Contacts of the helix formed by residues 14 - 23 (chain D) in PDB entry 2AXT
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 TRP 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY* 1.3 81.0 - - - +
15D PHE* 1.3 94.5 + - + +
16D ASP 3.0 2.2 - - - -
17D ILE* 2.8 24.5 + - + +
18D LEU* 2.7 24.7 + - - +
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Residues in contact with PHE 15 (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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483C UNK 3.6 31.0 - - + -
13D GLY 3.9 11.0 - - - +
14D TRP* 1.3 89.5 - - + +
16D ASP* 1.3 61.8 + - - +
18D LEU* 3.1 9.3 + - + +
19D ASP* 2.7 40.0 + - + +
32D TRP* 3.2 40.1 - + - -
25H TRP* 3.2 45.1 - + + -
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Residues in contact with ASP 16 (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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13D GLY* 3.7 27.5 + - - +
15D PHE* 1.3 86.0 - - - +
17D ILE* 1.3 56.3 + - + +
18D LEU 2.9 0.2 + - - -
19D ASP* 3.9 7.6 - - - +
20D ASP* 2.6 47.1 + - - +
25H TRP* 5.1 5.6 + - - -
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Residues in contact with ILE 17 (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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13D GLY 3.6 9.2 - - - +
14D TRP* 2.8 34.9 + - + +
16D ASP* 1.3 73.8 - - + +
18D LEU* 1.3 60.3 + - - +
20D ASP* 3.5 9.8 - - - +
21D TRP* 3.3 19.1 + - - +
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Residues in contact with LEU 18 (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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14D TRP 2.7 10.6 + - - +
15D PHE* 3.1 10.8 - - + +
17D ILE* 1.3 74.1 - - - +
19D ASP* 1.3 59.9 + - - +
20D ASP 3.0 1.1 - - - -
21D TRP* 2.7 37.0 + - + +
22D LEU* 2.8 37.7 + - + +
32D TRP* 3.6 28.7 - - + -
35D ILE* 5.6 2.7 - - + -
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Residues in contact with ASP 19 (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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483C UNK 4.2 2.9 - - - +
15D PHE* 2.7 22.7 + - + +
16D ASP* 3.4 13.9 - - - +
18D LEU* 1.3 71.9 - - - +
20D ASP* 1.3 71.4 + - - +
22D LEU* 3.4 3.0 + - - +
23D LYS* 2.9 61.0 + - - +
32D TRP* 3.0 31.0 + - + +
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Residues in contact with ASP 20 (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 ASP* 2.6 39.6 + - - +
17D ILE* 3.5 9.4 - - - +
19D ASP* 1.3 82.0 - - - +
21D TRP* 1.3 65.0 + - - +
23D LYS* 3.3 9.1 + - - +
24D ARG* 3.4 11.8 + - - +
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Residues in contact with TRP 21 (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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17D ILE 3.3 10.4 + - - +
18D LEU* 2.7 26.2 + - + +
20D ASP* 1.3 79.2 - - - +
22D LEU* 1.3 87.8 + - + +
24D ARG* 3.2 13.1 - - - +
26D ARG* 2.7 61.3 + - - +
30D VAL* 5.7 3.6 - - + -
18F VAL* 5.4 4.9 - - + -
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Residues in contact with LEU 22 (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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18D LEU* 2.8 38.0 + - + +
19D ASP* 3.8 3.1 - - - +
21D TRP* 1.3 98.5 - - + +
23D LYS* 1.3 61.0 + - + +
24D ARG 3.1 8.8 + - - +
26D ARG* 4.3 1.9 + - - +
29D PHE* 4.6 0.9 - - - -
30D VAL* 3.9 19.5 + - + +
31D GLY* 3.4 35.5 + - - +
32D TRP* 3.6 39.9 - - + +
35D ILE* 3.8 23.8 - - + -
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Residues in contact with LYS 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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483C UNK 3.2 22.3 - - - +
490C UNK 5.4 4.8 - - - +
19D ASP* 2.9 49.6 + - - +
20D ASP* 3.7 6.7 - - - +
21D TRP 3.3 0.4 - - - -
22D LEU* 1.3 78.2 - - + +
24D ARG* 1.3 59.0 + - - +
25D ASP 3.6 2.4 + - - -
29D PHE* 4.4 14.1 - - + -
32D TRP* 3.9 15.7 - - - +
131D GLU* 4.3 16.1 - - - +
135D LEU* 3.9 39.9 - - + +
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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