2.9 52.4 + - - +
26D ASP* 4.1 7.4 + - - +
28D LEU* 1.3 72.4 - - - +
30D LYS* 1.3 61.5 + - + +
31D TYR 3.1 1.6 - - - -
32D SER* 2.7 29.9 + - - +
33D LEU 5.0 2.8 - - - +
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Residues in contact with LYS 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 ASP* 3.0 34.3 + - + +
27D PHE* 3.3 11.0 - - + +
29D ASP* 1.3 77.0 - - + +
31D TYR* 1.3 76.9 + - + +
32D SER* 4.9 1.1 + - - -
51D GLU* 5.6 6.3 - - - +
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Residues in contact with TYR 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 PHE* 3.3 52.5 - + - -
28D LEU 3.3 2.0 + - - -
29D ASP 3.1 0.6 - - - -
30D LYS* 1.3 89.1 - - + +
32D SER* 1.3 72.9 + - - +
33D LEU* 3.2 24.8 + - + +
44D LYS* 3.8 24.3 + - - +
45D HIS* 3.7 21.9 - - - +
47D GLU* 3.4 23.1 + - + +
48D LEU* 3.3 43.1 + - + -
51D GLU* 2.4 27.7 + - - -
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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