Contacts of the helix formed by residues 38 - 49 (chain B) in PDB entry 5J8E
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 GLY 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B LEU 3.4 11.1 + - - -
36B THR 3.3 4.4 - - - -
37B ASN* 1.3 78.1 + - - +
39B VAL* 1.3 56.9 + - - +
40B VAL 3.4 2.5 - - - -
41B MET* 3.3 6.3 + - - -
42B ALA* 2.9 27.5 + - - +
61B ILE* 4.7 2.0 - - - -
76B LEU* 4.0 10.3 - - - -
79B ILE* 3.1 29.5 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 4.2 11.4 - - + -
37B ASN* 2.9 27.3 + - - +
38B GLY* 1.3 76.7 - - - +
40B VAL* 1.3 63.1 + - + +
42B ALA* 3.2 7.7 + - - +
43B GLN* 2.9 45.1 + - + +
61B ILE* 4.4 9.0 - - + -
62B LYS 3.9 21.1 - - - +
63B THR* 4.0 25.8 - - + +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.8 29.4 - - + -
25B VAL* 4.0 10.1 - - + -
27B ALA* 3.7 17.3 - - + +
28B PRO 3.3 26.5 - - - +
29B CYS* 4.0 10.1 - - + -
34B ASP 3.7 14.3 + - - +
35B LEU* 3.9 19.5 - - + +
37B ASN* 4.5 1.4 + - - -
38B GLY 3.4 0.2 - - - -
39B VAL* 1.3 77.0 - - + +
41B MET* 1.3 65.7 + - + +
43B GLN* 3.1 9.8 + - - +
44B VAL* 2.9 22.5 + - + +
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Residues in contact with MET 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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20B ILE* 5.4 1.6 - - + -
35B LEU* 3.4 33.4 + - + +
38B GLY* 3.3 9.7 + - - +
40B VAL* 1.3 79.5 - - + +
42B ALA* 1.3 58.0 + - - +
44B VAL* 3.2 7.5 + - - +
45B LEU* 2.9 34.8 + - - +
76B LEU* 3.5 27.6 - - + -
79B ILE* 4.5 7.9 - - + -
115B LEU* 3.8 14.4 - - + -
118B MET* 3.6 31.2 - - + +
119B LEU* 3.8 22.7 - - + -
122B ILE* 3.6 24.2 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 2.9 16.8 + - - +
39B VAL* 3.5 4.9 - - - +
40B VAL 3.2 0.2 - - - -
41B MET* 1.3 75.9 - - - +
43B GLN* 1.3 60.6 + - - +
45B LEU* 3.3 11.3 + - - +
46B GLN* 3.0 22.2 + - - +
57B TRP* 4.4 6.2 - - + -
58B LEU* 3.4 29.9 - - + +
61B ILE* 4.1 21.1 - - + -
79B ILE* 4.3 8.0 - - + +
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Residues in contact with GLN 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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25B VAL* 3.5 21.6 - - + +
26B ASP* 3.5 11.3 + - - +
27B ALA* 3.1 35.1 + - - +
39B VAL* 2.9 35.4 + - + +
40B VAL* 3.1 7.1 + - - +
42B ALA* 1.3 77.2 - - - +
44B VAL* 1.3 61.2 + - - +
46B GLN* 3.4 16.4 + - - +
47B LYS* 3.2 26.6 + - - +
58B LEU* 4.9 7.6 - - + -
63B THR* 6.2 0.4 - - - +
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Residues in contact with VAL 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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20B ILE* 3.9 26.7 - - + -
23B PHE* 3.8 35.9 - - + -
25B VAL* 4.0 18.2 - - + -
40B VAL* 2.9 26.7 + - + +
41B MET* 3.6 9.0 - - - +
43B GLN* 1.3 74.0 - - - +
45B LEU* 1.3 66.2 + - - +
47B LYS* 3.1 6.9 + - - +
48B ILE* 3.0 22.1 + - + +
122B ILE* 3.9 22.2 - - + -
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Residues in contact with LEU 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 MET 2.9 16.5 + - - +
42B ALA* 3.6 9.6 - - - +
44B VAL* 1.3 78.0 - - - +
46B GLN* 1.3 55.6 + - - +
48B ILE* 3.2 12.1 + - + +
49B ASP 2.9 25.5 + - - -
53B PHE* 3.3 49.4 - - + -
57B TRP* 5.1 3.8 - - + -
79B ILE* 3.7 30.3 - - + +
83B ILE* 3.9 23.3 - - + -
122B ILE* 4.2 23.3 - - + -
125B CYS* 4.6 11.4 - - + -
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Residues in contact with GLN 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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42B ALA 3.0 12.9 + - - +
43B GLN* 3.6 18.2 - - - +
44B VAL 3.2 0.2 - - - -
45B LEU* 1.3 73.7 - - - +
47B LYS* 1.3 63.9 + - + +
50B PRO* 2.9 45.2 + - + +
53B PHE* 3.3 30.4 + - - +
54B ASP* 4.1 2.4 - - - +
55B GLU* 4.1 21.6 - - - +
58B LEU* 4.2 14.4 - - + +
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Residues in contact with LYS 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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23B PHE* 3.8 36.6 - - + +
24B ASN 4.6 6.8 + - - -
25B VAL* 4.1 20.6 - - + +
26B ASP* 5.5 4.9 + - - -
43B GLN* 3.2 15.5 + - - +
44B VAL 3.1 8.1 + - - +
46B GLN* 1.3 81.6 - - + +
48B ILE* 1.3 65.2 + - - +
50B PRO* 3.8 6.3 - - - +
131B GLN* 3.6 5.9 + - - +
135B TYR* 3.0 14.2 + - - +
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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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19B TRP* 4.6 0.2 - - + -
23B PHE* 3.9 17.3 - - + -
44B VAL* 3.0 21.5 + - + +
45B LEU* 3.2 15.0 + - + +
47B LYS* 1.3 77.2 - - - +
49B ASP* 1.3 63.9 + - + +
53B PHE* 5.8 0.4 - - + -
86B TYR* 4.9 3.4 - - + -
122B ILE* 3.7 41.5 - - + +
125B CYS* 4.1 11.0 - - + +
126B ALA* 3.7 21.1 - - + +
129B CYS* 3.9 31.2 - - + +
131B GLN* 2.8 20.1 - - - +
135B TYR* 3.5 8.3 - - + -
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Residues in contact with ASP 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 LEU 2.9 7.4 + - - -
46B GLN 3.3 2.7 - - - -
48B ILE* 1.3 79.9 - - + +
50B PRO* 1.3 60.6 - - - +
51B ALA* 3.0 21.9 + - - +
52B TYR* 3.1 14.4 + - - +
53B PHE* 2.8 36.0 + - + +
86B TYR* 2.6 43.5 + - + +
90B ILE* 4.6 4.7 - - - +
130B GLU* 6.2 0.3 - - - +
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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