Contacts of the helix formed by residues 34 - 49 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU 3.8 11.1 + - - -
28B SER* 3.5 14.1 - - - -
29B LEU 4.8 0.2 - - - -
31B GLY 3.0 15.4 + - - -
32B GLN 3.4 0.4 - - - -
33B TRP* 1.3 78.5 - - - +
35B GLU* 1.3 66.9 + - - -
36B THR 3.2 3.1 - - - -
37B THR* 3.1 12.3 + - - -
38B GLY 3.1 4.2 + - - -
147B ARG* 3.0 15.1 + - - -
151B ALA* 5.6 0.2 - - - -
154B GLN* 5.4 1.3 - - - -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 2.8 25.1 + - - +
29B LEU* 5.3 0.9 - - - +
34B GLY* 1.3 70.2 - - - -
36B THR* 1.3 59.7 + - - +
38B GLY* 3.3 0.7 + - - -
39B MET* 2.9 29.8 + - - +
66B GLU* 3.1 13.5 - - - +
69B HIS* 3.0 39.1 + - + +
70B VAL* 3.7 25.1 - - + +
73B ILE* 4.1 15.3 - - + -
147B ARG* 3.0 29.4 + - - +
151B ALA* 4.5 2.1 - - - +
155B VAL* 6.4 0.4 - - - -
174B LEU* 4.5 6.5 - - - +
178B GLU* 4.1 18.3 - - - +
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.6 15.3 - - + +
126A TRP* 5.9 1.1 - - + -
29B LEU* 2.8 31.8 + - - +
30B GLY* 5.0 0.2 - - - -
34B GLY 3.2 0.4 - - - -
35B GLU* 1.3 75.5 - - - +
37B THR* 1.3 64.9 + - - +
39B MET* 3.7 17.4 - - + +
40B MET* 2.9 27.3 + - + +
70B VAL* 3.9 17.4 - - - +
118B LEU* 4.9 3.1 - - + +
126B TRP* 3.6 37.2 - - + -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLY 3.4 2.9 + - - -
32B GLN 2.8 27.9 + - - +
33B TRP* 4.4 1.8 - - + -
34B GLY 3.1 12.1 + - - -
36B THR* 1.3 79.6 - - - +
38B GLY* 1.3 57.9 + - - +
41B SER* 2.8 42.5 + - - +
126B TRP* 2.9 25.2 + - - +
130B TYR* 3.5 26.9 - - - +
131B VAL* 4.4 1.0 - - + +
143B PHE* 4.7 2.5 - - + -
147B ARG* 4.0 16.8 - - + -
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 3.1 8.9 + - - -
35B GLU 3.3 3.5 + - - -
37B THR* 1.3 80.2 - - - +
39B MET* 1.3 63.7 + - - +
42B PHE* 2.9 43.7 + - - -
66B GLU* 4.0 1.3 - - - -
147B ARG* 3.6 30.0 - - - +
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Residues in contact with MET 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 4.6 2.0 - - + +
40A MET* 4.4 10.5 - - - -
35B GLU 2.9 20.5 + - - +
36B THR* 3.4 17.2 + - + +
38B GLY* 1.3 71.1 - - - +
40B MET* 1.3 98.3 + - + +
43B LEU* 3.0 49.4 + - + +
63B GLY* 3.7 17.6 - - - +
66B GLU* 3.6 16.1 - - + +
67B MET* 3.7 46.2 - - + +
70B VAL* 4.4 3.6 - - + -
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 4.4 22.9 - - + +
39A MET* 4.1 13.5 - - + -
40A MET* 5.9 0.4 - - - +
70A VAL* 4.7 9.6 - - + -
118A LEU* 3.9 38.7 - - + +
36B THR* 2.9 22.3 + - + +
39B MET* 1.3 109.8 - - + +
41B SER* 1.3 60.9 + - - +
43B LEU* 4.9 4.3 - - - -
44B SER* 2.8 34.1 + - - -
47B TRP* 5.5 5.4 - - + -
126B TRP* 3.9 14.8 - - + -
131B VAL* 3.9 12.7 - - + +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 2.8 27.4 + - - +
38B GLY* 4.0 1.8 - - - -
40B MET* 1.3 73.9 - - - +
42B PHE* 1.3 68.1 + - - +
44B SER* 3.3 0.7 + - - -
45B GLN* 2.9 38.7 + - - +
131B VAL* 3.5 27.1 - - - +
132B THR 4.0 5.8 - - - -
143B PHE* 3.5 29.4 - - - -
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY* 2.9 24.4 + - - +
41B SER* 1.3 83.1 - - - +
43B LEU* 1.3 58.7 + - - +
45B GLN* 3.6 0.6 + - - -
46B GLY* 2.9 25.8 + - - -
59B LEU* 3.5 34.8 - - + +
62B THR* 3.6 23.8 - - + -
63B GLY* 3.6 5.2 - - - -
66B GLU* 3.6 18.6 - - + -
144B ASN* 3.2 43.3 - - + -
147B ARG* 4.1 17.3 - - + -
148B GLU* 3.2 29.4 - - + -
185B PHE* 3.6 13.7 - + - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 6.4 0.4 - - - -
67A MET* 5.1 6.3 - - + -
2B PHE* 4.2 21.3 - - + -
39B MET* 3.0 45.4 + - + +
40B MET* 4.4 4.0 - - - +
42B PHE* 1.3 76.4 - - - +
44B SER* 1.3 56.5 + - - +
46B GLY* 3.2 0.5 + - - -
47B TRP* 2.8 61.1 + - + -
60B LEU* 4.0 21.9 - - + +
63B GLY* 3.8 9.0 - - - +
64B THR* 3.8 29.2 - - - +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 6.0 0.4 - - - -
116A ALA 5.8 3.8 - - - -
118A LEU* 4.6 18.8 - - - -
40B MET* 2.8 24.4 + - - -
41B SER* 3.3 7.6 + - - -
43B LEU* 1.3 76.8 - - - +
45B GLN* 1.3 64.0 + - - +
47B TRP* 3.4 16.3 + - - +
48B ALA* 3.0 24.9 + - - +
131B VAL* 3.9 6.2 - - - +
133B SER* 3.6 17.8 + - - -
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 2.9 24.8 + - - +
42B PHE 3.9 1.8 - - - +
44B SER* 1.3 75.4 + - - +
46B GLY* 1.3 58.4 + - - +
48B ALA* 3.2 2.8 + - - +
49B SER* 3.0 29.3 + - - -
59B LEU* 3.3 19.6 - - + +
132B THR 2.9 23.9 + - - +
133B SER* 3.5 17.9 - - - +
137B LEU* 4.3 7.4 - - + +
140B ASP* 3.8 26.4 - - - +
143B PHE* 4.0 6.9 - - - -
144B ASN* 2.8 43.0 + - - -
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE 2.9 18.9 + - - -
43B LEU 3.2 1.3 + - - -
45B GLN* 1.3 77.4 - - - +
47B TRP* 1.3 51.6 - - - +
48B ALA 3.4 0.5 + - - -
49B SER 3.4 4.3 + - - -
56B LYS* 2.7 40.1 + - - +
59B LEU* 3.8 19.5 - - - +
60B LEU* 3.8 16.8 - - - -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS* 4.3 1.2 + - - -
67A MET* 4.7 2.0 - - - -
70A VAL* 3.8 25.8 - - + -
71A GLU* 2.9 51.5 + - + +
74A SER* 3.6 35.7 - - - -
75A THR* 5.0 11.9 + - - +
118A LEU* 6.1 1.6 - - + -
2B PHE* 4.0 21.1 - + - -
40B MET* 5.5 5.6 - - + -
43B LEU* 2.8 47.2 + - + +
44B SER* 3.9 12.6 - - - +
46B GLY* 1.3 75.7 - - - +
48B ALA* 1.3 59.6 + - - +
49B SER 4.2 0.2 - - - +
56B LYS* 3.4 13.0 + - - +
60B LEU* 3.7 21.1 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 3.4 45.9 + - + +
116A ALA 5.6 0.9 - - - +
44B SER 3.0 17.6 + - - +
45B GLN* 3.7 3.8 - - - +
46B GLY 3.2 0.2 - - - -
47B TRP* 1.3 77.3 - - - +
49B SER* 1.3 63.0 + - - +
50B THR* 3.5 9.8 + - - +
133B SER* 4.2 10.8 - - - +
135B GLY* 5.9 3.4 - - - -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN 3.0 15.1 + - - -
46B GLY* 3.4 7.3 + - - -
47B TRP 3.4 1.9 - - - +
48B ALA* 1.3 77.3 - - - +
50B THR* 1.3 59.7 + - - +
51B GLY* 3.0 20.3 + - - -
52B ALA 4.8 0.3 + - - -
56B LYS* 2.8 51.3 + - - +
59B LEU* 5.0 0.9 - - - -
137B LEU* 4.1 24.0 - - - +
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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
------------------------------------------------------------
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