Contacts of the helix formed by residues 30 - 45 (chain F) in PDB entry 4PIW
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 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F LYS* 3.7 21.1 - - - -
27F CYS 4.0 2.9 + - - -
28F GLY 3.4 1.8 - - - -
29F ASP* 1.3 76.6 - - - +
31F GLY* 1.3 66.5 + - - +
32F PHE 3.7 0.7 - - - -
33F THR* 3.5 9.8 + - - -
34F ARG* 3.4 26.3 + - - +
237F ASP* 3.8 11.9 - - - -
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Residues in contact with GLY 31 (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 LYS* 5.0 3.6 - - - +
30F GLY* 1.3 73.2 - - - +
32F PHE* 1.3 65.7 + - - +
33F THR 3.2 0.2 + - - -
34F ARG* 3.4 3.3 + - - +
35F ARG* 3.2 42.7 + - - +
237F ASP* 3.3 10.9 + - - -
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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
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16F TYR* 3.5 47.3 - + + -
19F SER* 3.7 18.4 - - - -
20F ALA* 3.7 25.1 - - + -
23F SER* 6.3 0.2 - - - -
31F GLY* 1.3 70.0 - - - -
33F THR* 1.3 60.8 + - - +
35F ARG* 3.4 31.5 - - - +
36F CYS* 2.9 33.6 + - - -
237F ASP* 3.0 15.5 + - - +
240F ALA* 3.5 19.7 - - - +
241F ALA* 3.8 14.8 - - + -
244F TRP* 3.8 25.4 - + + -
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Residues in contact with THR 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 ASP* 3.9 20.4 - - - +
30F GLY 3.5 18.5 + - - -
31F GLY 3.1 0.2 - - - -
32F PHE* 1.3 79.3 - - - +
34F ARG* 1.3 62.4 + - - +
37F GLN* 3.1 42.1 + - - +
51F LEU* 3.3 25.6 - - + +
207F ARG* 4.6 3.4 - - - +
235F MSE 3.9 17.0 + - + +
237F ASP* 3.1 14.7 + - - -
240F ALA* 3.4 13.9 - - - +
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Residues in contact with ARG 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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29F ASP* 2.5 54.2 + - - +
30F GLY 3.4 15.2 + - - +
31F GLY 3.4 4.9 + - - +
33F THR* 1.3 75.3 - - + +
35F ARG* 1.3 58.8 + - + +
37F GLN* 3.6 16.4 + - - +
38F GLN* 3.1 35.8 + - + +
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Residues in contact with ARG 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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19F SER* 5.4 0.4 + - - -
31F GLY* 3.2 23.9 + - - +
32F PHE* 3.4 53.4 - - - +
33F THR 3.1 0.4 - - - -
34F ARG* 1.3 77.2 - - + +
36F CYS* 1.3 60.9 + - - +
38F GLN* 3.2 14.4 + - - +
39F TRP 2.9 23.2 + - - -
244F TRP* 3.2 35.3 - - + -
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Residues in contact with CYS 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 PHE 2.9 25.0 + - - +
33F THR 3.7 4.5 - - - +
35F ARG* 1.3 75.6 - - - +
37F GLN* 1.3 63.4 + - - +
39F TRP* 3.3 2.8 + - - +
40F LEU* 3.1 30.0 + - + +
51F LEU* 3.8 13.5 - - + -
240F ALA* 3.3 24.9 - - - -
243F LEU* 4.0 12.6 - - + -
244F TRP* 3.5 29.2 - - - -
247F LEU* 3.9 15.9 - - + +
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Residues in contact with GLN 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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29F ASP* 5.1 3.3 + - - +
33F THR* 3.1 28.0 + - - +
34F ARG* 3.7 18.8 + - - +
36F CYS* 1.3 74.3 - - - +
38F GLN* 1.3 59.8 + - + +
40F LEU* 3.3 2.7 + - - +
41F GLU* 2.9 42.5 + - - +
49F VAL* 3.1 33.5 + - - +
50F LEU* 3.8 10.6 - - - +
51F LEU* 3.4 20.0 - - + +
207F ARG* 3.3 30.5 - - - +
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Residues in contact with GLN 38 (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 ARG* 3.1 25.1 + - - +
35F ARG* 3.2 14.4 + - - +
37F GLN* 1.3 77.1 - - + +
39F TRP* 1.3 61.0 + - - +
41F GLU* 4.2 13.0 - - - +
42F GLN* 3.3 33.3 + - + +
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Residues in contact with TRP 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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35F ARG 2.9 13.9 + - - +
36F CYS 3.4 9.9 - - - +
37F GLN 3.2 0.4 - - - -
38F GLN* 1.3 77.6 - - - +
40F LEU* 1.3 86.5 + - + +
42F GLN* 4.4 1.3 - - - +
43F ARG* 3.2 73.9 + - + +
44F PHE* 4.4 7.6 - + - -
157F VAL* 6.4 0.4 - - + -
158F MSE 4.2 6.5 - - - -
244F TRP* 4.1 23.1 - + + -
247F LEU* 3.3 48.4 + - + -
248F GLU* 5.2 1.6 - - - +
250F ALA* 3.6 20.4 - - + -
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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
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36F CYS* 3.1 20.6 + - + +
37F GLN 3.9 3.1 - - - +
39F TRP* 1.3 95.9 - - + +
41F GLU* 1.3 65.7 + - - +
43F ARG* 4.8 0.2 - - - -
44F PHE* 3.2 54.8 + - + +
46F SER* 3.9 2.6 + - - -
49F VAL* 3.7 33.0 - - + -
51F LEU* 4.2 15.5 - - + -
157F VAL* 5.7 2.7 - - + -
175F PHE* 4.5 11.2 - - + -
177F PHE* 4.2 19.5 - - + -
191F ALA* 4.5 0.4 - - + -
243F LEU* 5.6 0.2 - - + -
247F LEU* 4.6 14.1 - - + -
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Residues in contact with GLU 41 (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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37F GLN* 2.9 30.7 + - - +
38F GLN* 4.0 16.0 - - - +
39F TRP 3.4 0.2 - - - -
40F LEU* 1.3 77.9 - - - +
42F GLN* 1.3 69.3 + - - +
45F GLY* 3.1 20.1 + - - -
46F SER* 3.2 29.4 + - - +
47F ALA 4.0 6.2 - - - +
48F LYS* 3.3 18.7 - - - +
49F VAL* 3.2 37.8 + - + +
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Residues in contact with GLN 42 (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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38F GLN* 3.3 21.2 + - + +
39F TRP* 4.4 1.3 - - - +
40F LEU 3.3 0.2 - - - -
41F GLU* 1.3 89.5 + - - +
43F ARG* 1.3 66.7 + - - +
44F PHE 3.3 0.6 + - - -
45F GLY* 3.8 7.0 + - - -
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Residues in contact with ARG 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 TRP* 3.2 58.9 + - + +
40F LEU 4.4 0.9 - - - +
42F GLN* 1.3 80.6 - - - +
44F PHE* 1.3 81.0 + - + +
158F MSE 3.5 18.4 - - - +
165F ALA* 5.3 0.3 - - - +
250F ALA* 4.8 0.8 - - - +
251F ASP* 2.5 40.1 + - - -
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Residues in contact with PHE 44 (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 TRP* 4.4 7.6 - + - -
40F LEU* 3.2 33.1 + - + +
43F ARG* 1.3 99.5 - - + +
45F GLY* 1.3 63.1 + - - +
46F SER* 4.8 4.3 - - - +
157F VAL* 4.3 7.9 - - + -
158F MSE 3.8 43.7 - - - -
164F ARG* 5.8 0.2 - - - -
165F ALA* 3.6 35.4 + - + +
166F LEU 5.3 0.2 - - - -
168F THR* 3.4 20.9 + - - +
175F PHE* 3.6 39.5 - + - -
193F LEU* 5.1 2.7 - - + -
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Residues in contact with GLY 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 GLU 3.1 13.8 + - - -
42F GLN 3.8 5.3 + - - -
43F ARG 3.6 1.8 - - - -
44F PHE* 1.3 80.0 - - - +
46F SER* 1.3 62.3 + - - +
47F ALA 4.2 0.3 + - - -
168F THR* 3.9 10.9 - - - +
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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