Contacts of the helix formed by residues 31 - 46 (chain A) in PDB entry 1O69
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 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO 3.3 1.8 + - - -
30A LEU* 1.3 77.7 - - - +
32A GLU* 1.3 63.7 + - - +
33A PHE 3.3 2.9 - - - -
34A VAL* 3.0 4.1 + - - +
35A ASN* 2.9 26.5 + - - -
232A ASN* 3.5 14.2 - - - +
186B ILE* 3.7 33.1 - - - +
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Residues in contact with GLU 32 (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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24A SER* 4.0 9.2 + - - -
28A ALA* 3.3 24.7 - - + +
29A PRO* 3.4 30.6 + - + +
30A LEU 3.2 2.4 - - - -
31A GLY* 1.3 75.5 - - - +
33A PHE* 1.3 79.3 + - + +
35A ASN* 3.3 12.6 + - - +
36A ARG* 3.0 41.0 + - + +
232A ASN* 3.7 5.5 + - - +
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Residues in contact with PHE 33 (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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17A TYR* 3.7 24.9 - + + -
20A GLU* 3.3 37.0 - - + -
21A VAL* 3.3 28.5 - - + -
24A SER* 5.0 1.6 - - - -
32A GLU* 1.3 97.1 - - + +
34A VAL* 1.3 59.8 + - - +
36A ARG* 3.4 29.8 - - - -
37A PHE* 2.9 29.8 + - - +
232A ASN* 2.9 19.0 + - - +
235A GLY 3.7 6.2 - - - +
236A ALA* 3.6 30.3 - - + +
239A VAL* 3.7 12.1 - - + +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.0 8.1 + - - +
33A PHE* 1.3 72.2 - - - +
35A ASN* 1.3 68.1 + - - +
37A PHE* 3.2 7.1 + - - +
38A GLU* 3.0 25.8 + - - +
52A ALA* 3.8 14.1 - - + -
229A ARG* 3.4 36.1 - - - +
230A LEU* 3.6 26.2 - - + +
231A SER 3.6 20.6 - - - +
232A ASN* 3.3 8.8 + - - +
235A GLY* 4.4 4.9 - - - -
186B ILE* 4.0 15.7 - - + -
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Residues in contact with ASN 35 (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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29A PRO* 5.4 3.8 - - - +
30A LEU 3.7 12.8 + - - +
31A GLY* 2.9 21.9 + - - +
32A GLU* 3.4 10.9 - - - +
34A VAL* 1.3 80.0 - - - +
36A ARG* 1.3 59.5 + - + +
38A GLU* 3.3 16.4 + - - +
39A GLN* 2.9 28.3 + - - +
229A ARG* 4.9 6.5 - - - +
186B ILE* 5.0 3.4 - - - +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 4.0 19.0 + - - -
20A GLU* 4.5 5.1 + - - -
32A GLU* 3.0 32.5 + - + +
33A PHE* 3.4 37.1 - - - +
34A VAL 3.3 0.2 - - - -
35A ASN* 1.3 75.7 - - + +
37A PHE* 1.3 59.3 + - - +
39A GLN* 3.3 8.5 + - + +
40A SER* 2.8 30.3 + - - -
239A VAL* 3.8 31.2 - - + +
243A GLU* 4.8 1.2 + - - -
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Residues in contact with PHE 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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33A PHE 2.9 18.5 + - - +
34A VAL* 3.2 5.4 + - - +
36A ARG* 1.3 77.9 - - - +
38A GLU* 1.3 62.4 + - - +
40A SER* 2.9 21.5 + - - -
41A VAL* 3.1 12.9 + - + +
52A ALA* 4.3 2.9 - - + -
180A TYR* 3.4 50.5 - + - -
188A THR* 3.9 10.3 - - + -
191A GLY* 6.0 0.2 - - - -
192A GLY 5.1 2.0 - - - -
193A MET* 3.8 16.2 - - + -
230A LEU* 3.5 32.3 - - + -
235A GLY* 3.7 14.8 - - - +
238A GLY* 3.5 32.5 - - - -
239A VAL* 3.5 6.0 - - - +
242A MET* 3.8 7.2 - - + -
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Residues in contact with GLU 38 (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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34A VAL* 3.0 20.1 + - - +
35A ASN* 3.6 15.5 + - - +
37A PHE* 1.3 74.6 - - - +
39A GLN* 1.3 63.8 + - - +
41A VAL* 3.2 3.8 + - - +
42A LYS* 2.9 31.7 + - + +
50A ALA* 3.3 26.2 - - + +
52A ALA* 2.8 31.9 + - + +
193A MET* 3.8 14.1 - - - -
206A ARG* 3.1 18.7 + - - -
229A ARG* 2.8 20.9 + - - -
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Residues in contact with GLN 39 (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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35A ASN 2.9 14.2 + - - +
36A ARG* 3.5 12.1 - - - +
38A GLU* 1.3 77.1 - - - +
40A SER* 1.3 57.3 + - - +
42A LYS* 3.2 27.6 + - - +
43A ASP* 2.6 69.8 + - - +
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Residues in contact with SER 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 ARG 2.8 16.8 + - - -
37A PHE* 2.9 17.8 + - - -
39A GLN* 1.3 73.0 - - - +
41A VAL* 1.3 56.6 + - - +
43A ASP* 3.4 11.3 + - - +
44A TYR* 3.0 28.6 + - - +
239A VAL* 4.7 9.2 - - - -
242A MET* 3.2 33.9 - - - +
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Residues in contact with VAL 41 (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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37A PHE* 3.1 22.1 + - + +
38A GLU 3.7 5.8 - - - +
40A SER* 1.3 73.0 - - - +
42A LYS* 1.3 57.8 + - - +
44A TYR* 4.0 0.2 - - - +
45A SER* 2.7 39.3 + - - +
50A ALA* 4.9 0.4 - - + -
160A LEU* 5.4 1.6 - - + -
178A TYR* 3.8 31.9 - - + -
180A TYR* 3.3 22.2 - - - +
193A MET* 3.7 26.0 - - + -
195A ILE* 4.1 10.1 - - + -
242A MET* 4.0 17.0 - - + -
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Residues in contact with LYS 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 GLU* 2.9 25.2 + - + +
39A GLN* 3.5 28.2 + - - +
41A VAL* 1.3 76.8 - - - +
43A ASP* 1.3 55.9 + - - +
45A SER* 4.0 2.9 - - - -
46A LYS* 2.7 35.5 + - - +
47A SER* 3.3 22.2 - - - +
48A GLU* 3.4 22.2 + - - +
49A ASN* 4.3 4.0 - - - +
50A ALA* 3.8 25.9 + - + +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 2.6 50.6 + - - +
40A SER* 3.5 9.7 - - - +
42A LYS* 1.3 74.7 - - - +
44A TYR* 1.3 60.7 + - - +
46A LYS* 2.7 34.7 + - - +
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Residues in contact with TYR 44 (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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40A SER 3.0 8.0 + - - +
41A VAL 4.0 1.3 - - - +
42A LYS 3.3 0.2 - - - -
43A ASP* 1.3 79.7 - - - +
45A SER* 1.3 66.2 + - - +
46A LYS* 3.6 8.5 + - - +
160A LEU* 4.4 9.2 - - + -
161A GLY* 3.4 17.6 - - - -
163A PHE* 3.6 34.1 - + - -
168A ALA* 5.3 2.9 - - + -
242A MET* 3.6 24.9 - - + -
245A LEU* 3.6 36.8 - - + +
246A GLU* 2.7 38.5 + - + -
249A VAL* 4.5 0.3 - - - +
277A ARG* 3.3 13.7 + - - -
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Residues in contact with SER 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 VAL* 2.7 30.2 + - - +
44A TYR* 1.3 76.9 - - - +
46A LYS* 1.3 68.5 + - - +
47A SER* 3.0 22.3 + - - -
160A LEU* 5.9 0.2 - - - -
163A PHE* 6.0 0.2 - - - -
167A LYS* 6.0 0.3 - - - +
168A ALA* 3.6 17.9 + - - +
171A THR* 3.3 22.5 + - - +
178A TYR* 3.5 30.1 - - - -
195A ILE* 4.3 1.0 - - - +
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Residues in contact with LYS 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 LYS 2.7 15.6 + - - +
43A ASP* 2.7 28.7 + - - +
44A TYR 4.1 6.5 - - - +
45A SER* 1.3 80.9 - - - +
47A SER* 1.3 62.6 - - - +
48A GLU* 3.7 6.1 + - - +
163A PHE* 6.5 0.9 - - + -
171A THR* 4.9 1.6 - - - -
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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