Contacts of the helix formed by residues 34 - 49 (chain D) in PDB entry 1O9I
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 GLY 34 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU 3.8 12.9 + - - -
28D SER* 3.5 14.8 - - - -
29D LEU 4.8 0.7 - - - -
31D GLY 3.1 13.6 + - - -
32D GLN 3.5 0.2 - - - -
33D TRP* 1.3 79.5 - - - +
35D GLU* 1.3 67.1 + - - -
36D THR 3.3 2.9 - - - -
37D THR* 3.0 13.0 + - - -
38D GLY 3.1 4.2 + - - -
147D ARG* 3.0 14.1 + - - -
151D ALA* 5.5 0.7 - - - -
154D GLN* 5.3 1.1 - - - -
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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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28D SER* 2.8 24.2 + - - +
29D LEU* 5.3 0.4 - - - -
34D GLY* 1.3 70.3 - - - -
36D THR* 1.3 60.4 + - - +
38D GLY* 3.3 1.0 + - - -
39D MET* 2.8 29.8 + - - +
66D GLU* 3.1 13.8 - - - +
69D HIS* 3.0 39.4 + - + +
70D VAL* 3.7 25.4 - - + +
73D ILE* 4.2 15.0 - - + -
147D ARG* 3.0 31.7 + - - +
151D ALA* 4.4 1.9 - - - +
174D LEU* 4.5 6.5 - - - +
178D GLU* 4.2 18.0 - - - +
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Residues in contact with THR 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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29D LEU* 2.8 32.0 + - - +
30D GLY* 5.0 0.2 - - - -
34D GLY 3.3 0.8 - - - -
35D GLU* 1.3 77.0 - - - +
37D THR* 1.3 57.6 + - - +
39D MET* 4.3 17.3 - - + -
40D MET* 2.9 33.7 + - + +
70D VAL* 3.8 17.7 - - + +
118D LEU* 4.9 8.0 - - + +
126D TRP* 3.6 36.1 - - + -
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Residues in contact with THR 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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31D GLY 3.4 3.5 + - - -
32D GLN 2.8 28.3 + - - +
33D TRP* 4.4 2.0 - - + -
34D GLY 3.0 11.9 + - - -
36D THR* 1.3 79.6 - - - +
38D GLY* 1.3 62.0 + - - +
41D SER* 2.8 36.8 + - - +
126D TRP* 2.9 26.0 + - - +
130D TYR* 3.5 27.0 - - - +
131D VAL* 4.4 1.0 - - - +
143D PHE* 4.6 2.9 - - + -
147D ARG* 4.1 16.6 - - + -
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Residues in contact with GLY 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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34D GLY 3.1 8.1 + - - -
35D GLU 3.3 2.6 + - - -
37D THR* 1.3 80.4 - - - +
39D MET* 1.3 61.5 + - - +
42D PHE* 2.9 43.9 + - - -
66D GLU* 4.0 2.0 - - - -
147D ARG* 3.7 29.3 - - - +
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Residues in contact with MET 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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35D GLU 2.8 20.9 + - - +
36D THR* 3.7 16.6 - - + +
38D GLY* 1.3 71.6 - - - +
40D MET* 1.3 98.2 + - + +
43D LEU* 3.0 49.4 + - + +
63D GLY* 3.6 17.6 - - - +
66D GLU* 3.6 15.2 - - + +
67D MET* 3.4 49.8 - - + +
70D VAL* 4.4 4.3 - - + -
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Residues in contact with MET 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 THR* 2.9 23.2 + - + +
39D MET* 1.3 109.3 - - + +
41D SER* 1.3 54.8 + - - +
43D LEU* 4.4 4.9 - - - +
44D SER* 2.7 40.1 + - - -
47D TRP* 5.6 10.3 - - + -
126D TRP* 3.9 17.3 - - + -
131D VAL* 3.9 20.0 - - + +
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Residues in contact with SER 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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37D THR* 2.8 26.2 + - - +
38D GLY* 4.0 2.0 - - - -
40D MET* 1.3 74.5 - - - +
42D PHE* 1.3 67.0 + - - +
44D SER* 3.3 0.9 + - - -
45D GLN* 2.9 39.9 + - - +
131D VAL* 3.5 27.6 - - - +
132D THR 4.0 6.3 - - - -
143D PHE* 3.6 29.7 - - - -
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY* 2.9 28.6 + - - +
41D SER* 1.3 83.8 - - - +
43D LEU* 1.3 58.9 + - - +
45D GLN* 3.8 0.2 - - - +
46D GLY* 2.9 24.3 + - - -
59D LEU* 3.5 36.4 - - + +
62D THR* 3.6 24.2 - - + -
63D GLY* 3.7 4.7 - - - -
66D GLU* 3.5 19.1 - - + -
144D ASN* 3.2 45.3 - - + -
147D ARG* 4.2 9.4 - - + -
148D GLU* 3.4 29.4 - - + -
185D PHE* 3.6 14.1 - + - -
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Residues in contact with LEU 43 (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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2D PHE* 4.1 21.5 - - + -
39D MET* 3.0 44.4 + - + +
40D MET* 4.4 4.3 - - + +
42D PHE* 1.3 77.0 - - - +
44D SER* 1.3 57.4 + - - +
46D GLY* 3.2 0.9 + - - -
47D TRP* 2.8 63.4 + - + -
60D LEU* 4.0 21.8 - - + +
63D GLY* 3.9 23.6 - - - +
64D THR* 3.9 13.7 - - - +
67D MET* 5.8 3.6 - - + -
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Residues in contact with SER 44 (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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40D MET* 2.7 26.8 + - - -
41D SER* 3.3 7.1 + - - -
43D LEU* 1.3 76.1 - - - +
45D GLN* 1.3 64.3 + - - +
47D TRP* 3.4 15.8 + - - +
48D ALA* 3.0 24.8 + - - +
131D VAL* 4.0 7.1 - - - +
133D SER* 3.6 19.2 + - - -
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Residues in contact with GLN 45 (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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41D SER* 2.9 27.8 + - - +
42D PHE 3.8 2.5 - - - +
44D SER* 1.3 75.0 + - - +
46D GLY* 1.3 63.5 + - - +
48D ALA* 3.2 3.1 + - - +
49D SER* 3.0 24.4 + - - -
59D LEU* 3.4 17.7 - - + +
132D THR 2.9 26.6 + - - +
133D SER* 3.5 15.0 - - - +
137D LEU* 4.2 7.5 - - + +
140D ASP* 3.8 27.0 - - + +
143D PHE* 4.0 6.7 - - - -
144D ASN* 2.8 43.3 + - - -
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Residues in contact with GLY 46 (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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42D PHE 2.9 16.4 + - - -
43D LEU 3.6 3.1 - - - -
45D GLN* 1.3 76.7 - - - +
47D TRP* 1.3 51.4 + - - +
48D ALA 3.3 0.3 + - - -
49D SER* 3.3 4.6 + - - -
56D LYS* 2.7 40.3 + - - +
59D LEU* 3.8 19.4 - - - +
60D LEU* 3.9 17.7 - - - -
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Residues in contact with TRP 47 (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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254A ILE* 4.2 18.2 - - - +
2D PHE* 4.1 29.7 - + - -
40D MET* 5.6 10.1 - - + -
43D LEU* 2.8 53.5 + - + +
44D SER* 3.9 12.3 - - - +
46D GLY* 1.3 72.3 - - - +
48D ALA* 1.3 58.8 + - - +
49D SER 4.4 0.2 - - - +
56D LYS* 3.5 11.6 + - - +
60D LEU* 3.8 21.9 - - + +
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Residues in contact with ALA 48 (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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254A ILE* 5.7 3.5 - - - +
265A GLN* 3.8 11.9 + - - +
44D SER 3.0 17.9 + - - +
45D GLN* 3.7 4.3 - - - +
46D GLY 3.2 0.4 - - - -
47D TRP* 1.3 76.3 - - - +
49D SER* 1.3 62.1 + - - +
50D THR* 3.5 10.0 + - - +
133D SER* 4.2 11.7 - - - +
135D GLY* 5.8 6.1 - - - -
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Residues in contact with SER 49 (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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254A ILE* 6.0 0.2 - - - +
265A GLN* 3.7 14.2 + - - +
45D GLN 3.0 15.1 + - - -
46D GLY* 3.3 8.7 + - - -
47D TRP 4.4 0.5 - - - +
48D ALA* 1.3 78.0 - - - +
50D THR* 1.3 62.2 + - - +
51D GLY* 3.0 17.0 + - - -
52D ALA 4.7 0.7 + - - -
56D LYS* 2.7 50.7 + - - +
59D LEU* 5.1 0.7 - - - -
137D LEU* 4.1 18.0 - - - +
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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
------------------------------------------------------------
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