Contacts of the helix formed by residues 29 - 42 (chain D) in PDB entry 2XXA
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 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D LYS* 6.1 0.3 - - - +
27D LYS* 3.1 16.5 - - + +
28D ILE* 1.3 75.1 - - - +
30D ASP* 1.3 65.9 + - - +
31D ASP* 3.0 29.4 - - - +
32D LEU* 3.2 18.8 + - - +
33D PHE* 3.3 28.9 + - - -
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Residues in contact with ASP 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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29D ASP* 1.3 74.9 - - - +
31D ASP* 1.4 63.1 + - - +
33D PHE* 3.7 8.8 + - - +
34D GLU* 3.3 22.2 + - - +
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Residues in contact with ASP 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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29D ASP* 3.0 22.1 - - - +
30D ASP* 1.4 77.1 + - - +
32D LEU* 1.4 58.3 + - - +
34D GLU* 3.4 16.3 + - - +
35D GLU* 3.1 35.7 + - - +
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Residues in contact with LEU 32 (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 PHE* 4.5 28.1 - - + +
26D LYS* 3.8 43.5 - - + +
27D LYS 3.9 13.9 - - - +
28D ILE* 4.1 9.9 - - + -
29D ASP* 3.2 21.0 + - - +
30D ASP 3.5 0.2 - - - -
31D ASP* 1.4 75.8 - - - +
33D PHE* 1.4 60.0 + - + +
35D GLU* 3.2 18.2 + - + +
36D LEU* 3.0 28.3 + - + +
69D ALA* 5.6 2.2 - - + -
72D LEU* 3.8 28.7 - - + -
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Residues in contact with PHE 33 (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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28D ILE* 4.1 22.0 - - + -
29D ASP 3.3 24.2 + - - +
30D ASP* 3.9 10.1 - - - +
31D ASP 3.4 0.4 - - - -
32D LEU* 1.4 77.6 - - + +
34D GLU* 1.4 57.0 + - - +
36D LEU* 3.4 12.2 + - + +
37D GLU* 3.0 28.1 + - - +
54D ILE* 4.8 15.5 - - + +
57D LEU* 4.3 28.3 - - + -
58D THR* 3.7 28.7 - - + -
61D ALA* 4.7 9.4 - - + -
72D LEU* 4.1 26.0 - - + -
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Residues in contact with GLU 34 (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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35C ARG* 5.2 9.2 + - - +
30D ASP 3.3 12.1 + - - +
31D ASP* 3.5 18.2 - - - +
32D LEU 3.3 0.4 - - - -
33D PHE* 1.4 77.3 - - - +
35D GLU* 1.4 61.6 + - + +
37D GLU* 3.9 16.5 - - - +
38D GLU* 3.2 42.3 + - + +
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Residues in contact with GLU 35 (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 PHE* 5.1 6.4 - - + -
26D LYS* 2.9 35.4 + - - +
31D ASP* 3.1 25.4 + - - +
32D LEU* 3.2 24.3 + - + +
34D GLU* 1.4 77.5 - - - +
36D LEU* 1.4 58.8 + - - +
38D GLU* 4.0 8.2 + - - +
39D GLN* 3.5 38.5 + - - +
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Residues in contact with LEU 36 (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 PHE* 4.0 27.3 - - + -
32D LEU* 3.0 15.8 + - + +
33D PHE* 3.7 12.8 - - + +
34D GLU 3.3 0.2 - - - -
35D GLU* 1.4 75.3 - - - +
37D GLU* 1.4 58.7 + - - +
39D GLN* 3.4 6.5 + - + +
40D LEU* 3.0 50.9 + - + +
54D ILE* 6.0 2.0 - - + -
57D LEU* 4.1 23.3 - - + -
72D LEU* 5.2 25.1 - - + +
73D TYR* 6.3 0.9 - - - -
76D LEU* 4.2 22.9 - - + -
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Residues in contact with GLU 37 (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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35C ARG* 5.2 8.1 + - - -
33D PHE 3.0 17.1 + - - +
34D GLU* 3.9 19.0 - - - +
35D GLU 3.5 0.2 - - - -
36D LEU* 1.4 75.3 - - - +
38D GLU* 1.4 57.5 + - + +
40D LEU* 3.2 13.9 + - - +
41D LEU* 2.9 44.5 + - + +
50D THR* 4.4 2.7 - - + -
51D ARG* 4.3 20.6 + - - +
54D ILE* 3.5 31.4 - - + +
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Residues in contact with GLU 38 (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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35C ARG* 3.9 18.1 + - - +
45C LEU* 3.3 28.4 - - + +
49C ARG* 3.4 47.2 + - - +
34D GLU* 3.2 34.1 + - + +
35D GLU* 4.3 8.1 - - - +
36D LEU 3.4 0.2 - - - -
37D GLU* 1.4 78.5 - - + +
39D GLN* 1.4 58.1 + - + +
41D LEU* 4.4 4.3 - - + -
42D ILE* 3.2 24.8 + - - +
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Residues in contact with GLN 39 (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 ILE 5.5 0.9 + - - -
23D PHE* 3.4 37.9 - - + -
35D GLU* 3.5 22.8 + - - +
36D LEU* 3.4 7.7 + - + +
37D GLU 3.3 0.4 - - - -
38D GLU* 1.4 77.6 - - + +
40D LEU* 1.4 59.5 + - - +
42D ILE* 3.3 24.1 - - + +
43D ALA* 4.2 6.8 + - - +
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Residues in contact with LEU 40 (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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36D LEU* 3.0 40.4 + - + +
37D GLU* 3.2 12.5 + - - +
39D GLN* 1.4 77.0 - - - +
41D LEU* 1.3 63.1 + - - +
42D ILE 3.4 0.2 - - - -
43D ALA* 3.4 9.2 + - + +
45D VAL* 3.3 35.2 - - + +
50D THR* 3.8 20.6 - - + +
53D ILE* 5.1 13.9 - - + -
54D ILE* 4.7 11.4 - - + -
57D LEU* 5.4 1.3 - - + -
76D LEU* 4.3 24.5 - - + -
80D MET* 4.4 20.4 - - + -
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Residues in contact with LEU 41 (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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35C ARG* 5.3 5.2 - - - +
39C LEU* 4.1 37.2 - - + +
45C LEU* 3.8 21.8 - - + -
227C GLN* 3.5 12.3 + - - +
37D GLU* 2.9 41.1 + - + +
38D GLU* 4.4 6.7 - - + -
40D LEU* 1.3 72.5 - - - +
42D ILE* 1.4 54.4 + - - +
43D ALA 3.0 5.2 - - - -
44D ASP* 3.0 19.9 + - - -
45D VAL 4.3 1.5 + - - +
46D GLY 3.4 27.9 + - - +
47D VAL* 4.7 8.3 - - + -
50D THR* 4.2 11.4 - - + +
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Residues in contact with ILE 42 (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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44C ALA* 6.0 0.2 - - + -
45C LEU* 3.9 18.8 - - + +
46C PRO* 4.5 13.7 - - + -
49C ARG* 6.0 1.6 - - - +
227C GLN* 3.3 42.9 - - + +
228C ASP 5.2 0.2 + - - -
230C ALA* 5.9 3.8 - - + -
231C ASN* 6.2 2.5 - - - +
38D GLU 3.2 14.9 + - - +
39D GLN* 3.3 27.6 - - + +
41D LEU* 1.4 74.9 - - - +
43D ALA* 1.3 56.4 + - - +
44D ASP* 3.3 1.1 - - - +
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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