Contacts of the helix formed by residues 36 - 45 (chain B) in PDB entry 5CYJ
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 LYS 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 6.2 2.7 - - - -
34B ASP 4.2 7.6 + - - +
35B ILE* 1.3 81.3 - - - +
37B PRO* 1.3 69.3 - - + +
38B ARG* 3.2 44.6 - - + +
39B GLU* 2.9 48.1 + - + +
55B ILE* 3.8 3.2 - - - +
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Residues in contact with PRO 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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56A LYS* 6.2 0.2 - - - +
57A LEU* 3.6 36.6 - - + +
58A THR* 3.8 26.2 - - - +
59A SER* 4.4 4.7 - - - +
35B ILE 4.4 1.6 - - - +
36B LYS* 1.3 86.6 - - + +
38B ARG* 1.3 62.9 + - - +
39B GLU 3.2 0.9 + - - -
40B LEU* 3.2 13.2 + - - +
41B TYR* 3.3 10.6 + - - +
53B SER* 4.7 3.6 + - - +
54B LEU* 6.1 2.5 - - - -
55B ILE* 3.6 18.6 - - + +
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 3.2 43.5 - - + +
37B PRO* 1.3 79.6 - - - +
39B GLU* 1.3 69.8 + - + +
41B TYR* 3.2 14.5 + - + +
42B LEU* 2.8 39.8 + - + +
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Residues in contact with GLU 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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32B PRO* 5.7 0.2 - - - +
34B ASP 4.1 2.9 - - - +
35B ILE* 3.9 8.2 - - + -
36B LYS* 2.9 49.2 + - + +
38B ARG* 1.3 85.0 - - + +
40B LEU* 1.3 64.1 + - - +
42B LEU* 3.3 16.3 + - + +
43B LEU* 3.1 22.5 + - - +
86B PHE* 3.5 38.1 - - + -
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Residues in contact with LEU 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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28B VAL* 4.3 16.2 - - + -
31B LEU* 4.6 12.3 - - + -
35B ILE* 4.6 3.9 - - + +
36B LYS 3.8 1.2 + - - -
37B PRO 3.2 9.0 + - - +
39B GLU* 1.3 79.6 - - - +
41B TYR* 1.3 62.7 + - - +
43B LEU* 3.4 8.6 + - + -
44B PHE* 3.3 50.4 + - + +
53B SER* 3.8 24.2 + - - +
54B LEU 3.5 24.9 - - - +
55B ILE* 3.7 22.7 - - + -
64B GLY* 3.8 11.9 - - - -
66B VAL* 4.0 9.2 - - + -
86B PHE* 5.0 1.1 - - + -
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Residues in contact with TYR 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 PRO 3.3 6.4 + - - +
38B ARG* 3.2 20.6 + - + +
39B GLU 3.2 0.2 - - - -
40B LEU* 1.3 77.3 - - - +
42B LEU* 1.3 72.8 + - + +
44B PHE 3.2 1.0 + - - -
45B ARG* 2.8 72.3 + - + +
50B TYR* 3.4 38.8 - + - +
53B SER* 4.0 3.7 + - - +
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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 ARG* 2.8 31.9 + - + +
39B GLU* 3.3 20.4 + - + +
41B TYR* 1.3 88.3 - - + +
43B LEU* 1.3 64.7 + - - +
45B ARG* 3.5 21.0 + - - +
46B PRO* 3.9 4.7 - - - +
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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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39B GLU 3.1 12.8 + - - +
40B LEU* 3.6 14.1 - - + +
41B TYR 3.2 0.2 - - - -
42B LEU* 1.3 78.4 - - - +
44B PHE* 1.3 80.4 + - + +
46B PRO* 3.6 9.5 - - - +
47B PHE* 3.8 2.6 - - - -
81B MSE 3.4 38.0 - - + +
84B ILE* 4.4 13.5 - - + -
86B PHE* 4.0 25.6 - - + +
94B LEU* 3.7 26.2 - - + -
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Residues in contact with PHE 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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26B LEU* 4.1 19.3 - - + -
28B VAL* 4.3 13.5 - - + -
40B LEU* 3.3 21.8 + - + +
41B TYR 3.2 2.6 + - - -
43B LEU* 1.3 98.5 - - + +
45B ARG* 1.3 64.3 + - - +
46B PRO* 3.2 4.9 - - - -
47B PHE* 3.0 19.4 + + - +
50B TYR* 3.6 35.3 - - + +
66B VAL* 3.8 24.5 - - + -
68B PHE* 3.8 17.7 - + + -
77B ALA* 4.2 8.5 - - + -
81B MSE 3.1 26.5 - - + -
96B LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 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 TYR* 2.8 63.3 + - + +
42B LEU* 3.5 21.5 + - - +
44B PHE* 1.3 77.4 - - - +
46B PRO* 1.3 80.9 - - - +
47B PHE 3.2 4.7 + - - +
50B TYR* 4.2 12.3 - - + +
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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