Contacts of the helix formed by residues 31 - 46 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B GLU* 1.3 68.8 + - - +
33B PHE 3.1 3.4 - - - -
34B VAL* 3.0 11.1 + - - +
35B ASN* 3.0 33.6 + - - +
232B ASN* 3.4 24.1 - - - +
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Residues in contact with GLU 32 (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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20B GLU* 4.8 3.2 - - - +
24B SER 4.6 11.1 - - - +
31B GLY* 1.3 75.1 - - - +
33B PHE* 1.3 78.9 + - + +
35B ASN* 3.5 10.7 + - - +
36B ARG* 3.0 62.1 + - + +
232B ASN* 3.6 5.6 + - - +
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Residues in contact with PHE 33 (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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17B TYR* 3.6 33.0 - + + -
20B GLU* 3.4 31.4 - - + -
21B VAL* 3.4 28.0 - - + -
32B GLU* 1.3 97.1 - - + +
34B VAL* 1.3 60.6 + - - +
36B ARG* 3.5 31.0 - - - -
37B PHE* 2.9 30.0 + - - +
232B ASN* 2.9 14.0 + - - +
235B GLY 3.7 3.0 - - - +
236B ALA* 3.5 33.7 - - + +
239B VAL* 3.6 16.0 - - + +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 3.0 11.9 + - - +
33B PHE* 1.3 77.6 - - - +
35B ASN* 1.3 63.8 + - - +
37B PHE* 3.3 6.3 + - - +
38B GLU* 3.0 25.9 + - - +
52B ALA* 3.8 14.1 - - + -
229B ARG* 3.4 35.9 - - + +
230B LEU* 3.4 27.1 - - + +
231B SER 3.7 15.3 - - - +
232B ASN* 3.2 15.1 + - + +
235B GLY* 4.4 5.6 - - - -
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Residues in contact with ASN 35 (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* 3.0 23.3 + - - +
32B GLU* 3.5 10.4 - - - +
34B VAL* 1.3 77.5 - - - +
36B ARG* 1.3 57.5 + - + +
38B GLU* 3.4 15.6 + - - +
39B GLN* 2.9 27.8 + - - +
206B ARG* 5.8 0.2 + - - -
229B ARG* 4.8 8.3 + - - -
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Residues in contact with ARG 36 (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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17B TYR* 3.6 30.3 + - - -
20B GLU* 4.5 5.3 + - - -
32B GLU* 3.0 51.3 + - + +
33B PHE* 3.5 24.7 - - - +
34B VAL 3.3 0.2 - - - -
35B ASN* 1.3 73.4 - - + +
37B PHE* 1.3 61.2 + - - +
39B GLN* 3.3 7.6 + - - +
40B SER* 2.8 30.1 + - - -
239B VAL* 3.7 22.2 - - + +
243B GLU* 4.5 1.8 + - - -
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Residues in contact with PHE 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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33B PHE 2.9 19.5 + - - +
34B VAL* 3.5 5.8 - - - +
35B ASN 3.3 0.2 - - - -
36B ARG* 1.3 74.1 - - - +
38B GLU* 1.3 63.5 + - - +
40B SER* 2.8 22.9 + - - -
41B VAL* 3.1 9.8 + - + +
52B ALA* 4.1 3.4 - - + -
180B TYR* 3.4 51.6 - + + -
191B GLY* 5.6 1.8 - - - -
192B GLY 4.9 3.1 - - - -
193B MET* 3.6 18.8 - - + -
230B LEU* 3.6 33.4 - - + -
234B LEU 4.9 0.4 - - - -
235B GLY* 3.8 13.2 - - - +
238B GLY* 3.5 36.8 - - - -
239B VAL* 3.3 6.2 - - - +
242B MET* 3.7 6.7 - - + -
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Residues in contact with GLU 38 (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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34B VAL* 3.0 19.3 + - - +
35B ASN* 3.6 15.1 - - - +
37B PHE* 1.3 74.1 - - - +
39B GLN* 1.3 64.2 + - - +
41B VAL 3.2 1.9 + - - -
42B LYS* 3.0 30.2 + - + +
50B ALA* 3.3 29.6 - - + +
51B LEU* 3.4 0.2 - - - -
52B ALA* 2.8 32.8 + - + +
193B MET* 3.8 12.6 - - - -
206B ARG* 3.1 20.2 + - - -
229B ARG* 2.9 23.1 + - - -
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Residues in contact with GLN 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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35B ASN 2.9 17.1 + - - +
36B ARG* 3.6 9.0 - - + +
38B GLU* 1.3 78.3 - - - +
40B SER* 1.3 56.6 + - - +
42B LYS* 3.2 30.0 + - - +
43B ASP* 2.8 64.4 + - - +
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Residues in contact with SER 40 (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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36B ARG 2.8 17.8 + - - -
37B PHE* 2.8 19.3 + - - -
39B GLN* 1.3 72.9 - - - +
41B VAL* 1.3 57.2 + - - +
43B ASP* 3.4 11.5 + - - +
44B TYR* 3.0 29.3 + - - +
239B VAL* 4.6 9.6 - - - -
242B MET* 3.3 33.8 - - - +
243B GLU* 6.4 1.3 - - - -
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Residues in contact with VAL 41 (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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37B PHE* 3.1 15.2 + - + +
38B GLU 3.8 6.3 - - - +
40B SER* 1.3 79.8 + - - +
42B LYS* 1.3 55.7 + - - +
44B TYR* 3.9 0.6 - - - +
45B SER* 2.7 39.9 + - - +
50B ALA* 4.7 0.7 - - + -
160B LEU* 5.4 0.9 - - + -
178B TYR* 3.7 31.6 - - + -
180B TYR* 3.1 25.1 - - - +
193B MET* 3.6 19.1 - - + -
195B ILE* 3.8 19.5 - - + -
242B MET* 3.9 20.0 - - + -
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Residues in contact with LYS 42 (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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38B GLU* 3.0 24.0 + - + +
39B GLN* 3.5 32.2 + - - +
41B VAL* 1.3 78.1 - - - +
43B ASP* 1.3 57.5 + - - +
45B SER* 3.9 2.9 - - - -
46B LYS* 2.8 32.9 + - - +
47B SER* 3.4 19.7 - - - +
48B GLU* 3.1 27.6 + - - +
49B ASN* 4.0 5.9 - - - +
50B ALA* 3.7 22.1 + - + +
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Residues in contact with ASP 43 (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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39B GLN* 2.8 54.7 + - - +
40B SER* 3.6 10.0 - - - +
42B LYS* 1.3 74.0 - - - +
44B TYR* 1.3 56.3 + - - +
46B LYS* 3.0 27.1 + - - +
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Residues in contact with TYR 44 (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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40B SER 3.0 17.0 + - - +
41B VAL* 3.9 1.8 - - - +
43B ASP* 1.3 77.7 - - - +
45B SER* 1.3 63.8 + - - +
46B LYS* 3.2 17.1 + - - +
160B LEU* 4.2 9.9 - - + -
161B GLY* 3.4 22.5 - - - -
163B PHE* 3.6 28.6 - + - -
168B ALA* 5.0 3.1 - - + +
242B MET* 3.6 18.6 - - + -
245B LEU* 3.7 30.3 - - + +
246B GLU* 2.7 40.0 + - + -
249B VAL* 4.8 0.2 - - - +
277B ARG* 3.3 13.5 + - - -
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Residues in contact with SER 45 (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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41B VAL* 2.7 30.3 + - - +
44B TYR* 1.3 78.7 - - - +
46B LYS* 1.3 68.2 - - - +
47B SER* 3.1 23.2 + - - -
160B LEU* 5.9 0.2 - - - -
167B LYS* 6.0 0.2 - - - +
168B ALA* 3.7 17.4 + - - +
171B THR* 3.4 21.8 + - - +
178B TYR* 3.6 28.9 - - - -
195B ILE* 4.3 0.6 - - - +
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Residues in contact with LYS 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 LYS 2.8 13.5 + - - +
43B ASP* 3.0 24.2 + - - +
44B TYR* 3.2 13.7 + - - +
45B SER* 1.3 78.9 - - - +
47B SER* 1.3 65.2 + - - +
48B GLU* 3.6 7.4 + - - +
163B PHE* 6.4 0.2 - - - -
171B THR* 5.0 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