Contacts of the helix formed by residues 20 - 37 (chain F) in PDB entry 4R8A
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 PHE 20 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLU* 3.2 10.7 - - - +
19F PRO* 1.3 85.5 - - + +
21F TYR* 1.3 63.6 + - - +
22F TYR* 3.2 14.6 - + - -
23F LEU* 3.2 14.8 + - + -
24F HIS* 3.1 43.6 + - + +
57F GLU* 4.4 26.2 - - + +
58F ALA* 4.8 4.7 - - + -
61F ALA* 3.5 33.2 - - + -
83F GLU* 3.1 39.5 - - + -
84F ILE* 4.4 1.8 - - + -
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Residues in contact with TYR 21 (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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16F LEU* 5.0 16.4 - - - +
18F GLU* 3.1 24.7 + - + +
19F PRO* 3.8 9.2 - - + -
20F PHE* 1.3 76.2 - - - +
22F TYR* 1.3 90.7 + + + +
24F HIS* 3.4 11.3 + - - +
25F ASN* 3.0 44.7 + - - +
65F ARG* 4.5 13.9 + - - -
191F VAL* 3.5 35.5 - - + +
194F ASP* 6.1 1.1 - - - +
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Residues in contact with TYR 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PRO 3.4 22.9 - - - -
20F PHE* 4.1 7.7 - + - -
21F TYR* 1.3 107.5 - + + +
23F LEU* 1.3 65.4 - - + +
25F ASN* 3.5 6.3 + - - +
26F PHE* 3.1 22.7 + - - +
61F ALA* 3.3 48.4 + - + +
64F VAL* 3.6 16.4 - - + -
65F ARG* 3.2 45.9 + - - +
68F MET* 3.5 33.1 - - + +
83F GLU* 2.8 19.3 + - - -
84F ILE* 3.7 4.0 - - - +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PHE* 3.2 23.8 + - + +
22F TYR* 1.3 90.3 - - + +
24F HIS* 1.3 58.4 + - - +
26F PHE* 3.2 3.1 + - - +
27F ARG* 2.8 59.4 + - - +
52F PHE* 3.8 16.6 - - + -
57F GLU* 3.7 30.5 - - - +
60F GLN* 3.6 39.3 - - + +
61F ALA* 4.0 3.6 - - - +
64F VAL* 3.8 12.1 - - + -
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Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU* 3.4 39.3 + - + +
20F PHE* 3.1 25.2 + - + +
21F TYR* 3.6 8.5 - - - +
23F LEU* 1.3 77.6 - - + +
25F ASN* 1.3 58.9 + - - +
27F ARG* 3.4 35.2 + - - +
28F ALA* 2.9 28.9 + - - +
57F GLU* 4.3 7.2 - - - -
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Residues in contact with ASN 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TYR* 3.0 36.8 + - - +
22F TYR* 3.7 7.3 - - - +
24F HIS* 1.3 78.1 - - - +
26F PHE* 1.3 62.1 + - - +
28F ALA* 3.3 9.1 + - - +
29F VAL* 3.1 27.9 + - - +
68F MET* 5.2 4.9 - - + +
187F TRP* 4.8 4.1 + - + +
190F PHE* 3.4 47.0 - - + +
191F VAL* 4.3 7.9 - - - +
194F ASP* 4.4 10.2 + - - +
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Residues in contact with PHE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TYR 3.1 14.8 + - - +
23F LEU 3.5 7.0 - - - +
25F ASN* 1.3 73.4 - - - +
27F ARG* 1.3 65.1 + - - +
29F VAL* 3.3 10.2 + - + +
30F LEU* 3.1 48.0 + - + +
48F PHE* 4.8 9.0 - + - -
52F PHE* 3.5 43.5 - + - -
63F LEU* 5.7 1.3 - - + -
64F VAL* 3.6 25.6 - - + -
67F VAL* 4.7 13.5 - - + -
68F MET* 4.9 2.2 - - + +
172F CYS* 4.6 16.8 - - + -
175F LEU* 5.1 5.4 - - + -
187F TRP* 3.9 35.7 - + - -
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Residues in contact with ARG 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 2.8 38.2 + - + +
24F HIS* 3.6 29.8 + - - +
26F PHE* 1.3 69.6 - - - +
28F ALA* 1.3 60.6 + - - +
30F LEU* 3.2 9.4 + - + +
31F ALA* 2.9 31.1 + - - +
52F PHE* 4.4 9.6 - - + -
57F GLU* 3.0 39.2 + - - -
60F GLN* 2.6 35.6 + - - +
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS 2.9 17.6 + - - +
25F ASN* 3.4 10.3 - - - +
26F PHE 3.3 0.2 - - - -
27F ARG* 1.3 77.2 - - - +
29F VAL* 1.3 56.3 + - - +
31F ALA* 3.5 4.9 + - - +
32F TRP* 3.0 29.5 + - - +
179F TYR* 4.9 1.5 - - - +
190F PHE* 4.7 11.9 - - + -
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Residues in contact with VAL 29 (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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25F ASN 3.1 14.8 + - - +
26F PHE* 3.6 10.1 - - + +
27F ARG 3.3 0.2 - - - -
28F ALA* 1.3 73.2 - - - +
30F LEU* 1.3 61.4 + - + +
32F TRP* 3.3 2.1 + - - +
33F ILE* 2.9 42.3 + - + +
175F LEU* 4.3 14.1 - - + +
176F ARG* 5.2 1.8 - - - -
179F TYR* 3.9 37.2 - - + -
180F PHE* 5.8 1.1 - - + -
187F TRP* 4.5 20.0 - - + +
190F PHE* 3.6 28.5 - - + -
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Residues in contact with LEU 30 (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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26F PHE* 3.1 34.3 + - + +
27F ARG* 3.2 11.4 + - + +
29F VAL* 1.3 78.3 - - + +
31F ALA* 1.3 56.8 + - - +
33F ILE* 3.3 6.1 + - - +
34F GLY* 2.9 23.7 + - - -
48F PHE* 5.0 2.2 - - + -
49F ILE* 4.0 44.4 - - + +
52F PHE* 3.5 37.5 - - + -
175F LEU* 3.6 33.9 - - + -
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Residues in contact with ALA 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ARG 2.9 16.7 + - - +
28F ALA* 3.9 5.4 - - - +
30F LEU* 1.3 73.2 - - - +
32F TRP* 1.3 65.9 + - - +
34F GLY* 3.1 3.5 + - - +
35F GLU* 3.0 38.5 + - - +
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Residues in contact with TRP 32 (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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28F ALA 3.0 18.2 + - - +
29F VAL 3.5 4.7 - - - +
31F ALA* 1.3 75.6 - - - +
33F ILE* 1.3 61.8 + - + +
35F GLU* 3.3 11.0 + - - +
36F ARG* 3.2 74.6 + - - +
37F TYR* 3.7 18.8 - + - -
179F TYR* 3.5 36.4 + + + -
205F PHE* 3.8 17.9 - + - -
411F PHE 3.1 29.2 + - - -
412F HIS* 3.9 7.5 - - - +
413F PRO* 4.5 10.1 - - + -
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Residues in contact with ILE 33 (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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29F VAL* 2.9 27.5 + - + +
30F LEU* 3.5 7.0 - - - +
31F ALA 3.2 0.2 - - - -
32F TRP* 1.3 74.3 - - + +
34F GLY* 1.3 66.1 - - - +
37F TYR* 3.0 47.3 + - + +
38F ALA* 4.2 0.2 - - - -
41F LEU* 4.4 25.1 - - + +
49F ILE* 4.4 12.1 - - + -
175F LEU* 3.7 26.9 - - + +
178F MET* 3.6 32.1 - - + -
179F TYR* 3.9 11.0 - - + +
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Residues in contact with GLY 34 (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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30F LEU 2.9 15.0 + - - -
31F ALA* 3.1 5.8 + - - -
33F ILE* 1.3 79.1 - - - +
35F GLU* 1.3 60.5 + - - +
38F ALA* 3.3 21.9 - - - +
41F LEU* 5.7 3.4 - - - -
49F ILE* 5.4 6.1 - - - -
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Residues in contact with GLU 35 (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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31F ALA* 3.0 29.3 + - + +
32F TRP* 3.8 6.3 - - - +
34F GLY* 1.3 80.2 - - - +
36F ARG* 1.3 89.5 + - + +
37F TYR 3.7 0.2 + - - -
38F ALA* 4.1 8.0 + - - +
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Residues in contact with ARG 36 (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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32F TRP* 3.2 68.2 + - - +
35F GLU* 1.3 99.6 + - + +
37F TYR* 1.3 78.7 + - + +
38F ALA 3.5 1.1 + - - -
39F ASP* 4.2 6.8 - - - +
40F LEU* 4.8 2.9 - - - +
205F PHE* 4.3 5.7 + - - -
206F SER 4.0 7.3 + - - -
207F ALA* 3.1 43.0 + - - +
208F ASP* 4.9 3.4 - - - +
209F SER 3.5 23.0 + - - +
210F ARG* 5.8 4.1 - - + +
411F PHE 4.9 0.2 - - - -
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Residues in contact with TYR 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TRP* 3.7 26.9 - + - -
33F ILE* 3.0 39.0 + - + +
36F ARG* 1.3 91.3 - - + +
38F ALA* 1.3 64.6 + - - +
39F ASP 3.3 2.5 - - - -
40F LEU* 3.3 33.3 + - + +
41F LEU* 3.5 13.7 + - - +
178F MET* 3.2 36.7 + - + +
179F TYR 4.2 1.2 + - - -
209F SER 4.4 0.4 + - - -
210F ARG* 3.7 8.4 - - + -
211F GLY* 2.8 33.3 + - - -
212F PHE* 3.6 23.8 - - + -
411F PHE* 3.9 14.0 + - - +
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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
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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