Contacts of the helix formed by residues 31 - 47 (chain F) in PDB entry 3AOI
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 1.3 72.1 - - - +
32F PHE* 1.3 55.1 + - - +
33F GLY 3.4 1.8 - - - -
34F VAL* 2.7 24.3 - - - +
35F THR* 2.5 24.4 + - - -
193F ASP* 2.3 31.1 + - - -
42G ARG* 3.5 10.0 + - - -
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Residues in contact with PHE 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 3.6 21.5 - - + -
29F GLU* 3.0 47.5 + - + +
30F ARG 3.5 1.5 - - - -
31F GLY* 1.3 80.6 - - - +
33F GLY* 1.3 68.4 + - - +
34F VAL 3.0 2.2 - - - -
35F THR* 3.2 13.1 - - - -
36F LEU* 2.8 29.0 + - + +
193F ASP* 4.0 0.6 - - - -
42G ARG 5.1 2.0 - - - -
43G ILE* 4.2 20.4 - - + -
46G SER* 4.6 18.4 - - - -
47G SER* 4.0 31.2 - - - -
217G ILE* 5.6 0.9 - - + -
221G HIS* 3.7 28.5 - + + -
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Residues in contact with GLY 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 4.3 6.1 - - - +
31F GLY 3.4 0.6 - - - -
32F PHE* 1.3 79.5 - - - +
34F VAL* 1.3 55.1 + - - +
37F GLY* 2.9 22.5 + - - -
181F VAL* 4.2 4.3 - - - -
193F ASP* 3.9 20.5 - - - +
195F LEU* 3.0 43.1 - - - +
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLY* 2.7 35.2 - - - +
33F GLY* 1.3 74.9 - - - +
35F THR* 1.3 63.3 + - - +
36F LEU 3.1 2.9 + - - -
38F ASN* 3.4 21.0 + - - +
39F PRO* 4.0 0.3 - - - +
179F PHE* 4.4 11.7 - - + -
181F VAL* 4.2 10.5 - - + +
193F ASP* 4.7 1.9 + - - +
38G ASN* 5.9 0.3 + - - -
42G ARG* 3.5 21.0 - - - +
939H ARG* 4.7 15.0 - - - +
979H THR 4.1 16.7 - - - +
980H GLY 4.1 15.7 - - - +
981H GLU* 3.9 17.0 - - - +
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Residues in contact with THR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLY 2.5 24.9 + - - -
32F PHE* 2.8 18.1 + - - -
34F VAL* 1.3 78.3 - - - +
36F LEU* 1.3 59.5 + - - +
39F PRO* 2.9 23.4 - - - +
39G PRO* 3.4 27.4 - - + +
42G ARG* 3.7 22.3 + - + +
43G ILE* 3.4 31.2 - - + -
218G LEU* 4.7 7.5 - - + +
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 4.0 9.4 - - + -
28F LEU* 4.0 25.1 - - + -
32F PHE* 2.8 12.9 + - + +
35F THR* 1.3 78.0 - - - +
37F GLY* 1.3 59.2 + - - +
39F PRO* 2.7 23.1 - - + +
40F LEU* 3.3 24.6 + - + +
195F LEU* 3.9 9.4 - - + -
218F LEU* 5.1 3.1 - - + -
218G LEU* 4.5 17.9 - - + -
221G HIS* 4.3 23.6 - - + +
222G LEU* 3.9 27.8 - - + -
225G PHE* 3.8 24.9 - - + -
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Residues in contact with GLY 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F GLY 2.9 20.6 + - - -
34F VAL 3.7 0.6 + - - -
36F LEU* 1.3 77.3 - - - +
38F ASN* 1.3 59.5 + - - +
40F LEU* 3.8 5.5 + - - +
41F ARG* 3.2 21.5 + - - +
179F PHE* 3.7 18.9 - - - +
195F LEU* 3.4 18.6 - - - +
197F LEU* 5.0 4.6 - - - +
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Residues in contact with ASN 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL 3.4 9.2 + - - +
37F GLY* 1.3 71.9 - - - +
39F PRO* 1.4 77.4 - - + +
41F ARG* 3.0 11.9 + - - +
42F ARG* 2.8 27.1 + - - +
179F PHE* 3.8 7.4 - - + -
35G THR* 6.0 0.6 - - - +
38G ASN* 4.4 5.0 - - - +
39G PRO* 5.6 1.4 - - - +
977H GLY* 3.0 22.7 + - - +
978H ARG 2.6 30.5 + - - -
979H THR* 3.1 20.1 + - - +
980H GLY* 3.2 23.8 + - - -
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Residues in contact with PRO 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F VAL 4.0 0.4 - - - +
35F THR 2.9 26.5 - - - +
36F LEU* 2.7 22.0 - - + +
38F ASN* 1.4 89.1 - - + +
40F LEU* 1.3 53.2 + - - +
42F ARG* 3.2 4.4 + - + +
43F ILE* 2.7 37.0 + - - +
218F LEU* 4.4 17.7 - - + -
35G THR* 3.9 26.2 - - + +
38G ASN* 6.3 0.2 - - - +
39G PRO* 3.3 24.0 - - + -
218G LEU* 5.9 2.2 - - + -
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 3.3 25.3 + - + +
37F GLY* 4.0 4.5 - - - +
38F ASN 3.2 0.4 - - - -
39F PRO* 1.3 76.0 - - - +
41F ARG* 1.3 57.0 + - - +
43F ILE* 3.3 7.6 + - + +
44F LEU* 2.8 39.0 + - + +
195F LEU* 5.3 1.6 - - + -
197F LEU* 4.5 18.6 - - + -
211F LEU* 4.4 13.2 - - + -
214F ALA* 4.4 3.7 - - + +
215F VAL* 4.0 29.4 - - + +
218F LEU* 3.9 26.2 - - + -
222G LEU* 4.5 3.4 - - + -
225G PHE* 3.8 29.6 - - + -
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Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F GLY 3.2 13.5 + - - +
38F ASN* 3.0 20.3 + - - +
40F LEU* 1.3 78.9 - - - +
42F ARG* 1.3 62.8 + - - +
43F ILE 3.1 1.2 + - - -
44F LEU* 3.2 5.4 + - - +
45F LEU* 3.2 46.4 - - + +
177F VAL* 2.6 64.8 + - + +
178F ALA* 5.9 0.2 - - - +
179F PHE* 4.7 9.2 - - + -
855H VAL 4.4 3.0 + - - -
856H GLU 4.2 14.8 + - - -
858H MET 4.8 1.2 + - - -
860H HIS* 3.4 54.7 + - - +
864H GLY 4.1 3.4 + - - -
866H PRO* 4.0 13.1 - - - +
977H GLY* 4.7 2.1 - - - -
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASN* 2.8 22.6 + - - +
39F PRO* 3.6 6.3 - - - +
41F ARG* 1.3 73.8 - - + +
43F ILE* 1.3 52.6 + - - +
45F LEU 4.3 0.2 - - - -
46F SER* 2.6 33.6 + - - -
31G GLY* 2.5 36.9 + - - -
34G VAL* 2.6 39.8 - - - +
35G THR* 3.2 22.8 + - - +
856H GLU* 4.1 23.0 + - + +
857H ASP* 2.6 35.6 + - - +
977H GLY 3.3 25.4 - - - +
978H ARG* 3.5 21.4 + - - +
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Residues in contact with ILE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PRO 2.7 33.8 + - - +
40F LEU* 3.6 12.1 - - + +
42F ARG* 1.3 75.0 - - - +
44F LEU* 1.3 67.6 + - - +
45F LEU 2.8 2.3 + - - -
46F SER* 3.1 0.4 + - - -
47F SER* 2.8 55.0 + - - +
48F ILE* 3.8 1.9 + - - -
214F ALA* 4.1 13.5 - - + +
217F ILE* 3.9 26.0 - - + -
218F LEU* 3.9 36.3 - - + -
221F HIS* 6.5 1.1 - - + -
32G PHE* 5.3 4.3 - - + -
35G THR* 4.2 10.8 - - + +
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 2.8 33.7 + - + +
41F ARG 3.5 4.7 - - - +
43F ILE* 1.3 73.2 - - - +
45F LEU* 1.3 59.2 + - - +
48F ILE* 3.0 26.0 - - + +
172F SER* 4.1 1.0 + - - -
174F VAL* 3.5 16.3 - - + +
177F VAL* 3.6 28.7 - - + -
197F LEU* 4.2 9.2 - - + -
199F ILE* 3.4 44.4 - - + -
210F ALA* 3.7 29.8 - - + +
211F LEU* 4.0 7.6 - - + +
214F ALA* 4.2 8.0 - - + +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ARG* 3.2 42.1 + - + +
42F ARG 4.7 0.2 - - - +
43F ILE 2.8 4.6 + - - -
44F LEU* 1.3 77.2 - - - +
46F SER* 1.3 60.9 + - - +
48F ILE 5.1 0.6 + - - -
149F GLY* 6.0 0.2 - - - -
172F SER* 2.8 29.0 + - - +
174F VAL* 4.5 9.0 - - + +
175F ARG 5.1 9.0 - - - +
176F ARG* 5.7 0.2 - - - -
177F VAL* 3.1 43.1 - - + +
855H VAL* 4.0 32.3 - - + +
856H GLU* 4.4 18.2 - - - +
866H PRO* 5.4 1.6 - - + -
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Residues in contact with SER 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ARG 2.6 20.5 + - - -
43F ILE 3.1 0.2 + - - -
45F LEU* 1.3 81.0 - - - +
47F SER* 1.3 69.0 + - - +
48F ILE 3.9 1.3 - - - +
148F VAL* 3.8 12.0 - - - +
149F GLY* 4.3 12.6 + - - -
29G GLU* 5.7 0.7 - - - +
30G ARG 5.2 1.1 - - - -
32G PHE* 4.3 11.5 - - - -
855H VAL* 6.2 0.2 - - - -
856H GLU* 3.2 43.8 + - - -
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ILE* 2.8 41.7 + - - +
46F SER* 1.3 82.4 + - - +
48F ILE* 1.3 61.1 + - - +
49F PRO* 3.4 4.7 - - - +
148F VAL* 2.9 23.5 - - - +
217F ILE* 3.6 17.2 - - - +
29G GLU* 5.9 2.2 - - - -
32G PHE* 3.5 22.0 - - - -
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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