Contacts of the helix formed by residues 36 - 50 (chain F) in PDB entry 1E50
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 PRO 36 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35F ARG* 1.3 104.4 - - + +
37F HIS* 1.3 66.3 + - - +
38F GLU* 4.5 10.8 - - + +
39F GLU* 2.9 30.7 + - + +
40F ARG 3.0 10.6 + - - -
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Residues in contact with HIS 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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35F ARG 3.4 3.6 + - - -
36F PRO* 1.3 72.0 - - - +
38F GLU* 1.3 77.6 + - - +
40F ARG* 3.4 12.4 + - - +
41F GLN* 3.0 46.2 + - - +
117F GLN* 2.6 30.5 + - - +
118F ARG* 4.0 10.8 - - - -
119F LEU* 3.8 24.4 - - + +
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Residues in contact with GLU 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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36F PRO* 3.2 9.5 - - + +
37F HIS* 1.3 98.2 + - - +
39F GLU* 1.3 61.8 + - - +
41F GLN* 3.3 18.8 + - - +
42F ALA* 3.3 17.3 + - - +
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Residues in contact with GLU 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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32F PHE* 4.8 0.5 - - - -
35F ARG* 3.3 47.5 + - + +
36F PRO* 2.9 22.3 + - + +
38F GLU* 1.3 78.6 - - - +
40F ARG* 1.3 59.9 + - - +
42F ALA* 2.9 10.9 + - + +
43F ARG* 2.9 68.7 + - + +
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Residues in contact with ARG 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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28F LYS* 6.1 0.4 - - - +
29F TYR* 3.1 37.6 + - + -
30F THR 3.7 7.3 - - - -
31F GLY 2.8 25.9 + - - -
32F PHE* 3.0 24.4 + - + +
33F ARG* 3.6 24.7 + - - +
35F ARG* 3.3 29.8 - - + +
36F PRO 3.0 7.1 + - - +
37F HIS* 3.7 14.4 + - - +
39F GLU* 1.3 76.0 - - - +
41F GLN* 1.3 57.7 + - - +
43F ARG* 3.8 9.4 - - - +
44F PHE* 3.0 31.4 + - - +
119F LEU* 3.5 38.8 - - + +
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Residues in contact with GLN 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 HIS* 3.0 39.6 + - - +
38F GLU* 3.3 30.6 - - - +
39F GLU 3.1 0.2 - - - -
40F ARG* 1.3 75.8 - - - +
42F ALA* 1.3 62.3 + - - +
44F PHE* 3.9 2.4 - - - +
45F GLN* 3.2 28.9 + - + +
116F LEU 3.2 21.0 + - - +
117F GLN* 3.1 40.5 + - - +
119F LEU* 4.0 13.4 - - + +
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Residues in contact with ALA 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 GLU 3.3 9.2 + - - +
39F GLU* 2.9 12.9 + - + +
41F GLN* 1.3 76.8 - - - +
43F ARG* 1.3 68.5 + - + +
45F GLN* 2.9 10.4 + - - +
46F ASN* 2.8 31.6 + - - +
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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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29F TYR* 3.8 1.1 - - - +
32F PHE* 3.5 59.4 - - + -
35F ARG* 5.7 1.0 - - - +
39F GLU* 2.9 59.5 + - + +
40F ARG* 3.8 5.4 - - - +
42F ALA* 1.3 71.5 - - - +
44F PHE* 1.3 55.3 + - - +
46F ASN* 3.1 10.9 + - - +
47F ALA* 2.7 38.1 + - - +
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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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29F TYR* 3.3 35.8 + + + -
40F ARG 3.0 16.5 + - - +
41F GLN 3.9 4.0 - - - +
43F ARG* 1.3 79.3 - - - +
45F GLN* 1.3 66.2 + - - +
47F ALA* 3.8 3.3 - - - +
48F CYS* 3.0 48.9 + - - -
53F SER* 3.5 20.2 - - - -
55F ILE* 4.5 1.8 - - + -
95F VAL* 3.8 15.7 - - + -
97F LEU* 4.3 3.4 - - + -
114F ILE* 3.7 43.1 - - + -
116F LEU* 4.0 16.8 - - + -
119F LEU* 3.9 20.6 - - + -
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Residues in contact with GLN 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 GLN* 3.2 15.4 + - + +
42F ALA* 2.9 13.1 + - - +
44F PHE* 1.3 82.7 - - + +
46F ASN* 1.3 66.4 + - - +
48F CYS* 3.7 4.5 - - - +
49F ARG* 3.2 35.3 + - - +
88F LEU* 4.1 20.2 - - - +
116F LEU* 3.5 45.5 - - + +
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Residues in contact with ASN 46 (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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42F ALA* 2.8 26.4 + - - +
43F ARG* 3.5 12.3 - - - +
45F GLN* 1.3 72.0 - - - +
47F ALA* 1.3 65.8 + - - +
49F ARG* 2.7 49.9 + - - +
50F ASP* 3.0 24.4 + - - +
52F ARG* 5.5 1.3 - - - +
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Residues in contact with ALA 47 (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 TYR* 5.3 5.8 - - + +
32F PHE* 6.0 0.9 - - + -
43F ARG 2.7 21.1 + - - +
44F PHE* 3.8 6.7 - - - +
46F ASN* 1.3 72.4 - - - +
48F CYS* 1.3 55.1 + - - +
50F ASP* 3.3 5.1 + - - +
51F GLY 3.3 4.5 + - - -
52F ARG* 2.6 80.6 + - + +
53F SER* 4.8 5.4 - - - +
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Residues in contact with CYS 48 (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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44F PHE* 3.0 60.4 + - - +
45F GLN* 3.7 5.6 - - - +
46F ASN 3.0 0.2 + - - -
47F ALA* 1.3 71.6 - - - +
49F ARG* 1.3 60.3 + - + +
50F ASP 3.0 1.6 - - - -
51F GLY* 2.7 25.8 + - - -
52F ARG 3.3 7.4 + - - +
68F PHE* 4.4 6.5 - - - -
86F VAL* 3.6 27.3 - - + +
88F LEU* 6.4 1.8 - - + -
95F VAL* 4.5 5.2 - - + -
97F LEU* 4.1 20.0 - - + -
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Residues in contact with ARG 49 (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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45F GLN* 3.2 22.0 + - - +
46F ASN* 2.7 38.0 + - - +
48F CYS* 1.3 80.7 - - + +
50F ASP* 1.3 69.1 + - - +
51F GLY 3.1 0.4 - - - -
80F THR* 3.8 13.6 + - - +
81F PRO* 3.0 22.6 - - - +
86F VAL* 4.8 6.5 - - + -
88F LEU* 4.6 19.7 - - + -
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Residues in contact with ASP 50 (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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46F ASN* 3.0 27.2 + - - +
47F ALA* 3.4 8.1 + - - +
48F CYS 3.0 1.2 - - - -
49F ARG* 1.3 87.0 + - - +
51F GLY* 1.3 60.6 - - - +
52F ARG* 3.5 13.5 + - - +
69F PHE* 3.8 10.4 - - - -
80F THR* 5.3 5.5 + - - +
81F PRO* 4.2 4.0 - - - -
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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
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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