Contacts of the helix formed by residues 39 - 50 (chain A) in PDB entry 4F56
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 SER 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 3.0 17.4 + - - -
38A SER* 1.3 73.3 - - - +
40A MET* 1.3 63.3 + - - +
41A ALA* 3.6 7.8 + - - +
42A ASP* 3.0 36.8 + - - -
43A PHE 3.1 16.3 + - - -
287A PHE* 3.4 7.6 - - - -
289A PHE* 3.6 4.0 - - - -
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER 3.2 7.8 + - - +
39A SER* 1.3 71.6 - - - +
41A ALA* 1.3 57.3 + - - +
43A PHE* 3.3 8.5 + - - +
44A ARG* 2.8 42.1 + - - +
274A PHE* 4.6 1.1 - - + -
289A PHE* 3.4 38.5 - - + -
296A THR* 4.3 9.9 - - + +
299A GLU* 3.4 38.1 - - - +
300A ALA* 3.7 37.5 - - + -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 3.2 6.4 + - - +
40A MET* 1.3 79.0 - - - +
42A ASP* 1.3 65.1 + - - +
44A ARG* 3.3 7.1 + - - +
45A LYS* 3.0 28.8 + - + +
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 4.7 2.1 + - - -
39A SER* 3.0 30.4 + - - +
41A ALA* 1.3 75.4 - - - +
43A PHE* 1.3 66.3 + - - +
45A LYS* 3.2 36.9 + - - +
46A PHE* 3.4 18.7 + - + -
287A PHE* 3.7 15.0 - - + -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 3.1 7.2 + - - +
40A MET* 3.6 13.9 - - - +
42A ASP* 1.3 76.6 - - - +
44A ARG* 1.3 69.9 + - + +
46A PHE* 3.0 7.1 + - - +
47A PHE* 2.8 44.5 + + + -
244A LEU* 4.0 24.7 - - + -
246A LEU* 4.0 29.2 - - + -
272A ALA* 3.7 30.3 - - + -
274A PHE* 4.6 1.3 - + - -
287A PHE* 3.4 20.0 - + + -
289A PHE* 3.7 22.9 - + + -
300A ALA* 3.5 30.7 - - + -
301A LEU* 4.8 1.3 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 2.8 37.1 + - - +
41A ALA* 3.3 6.0 + - - +
42A ASP 3.3 0.2 - - - -
43A PHE* 1.3 77.2 - - + +
45A LYS* 1.3 57.0 + - - +
47A PHE* 3.6 14.1 - - + +
48A ALA* 2.9 30.3 + - - +
299A GLU* 3.5 17.6 + - - -
300A ALA 2.9 35.8 + - - +
302A ALA* 2.7 42.8 + - - +
113B GLU* 3.0 39.0 + - - +
114B PRO 4.5 2.6 + - - -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.0 15.5 + - - +
42A ASP* 3.6 31.6 + - - +
43A PHE 3.2 0.8 - - - -
44A ARG* 1.3 78.4 - - - +
46A PHE* 1.3 62.3 + - + +
48A ALA* 3.5 9.4 + - - +
49A LYS* 3.7 19.1 + - - +
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 3.4 19.4 + - + -
43A PHE 3.0 6.3 + - - +
45A LYS* 1.3 74.7 - - + +
47A PHE* 1.3 67.0 + - - +
49A LYS* 3.0 7.5 + - + +
50A ALA* 3.0 23.4 + - - +
243A ASP 5.9 0.9 - - - +
244A LEU* 4.0 18.6 - - + -
270A PRO* 3.9 22.4 - - + -
286A ARG* 3.8 22.7 - - + -
287A PHE* 3.8 27.6 - + - -
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 2.8 29.6 + + + +
44A ARG* 3.3 15.9 + - - +
46A PHE* 1.3 76.9 - - - +
48A ALA* 1.3 58.0 + - - +
49A LYS 3.2 0.7 + - - -
50A ALA* 3.5 2.4 + - - +
53A ILE* 3.6 29.2 - - + -
124A CYS* 3.8 16.4 - - - -
127A ARG* 3.8 11.2 - - - -
128A LEU* 4.2 11.2 - - + -
133A ARG* 2.8 25.1 + - - -
244A LEU* 3.7 11.6 - - + +
246A LEU* 6.1 0.2 - - + -
300A ALA 3.6 12.6 - - - -
301A LEU* 3.6 35.4 - - + -
302A ALA 3.4 23.6 - - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG 2.9 17.3 + - - +
45A LYS* 3.7 8.5 - - - +
46A PHE 3.2 0.4 - - - -
47A PHE* 1.3 78.8 - - - +
49A LYS* 1.3 70.8 + - + +
133A ARG* 3.4 18.0 + - - +
113B GLU* 5.8 3.8 - - - +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS 3.7 12.8 + - - +
46A PHE* 3.0 8.6 + - + +
48A ALA* 1.3 89.6 - - + +
50A ALA* 1.3 66.2 + - - +
51A LYS* 3.5 14.0 + - - +
133A ARG* 4.2 1.6 + - - -
243A ASP* 4.5 1.2 - - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE 3.0 14.7 + - - +
47A PHE 3.5 7.3 + - - +
49A LYS* 1.3 76.3 - - - +
51A LYS* 1.3 60.3 + - - +
52A HIS 3.5 0.4 - - - -
53A ILE* 3.8 21.8 - - + -
128A LEU* 4.6 2.8 - - - +
133A ARG* 2.8 31.5 + - - +
243A ASP* 3.6 18.6 - - - +
244A LEU* 3.9 17.7 - - + -
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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