Contacts of the helix formed by residues 35 - 52 (chain B) in PDB entry 1PLN
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 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B CYS* 1.3 66.0 + - - +
37B LEU 3.3 3.1 - - - +
38B ILE* 2.9 50.2 + - + +
39B LEU* 2.9 13.2 + - + +
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Residues in contact with CYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.3 27.1 - - + -
38A ILE* 4.7 20.2 - - - -
41A CYS* 3.7 9.2 - - - -
35B PHE* 1.3 78.8 - - - +
37B LEU* 1.3 57.9 + - - +
39B LEU* 3.2 13.4 + - - +
40B ILE* 2.9 33.1 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.1 34.3 - - + -
35B PHE 3.3 1.0 - - - -
36B CYS* 1.3 72.9 - - - +
38B ILE* 1.3 62.5 + - + +
40B ILE* 3.3 13.2 + - + +
41B CYS* 2.9 33.8 + - - -
36C CYS* 3.5 37.7 - - + -
37C LEU* 4.1 24.9 - - + -
40C ILE* 4.0 6.8 - - + +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 2.9 38.0 + - + +
37B LEU* 1.3 75.0 - - + +
39B LEU* 1.3 60.4 + - - +
41B CYS* 3.2 11.8 + - + +
42B LEU* 2.9 29.7 + - + +
36C CYS* 6.0 4.5 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A CYS* 3.8 25.8 - - + -
45A ILE* 5.8 5.2 - - + -
35B PHE* 2.9 11.7 + - + +
36B CYS* 3.3 14.4 - - - +
38B ILE* 1.3 75.9 - - - +
40B ILE* 1.3 55.8 + - - +
42B LEU* 3.2 18.7 + - + +
43B LEU* 2.9 54.5 + - + +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.1 25.8 - - + +
40A ILE* 3.9 25.1 - - + -
41A CYS* 3.4 19.3 - - - -
44A LEU* 3.8 20.4 - - + -
36B CYS 2.9 21.9 + - - +
37B LEU* 3.4 19.5 - - + +
39B LEU* 1.3 73.4 - - - +
41B CYS* 1.3 56.7 + - - +
43B LEU* 3.3 2.1 + - - +
44B LEU* 2.9 42.9 + - + +
40C ILE* 3.9 22.0 - - + -
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Residues in contact with CYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 2.9 26.4 + - - -
38B ILE* 3.3 13.0 - - + +
40B ILE* 1.3 75.1 - - - +
42B LEU* 1.3 57.0 + - - +
44B LEU* 3.2 4.8 + - - +
45B ILE* 2.9 36.7 + - + +
36C CYS* 3.9 11.2 - - - -
39C LEU* 3.8 28.7 - - + -
40C ILE* 3.4 24.7 - - - -
43C LEU* 3.5 13.7 - - + +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 2.9 18.0 + - + +
39B LEU* 3.2 26.2 + - + +
41B CYS* 1.3 71.1 - - - +
43B LEU* 1.3 61.6 + - + +
45B ILE* 3.2 21.2 + - + +
46B CYS* 2.9 42.5 + - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A CYS* 4.6 3.1 - - + +
44A LEU* 3.9 34.1 - - + +
45A ILE* 4.0 24.5 - - + +
48A ILE* 3.8 28.7 - - + -
39B LEU* 2.9 48.5 + - + +
40B ILE 3.7 4.5 - - - +
42B LEU* 1.3 79.5 - - + +
44B LEU* 1.3 56.3 + - - +
46B CYS* 3.2 11.4 + - + +
47B ILE* 2.9 33.8 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.8 31.0 - - + -
40B ILE* 2.9 27.6 + - + +
41B CYS 3.5 8.3 - - - +
43B LEU* 1.3 72.8 - - - +
45B ILE* 1.3 60.2 + - - +
47B ILE* 3.2 11.0 + - + +
48B ILE* 2.9 33.6 + - - +
40C ILE* 3.5 45.3 - - + +
43C LEU* 3.8 17.3 - - + -
44C LEU* 3.9 17.0 - - + +
47C ILE* 4.2 14.4 - - + +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B CYS* 2.9 28.4 + - + +
42B LEU* 3.2 18.8 + - + +
44B LEU* 1.3 72.9 - - - +
46B CYS* 1.3 59.9 + - - +
48B ILE* 3.1 13.4 + - + +
49B VAL* 2.9 42.2 + - + +
39C LEU* 6.0 3.1 - - + -
43C LEU* 3.9 19.3 - - + -
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Residues in contact with CYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 18.8 - - + -
42B LEU* 2.9 34.6 + - - -
43B LEU* 3.4 14.8 - - - +
45B ILE* 1.3 76.7 - - - +
47B ILE* 1.3 55.2 + - - +
49B VAL* 3.3 9.3 + - - +
50B MET* 2.9 32.8 + - + +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.9 30.3 - - + +
47A ILE* 4.2 18.6 - - + -
48A ILE* 3.8 19.5 - - + -
51A LEU* 4.1 17.0 - - + -
43B LEU 2.9 21.1 + - - +
44B LEU* 3.2 15.9 + - + +
46B CYS* 1.3 74.4 - - - +
48B ILE* 1.3 58.1 + - - +
50B MET* 3.1 3.6 + - - +
51B LEU* 2.8 49.9 + - + +
47C ILE* 4.0 16.8 - - + -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 2.9 19.6 + - - +
45B ILE* 3.1 14.6 + - + +
47B ILE* 1.3 74.5 - - - +
49B VAL* 1.3 58.7 + - + +
51B LEU* 3.2 8.1 + - - +
52B LEU* 2.8 41.7 + - + +
43C LEU* 3.7 41.5 - - + +
46C CYS* 3.9 14.8 - - + -
47C ILE* 3.9 17.5 - - + +
50C MET* 3.8 22.8 - - + +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 2.9 33.6 + - + +
46B CYS* 3.6 11.2 - - - +
47B ILE 3.3 0.2 - - - -
48B ILE* 1.3 72.6 - - + +
50B MET* 1.3 65.9 + - - +
52B LEU* 3.0 26.2 - - - +
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Residues in contact with MET 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.5 6.7 - - + -
51A LEU* 3.5 53.4 - - + +
52A LEU* 3.8 34.8 - - + -
46B CYS* 2.9 21.1 + - + +
47B ILE 3.1 4.2 + - - +
49B VAL* 1.3 82.7 - - + +
51B LEU* 1.3 61.3 + - - +
52B LEU* 4.7 1.0 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.9 15.5 - - + -
47B ILE* 2.8 33.1 + - + +
48B ILE* 3.2 6.3 + - + +
50B MET* 1.3 79.9 - - - +
52B LEU* 1.3 60.6 + - - +
47C ILE* 3.9 34.5 - - + -
50C MET* 3.9 30.8 - - + +
51C LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 2.8 26.9 + - + +
49B VAL* 3.0 18.4 - - - +
50B MET 4.6 1.1 - - - +
51B LEU* 1.3 76.1 - - - +
50C MET* 4.1 35.0 - - + -
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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