Contacts of the helix formed by residues 34 - 49 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU 3.8 11.1 + - - -
28A SER* 3.4 14.6 - - - -
29A LEU 4.9 0.2 - - - -
31A GLY 3.1 16.7 + - - -
32A GLN 3.5 0.4 - - - -
33A TRP* 1.3 77.5 - - - +
35A GLU* 1.3 67.2 + - - -
36A THR 3.2 3.4 - - - -
37A THR* 3.1 13.1 + - - -
38A GLY 3.1 4.2 + - - -
147A ARG* 3.0 13.9 + - - -
151A ALA* 5.5 0.4 - - - -
154A GLN* 5.3 1.3 - - - -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 2.8 23.4 + - - +
29A LEU* 5.3 0.9 - - - +
34A GLY* 1.3 73.8 - - - -
36A THR* 1.3 57.4 + - - +
38A GLY* 3.2 0.9 + - - -
39A MET* 2.9 29.8 + - - +
66A GLU* 3.1 14.0 - - - +
69A HIS* 3.0 40.5 + - + +
70A VAL* 3.7 24.7 - - + +
73A ILE* 4.2 14.6 - - + -
147A ARG* 3.0 30.1 + - - +
151A ALA* 4.5 1.7 - - - +
155A VAL* 6.0 0.8 - - - +
174A LEU* 4.5 8.4 - - - +
178A GLU* 4.1 16.0 - - - +
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.8 31.4 + - - +
34A GLY 3.2 0.6 - - - -
35A GLU* 1.3 73.9 - - - +
37A THR* 1.3 66.1 + - - +
39A MET* 3.7 17.2 - - + +
40A MET* 2.9 26.5 + - + +
70A VAL* 3.8 18.7 - - - +
118A LEU* 5.0 2.8 - - + +
126A TRP* 3.5 38.1 - - + -
40B MET* 4.4 14.6 - - + +
126B TRP* 6.0 0.9 - - + -
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY 3.4 4.2 + - - -
32A GLN 2.8 28.6 + - - +
33A TRP* 4.3 1.3 - - + -
34A GLY 3.1 12.1 + - - -
36A THR* 1.3 78.0 - - - +
38A GLY* 1.3 62.1 + - - +
41A SER* 2.8 37.1 + - - +
126A TRP* 2.9 25.3 + - - +
130A TYR* 3.5 26.7 - - - +
131A VAL* 4.3 0.4 - - + +
143A PHE* 4.7 2.7 - - + -
147A ARG* 4.1 16.8 - - + -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.1 11.9 + - - -
35A GLU 3.2 3.3 + - - -
37A THR* 1.3 76.8 - - - +
39A MET* 1.3 64.0 + - - +
42A PHE* 2.9 44.7 + - - -
66A GLU* 3.9 1.8 - - - -
147A ARG* 3.7 29.1 - - - +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU 2.9 15.5 + - - +
36A THR* 3.7 22.9 - - + +
38A GLY* 1.3 75.6 - - - +
40A MET* 1.3 77.2 + - - +
43A LEU* 3.1 44.0 + - + +
63A GLY* 4.0 5.3 - - - +
66A GLU* 3.6 18.8 - - + +
67A MET* 3.5 42.2 - - + +
70A VAL* 4.2 13.2 - - + -
39B MET* 5.3 1.1 - - - +
40B MET* 4.1 21.3 - - + +
43B LEU* 6.4 0.7 - - - -
67B MET* 3.9 11.4 - - + -
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 2.9 22.1 + - + +
39A MET* 1.3 98.8 - - + +
41A SER* 1.3 60.4 + - - +
43A LEU* 4.8 3.1 - - - -
44A SER* 2.8 33.4 + - - -
47A TRP* 5.3 6.1 - - + -
126A TRP* 3.9 15.5 - - + -
131A VAL* 3.9 19.9 - - + +
36B THR* 4.6 18.2 - - + -
39B MET* 4.4 12.8 - - + -
40B MET* 5.9 0.2 - - - +
67B MET* 4.5 6.1 - - + -
70B VAL* 4.6 16.2 - - + -
118B LEU* 3.9 33.9 - - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 2.8 25.5 + - - +
38A GLY* 3.9 2.0 - - - -
40A MET* 1.3 75.4 - - - +
42A PHE* 1.3 71.3 + - - +
44A SER* 3.2 1.0 + - - -
45A GLN* 2.9 37.0 + - - +
131A VAL* 3.5 27.6 - - - +
132A THR 4.0 5.8 - - - -
143A PHE* 3.6 30.0 - - - -
147A ARG* 5.6 0.2 - - - -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 2.9 30.6 + - - +
41A SER* 1.3 82.3 - - - +
43A LEU* 1.3 58.2 + - - +
45A GLN* 3.8 0.3 - - - +
46A GLY* 2.8 26.9 + - - -
59A LEU* 3.5 33.4 - - + +
62A THR* 3.6 22.9 - - + -
63A GLY* 3.6 5.2 - - - -
66A GLU* 3.6 18.6 - - + -
144A ASN* 3.2 44.6 - - + -
147A ARG* 4.2 10.3 - - + -
148A GLU* 3.3 28.9 - - + -
185A PHE* 3.7 14.1 - + - -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 4.2 16.2 - - + -
39A MET* 3.1 29.6 + - + +
40A MET* 4.4 5.4 - - - +
42A PHE* 1.3 74.3 - - - +
44A SER* 1.3 59.7 + - - +
46A GLY* 3.2 1.0 + - - -
47A TRP* 2.8 59.7 + - + -
60A LEU* 4.1 21.7 - - + +
63A GLY* 3.8 24.2 - - - +
64A THR* 3.9 13.9 - - - +
67A MET* 4.4 3.1 - - - -
4B HIS* 5.8 0.2 - - + -
67B MET* 3.8 29.4 - - + -
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 2.8 24.2 + - - -
41A SER* 3.2 7.3 + - - -
43A LEU* 1.3 77.1 - - - +
45A GLN* 1.3 65.0 + - - +
47A TRP* 3.4 16.3 + - - +
48A ALA* 3.0 25.3 + - - +
131A VAL* 3.9 5.9 - - - +
133A SER* 3.5 19.4 + - - -
74B SER* 6.0 0.4 - - - -
116B ALA 5.8 3.4 - - - -
118B LEU* 4.6 18.4 - - - -
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 2.9 27.3 + - - +
42A PHE 3.9 2.7 - - - +
44A SER* 1.3 74.6 + - - +
46A GLY* 1.3 63.9 + - - +
48A ALA* 3.2 2.9 + - - +
49A SER* 3.0 23.9 + - - -
59A LEU* 3.4 18.3 - - + +
132A THR 2.9 23.1 + - - +
133A SER* 3.5 18.2 - - - +
137A LEU* 4.3 8.3 - - + +
140A ASP* 3.7 27.7 - - - +
143A PHE* 3.9 6.7 - - - -
144A ASN* 2.8 44.0 + - - -
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE 2.8 19.3 + - - -
43A LEU 3.2 1.3 + - - -
45A GLN* 1.3 78.1 - - - +
47A TRP* 1.3 52.0 + - - +
49A SER 3.3 4.7 + - - -
56A LYS* 2.7 40.4 + - - +
59A LEU* 3.7 18.8 - - - +
60A LEU* 3.9 16.4 - - - -
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Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 4.0 20.0 - + - -
40A MET* 5.3 6.3 - - + -
43A LEU* 2.8 47.5 + - + +
44A SER* 3.8 11.9 - - - +
46A GLY* 1.3 76.2 - - - +
48A ALA* 1.3 59.9 + - - +
49A SER 4.3 0.5 - - - +
56A LYS* 3.6 11.1 + - - +
60A LEU* 3.7 21.6 - - + +
4B HIS* 4.3 1.2 + - - -
67B MET* 4.2 4.7 - - - -
70B VAL* 3.8 25.6 - - + -
71B GLU* 2.9 52.4 + - + +
74B SER* 3.7 35.4 - - - -
75B THR* 5.1 9.9 + - - +
118B LEU* 6.0 1.3 - - + -
252C PRO* 6.6 0.2 - - + -
254C ILE* 4.3 16.8 - - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER 3.0 16.9 + - - +
45A GLN* 3.7 4.3 - - - +
46A GLY 3.2 0.2 - - - -
47A TRP* 1.3 76.3 - - - +
49A SER* 1.3 63.4 + - - +
50A THR* 3.4 10.8 + - - +
133A SER* 4.2 11.9 - - - +
135A GLY* 5.8 3.8 - - - -
115B ASN* 3.5 42.5 + - + +
254C ILE* 5.8 2.6 - - - +
265C GLN* 4.0 9.1 + - - +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN 3.0 14.6 + - - -
46A GLY* 3.3 8.7 + - - -
47A TRP 4.3 0.2 - - - +
48A ALA* 1.3 77.8 - - - +
50A THR* 1.3 62.2 + - - +
51A GLY* 3.1 16.6 + - - -
52A ALA 4.7 0.5 + - - -
56A LYS* 2.8 52.2 + - - +
59A LEU* 5.1 0.7 - - - -
137A LEU* 4.2 17.1 - - - +
254C ILE* 6.0 0.5 + - - +
265C GLN* 3.8 14.2 + - - +
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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
------------------------------------------------------------
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