Contacts of the helix formed by residues 41 - 55 (chain F) in PDB entry 1R8Y
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 THR 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F SER 3.5 1.1 + - - -
40F ARG* 1.3 74.1 - - - +
42F ALA* 1.3 65.5 + - - +
43F GLU* 3.9 8.6 - - - +
44F TYR* 3.3 16.6 + - - +
45F LYS* 3.4 11.1 + - - +
191F ASN 4.4 3.1 - - - +
192F ILE* 2.7 29.9 + - - +
193F TYR 2.8 25.4 + - - +
194F TYR 3.8 0.7 - - - +
195F LYS* 3.6 26.5 - - + +
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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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40F ARG 3.4 4.4 + - - -
41F THR* 1.3 69.5 - - - +
43F GLU* 1.3 67.1 + - - +
45F LYS* 3.6 5.0 + - - +
46F ALA* 3.0 28.7 + - - +
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F THR* 3.9 12.8 - - - +
42F ALA* 1.3 76.6 - - - +
44F TYR* 1.3 61.6 + - - +
46F ALA* 3.7 4.8 + - - +
47F TRP* 3.2 21.1 + - - +
192F ILE 4.8 0.9 - - - +
270F PHE* 3.7 30.3 - - + +
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Residues in contact with TYR 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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40F ARG* 3.8 15.3 - - + -
41F THR* 3.3 16.7 + - - +
42F ALA 3.2 0.4 - - - -
43F GLU* 1.3 74.7 - - - +
45F LYS* 1.3 68.4 + - - +
46F ALA 3.1 1.3 - - - -
47F TRP* 2.8 15.4 + + - +
48F LEU* 2.9 43.6 + - + +
70F ASP* 2.7 39.3 + - - +
73F MET* 4.2 2.9 - - + -
136F LEU* 3.4 18.7 - - + +
192F ILE 3.9 1.8 - - - +
193F TYR* 3.4 54.7 - + + -
194F TYR* 4.2 6.3 - + - -
270F PHE* 3.5 25.5 - + + -
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Residues in contact with LYS 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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40F ARG* 4.1 14.7 - - - +
41F THR 3.4 7.1 + - - +
42F ALA* 4.2 6.3 - - - +
44F TYR* 1.3 79.9 - - - +
46F ALA* 1.3 64.3 + - - +
48F LEU* 4.7 0.7 - - - +
49F LEU* 3.0 48.2 + - + +
73F MET* 2.9 54.6 + - + +
76F GLU* 5.1 4.2 + - - -
77F GLU* 3.1 32.9 + - - +
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Residues in contact with ALA 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 3.0 19.8 + - - +
43F GLU* 3.7 6.1 - - - +
45F LYS* 1.3 78.1 - - - +
47F TRP* 1.3 59.0 + - - +
49F LEU* 4.1 1.9 - - - +
50F GLY* 2.9 27.2 + - - -
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Residues in contact with TRP 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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43F GLU 3.2 11.0 + - - +
44F TYR* 2.8 20.3 + + - +
46F ALA* 1.3 72.5 - - - +
48F LEU* 1.3 92.4 - - + +
50F GLY* 3.0 2.0 + - - -
51F LEU* 2.8 56.6 + - + +
136F LEU* 4.3 6.7 - - + -
171F VAL* 3.7 15.9 - - + -
193F TYR* 4.9 0.4 - + - -
267F LEU* 3.3 32.0 - - + +
270F PHE* 3.2 55.9 - + + -
285F ILE* 3.7 25.6 - - + -
287F VAL* 5.4 0.7 - - + -
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Residues in contact with LEU 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 TYR* 2.9 34.6 + - + +
45F LYS 4.4 1.6 - - - +
47F TRP* 1.3 103.0 - - + +
49F LEU* 1.3 63.8 + - - +
51F LEU* 3.3 5.4 + - + +
52F LEU* 3.0 51.0 + - + +
70F ASP* 5.4 0.2 - - + -
73F MET* 3.6 28.3 - - + -
74F LEU* 4.1 16.2 - - + -
134F ILE* 4.7 17.5 - - + -
136F LEU* 4.3 11.0 - - + -
171F VAL* 5.2 4.0 - - + -
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Residues in contact with LEU 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 LYS* 3.0 41.4 + - + +
46F ALA* 4.1 2.5 - - - +
48F LEU* 1.3 77.9 - - - +
50F GLY* 1.3 63.1 + - - +
52F LEU* 4.3 2.4 - - - +
53F ARG* 3.2 47.2 + - - +
73F MET* 3.9 9.4 - - - -
74F LEU* 3.9 28.0 - - + -
77F GLU* 3.3 41.7 - - + +
79F PHE* 3.9 11.0 - - + -
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Residues in contact with GLY 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 ALA 2.9 17.2 + - - -
47F TRP* 3.0 4.9 + - - -
49F LEU* 1.3 77.2 - - - +
51F LEU* 1.3 50.8 + - - +
53F ARG* 3.8 1.5 - - - +
54F GLN* 2.8 38.0 + - - +
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Residues in contact with LEU 51 (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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47F TRP* 2.8 53.1 + - + +
48F LEU* 3.8 5.8 - - + +
50F GLY* 1.3 71.7 - - - +
52F LEU* 1.3 68.8 + - + +
54F GLN* 3.0 9.7 + - + +
55F HIS* 2.9 53.7 + - + +
169F LEU* 4.5 4.7 - - + -
171F VAL* 3.9 25.4 - - + -
267F LEU* 5.9 0.7 - - + -
287F VAL* 4.2 21.3 - - + -
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Residues in contact with LEU 52 (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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48F LEU* 3.0 38.1 + - + +
49F LEU* 4.3 0.9 - - + +
51F LEU* 1.3 78.9 - - + +
53F ARG* 1.3 61.1 + - - +
55F HIS 3.4 0.7 + - - -
56F GLY 3.3 2.6 + - - -
57F CYS* 2.9 40.3 + - + +
60F VAL* 4.6 5.2 - - + -
74F LEU* 3.5 38.8 - - + -
79F PHE* 3.8 27.1 - - + -
132F ALA* 3.8 28.7 - - + -
134F ILE* 4.8 6.3 - - + -
169F LEU* 4.9 5.8 - - + -
171F VAL* 5.1 5.2 - - + -
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Residues in contact with ARG 53 (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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49F LEU* 3.2 38.9 + - - +
50F GLY* 4.1 1.6 - - - +
52F LEU* 1.3 74.1 - - - +
54F GLN* 1.3 67.3 + - - +
55F HIS 3.1 1.6 - - - -
56F GLY* 3.1 14.2 + - - +
57F CYS 4.8 1.6 - - - +
77F GLU* 3.1 49.1 + - - +
79F PHE* 4.1 19.9 - - + -
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Residues in contact with GLN 54 (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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50F GLY 2.8 20.6 + - - +
51F LEU* 3.1 12.1 - - + +
53F ARG* 1.3 79.0 - - - +
55F HIS* 1.3 64.1 + - + +
56F GLY 3.5 1.7 + - - -
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Residues in contact with HIS 55 (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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51F LEU* 2.9 39.2 + - + +
54F GLN* 1.3 81.0 - - + +
56F GLY* 1.3 61.3 + - - +
57F CYS* 3.2 11.4 + - - -
169F LEU* 3.4 45.6 - - + +
287F VAL* 5.0 4.3 - - + -
289F LYS* 5.6 8.7 - - + +
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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