Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 5J13
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 ASP 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN 4.0 0.2 + - - -
34A CYS* 1.3 69.1 - - - +
36A PHE* 1.3 64.6 + - - +
37A GLU* 3.5 8.3 + - - +
38A LYS* 3.1 39.2 + - - +
39A ILE* 3.2 26.4 + - - +
109A TRP* 3.0 37.0 + - + +
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Residues in contact with PHE 36 (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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31A PHE 3.3 26.2 - - - -
32A THR 3.9 12.3 - - - -
34A CYS* 3.4 24.1 + - + -
35A ASP* 1.3 70.0 + - - +
37A GLU* 1.3 63.0 + - + +
39A ILE* 3.3 3.4 + - + +
40A LYS* 2.9 30.2 + - - +
72A ARG* 3.9 32.5 - - + -
73A PRO* 3.7 29.2 - - + -
76A LEU* 4.0 12.6 - - + -
151A PHE* 3.9 23.2 - + + -
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Residues in contact with GLU 37 (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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35A ASP* 3.4 7.7 + - - +
36A PHE* 1.3 78.9 - - + +
38A LYS* 1.3 62.5 + - + +
40A LYS* 3.4 11.7 + - + +
41A ALA* 3.1 26.2 + - - +
155A LEU* 4.8 18.4 - - + -
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Residues in contact with LYS 38 (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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35A ASP* 3.1 31.1 + - - +
36A PHE 3.2 0.4 - - - -
37A GLU* 1.3 81.4 - - + +
39A ILE* 1.3 59.6 + - - +
41A ALA* 3.3 10.5 + - + +
42A ALA* 3.0 27.0 + - - +
109A TRP* 3.4 54.8 + - + -
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Residues in contact with ILE 39 (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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34A CYS* 4.1 7.0 - - + -
35A ASP 3.2 16.6 + - - +
36A PHE* 3.3 7.8 + - - +
38A LYS* 1.3 72.5 - - - +
40A LYS* 1.3 65.0 + - - +
42A ALA* 3.3 8.1 + - - +
43A TYR* 3.0 21.3 + - - +
47A ILE* 5.1 0.2 - - - +
76A LEU* 3.9 21.5 - - + -
105A ALA* 4.3 13.2 - - + +
106A LEU* 4.1 7.9 - - + -
109A TRP* 3.8 20.4 - - + -
110A CYS* 3.9 27.6 - - - -
148A TRP* 3.8 20.5 - - + -
151A PHE* 3.7 17.5 - - + -
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Residues in contact with LYS 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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36A PHE 2.9 16.4 + - - +
37A GLU* 3.5 10.1 - - + +
39A ILE* 1.3 77.6 - - - +
41A ALA* 1.3 61.9 + - - +
43A TYR* 3.1 8.1 + - - +
44A LEU* 3.0 37.2 + - + +
72A ARG* 6.1 0.9 - - - +
151A PHE* 4.0 14.5 - - + +
152A ASN* 3.3 50.3 + - - +
153A ARG 4.6 6.4 + - - +
154A PRO* 4.8 7.3 - - - +
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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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37A GLU 3.1 14.0 + - - +
38A LYS* 3.3 16.1 + - + +
40A LYS* 1.3 77.3 - - - +
42A ALA* 1.3 60.6 + - - +
44A LEU* 3.5 9.4 + - - +
45A SER* 3.0 28.3 + - - -
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Residues in contact with ALA 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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38A LYS 3.0 14.1 + - - +
39A ILE* 3.5 9.6 - - - +
41A ALA* 1.3 73.6 - - - +
43A TYR* 1.3 60.3 - - - +
45A SER* 3.2 7.1 + - - -
46A THR* 3.0 28.6 + - - +
47A ILE* 3.3 12.2 + - + +
105A ALA* 4.1 24.2 - - + -
109A TRP* 5.2 5.2 - - - +
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Residues in contact with TYR 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 ILE 3.0 13.8 + - - +
40A LYS 3.1 7.4 + - - +
42A ALA* 1.3 78.4 - - - +
44A LEU* 1.3 68.9 + - + +
45A SER 3.3 0.7 + - - -
46A THR 3.5 0.2 + - - -
47A ILE* 3.4 16.2 + - + +
48A SER* 2.9 64.7 + - - -
51A LEU* 3.9 13.9 - - + +
145A GLN* 4.5 10.9 + - - +
148A TRP* 3.5 52.4 - + + +
149A ARG* 4.9 3.3 + - - +
152A ASN* 3.2 36.8 - - + +
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Residues in contact with LEU 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 LYS* 3.0 38.6 + - + +
41A ALA* 4.0 8.1 - - - +
43A TYR* 1.3 85.9 - - + +
45A SER* 1.3 60.8 + - - +
48A SER* 4.7 7.6 - - - -
49A LYS* 4.3 10.7 - - - +
152A ASN* 3.4 21.8 - - - +
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Residues in contact with SER 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 19.1 + - - -
42A ALA* 3.2 8.7 + - - -
44A LEU* 1.3 79.8 - - - +
46A THR* 1.3 71.0 + - - +
49A LYS* 3.4 26.1 + - - +
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Residues in contact with THR 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 ALA* 3.0 11.3 + - - +
43A TYR 3.5 0.8 + - - -
45A SER* 1.3 92.0 + - - +
47A ILE* 1.3 68.0 + - - +
48A SER 3.3 1.8 - - - -
49A LYS* 3.2 19.3 + - - +
50A ASP* 3.4 13.3 + - - +
101A LYS* 3.4 42.0 - - + -
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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