Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 2JM5
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 ASN 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.9 2.0 - - - +
37A SER* 3.5 25.3 + - - +
38A GLU 3.0 0.6 - - - -
39A GLU* 1.3 83.7 - - - +
41A ILE* 1.3 65.8 + - - +
42A GLU 3.1 0.7 - - - -
43A PHE* 2.9 21.7 + - - +
44A TRP* 3.4 5.7 + - - -
70A PHE* 6.1 0.2 - - - -
78A GLU 5.4 1.4 - - - +
79A VAL* 4.5 19.7 - - - +
80A ASN* 5.2 9.6 + - - +
108A VAL* 3.3 29.1 - - + +
111A LEU* 5.6 6.9 - - - +
112A MET* 3.7 19.3 - - + +
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Residues in contact with ILE 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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19A LEU* 3.6 23.1 - - + -
25A LEU* 3.8 27.6 - - + +
28A PHE* 3.7 17.5 - - + -
29A THR* 3.6 23.8 - - - +
32A LEU* 3.5 12.3 - - + +
38A GLU 3.2 13.0 + - - +
40A ASN* 1.3 79.3 - - - +
42A GLU* 1.3 70.7 + - + +
44A TRP* 3.5 27.9 - - + -
45A ILE* 3.1 33.6 + - + +
112A MET* 3.4 13.2 - - - -
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Residues in contact with GLU 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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29A THR* 4.7 5.7 + - - -
33A LYS* 4.2 8.8 + - - -
38A GLU* 3.0 33.4 + - - +
39A GLU* 3.6 7.9 - - + -
41A ILE* 1.3 80.2 - - + +
43A PHE* 1.3 59.6 + - - +
45A ILE* 3.6 34.9 - - + +
46A ALA* 2.9 28.4 + - - +
70A PHE* 4.8 4.4 - - + -
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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 GLU 2.8 18.0 + - - +
40A ASN* 2.9 15.0 - - - +
42A GLU* 1.3 79.1 - - - +
44A TRP* 1.3 67.3 + - + +
46A ALA* 3.2 4.5 + - - +
47A CYS* 3.0 39.1 + - - -
66A ILE* 4.5 5.4 - - + +
70A PHE* 3.5 25.6 - + + -
71A ILE* 3.4 35.4 - - + -
79A VAL* 3.4 28.7 - - + -
81A LEU* 4.8 1.6 - - + -
101A PHE* 4.5 0.9 - + + -
104A ALA* 3.7 26.0 - - + -
105A GLN 4.3 1.6 - - - -
108A VAL* 3.4 31.0 - - + -
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Residues in contact with TRP 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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19A LEU* 3.3 44.6 - - + -
25A LEU* 5.1 6.1 - - + -
40A ASN 3.4 2.6 + - - -
41A ILE* 3.5 18.6 - - + -
43A PHE* 1.3 81.5 - - + +
45A ILE* 1.3 94.6 + - + +
47A CYS* 3.1 7.9 + - + +
48A GLU* 2.8 40.3 + - + +
105A GLN* 3.2 61.7 + - + -
108A VAL* 3.9 15.9 - - + -
109A TYR* 3.8 6.1 - - - +
112A MET* 3.3 27.2 - - + +
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Residues in contact with ILE 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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25A LEU* 4.2 22.2 - - + -
41A ILE* 3.1 33.1 + - + +
42A GLU* 3.6 33.4 - - + +
43A PHE 3.3 0.2 - - - -
44A TRP* 1.3 92.1 - - + +
46A ALA* 1.3 57.9 + - - +
48A GLU* 3.5 4.6 + - - +
49A ASP* 2.9 31.4 + - + +
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Residues in contact with ALA 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 GLU 2.9 15.5 + - - +
43A PHE 3.3 10.1 - - - +
45A ILE* 1.3 77.7 - - - +
47A CYS* 1.3 56.9 + - - +
49A ASP* 3.2 9.3 + - - +
50A PHE* 2.9 29.6 + - - +
62A LYS* 5.6 0.2 - - - +
66A ILE* 3.4 24.4 - - + +
70A PHE* 4.6 10.8 - - + -
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Residues in contact with CYS 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* 3.0 32.1 - - - -
44A TRP* 3.1 17.2 + - + +
46A ALA* 1.3 79.2 - - - +
48A GLU* 1.3 65.8 + - - +
50A PHE* 3.2 11.7 + - - +
51A LYS* 2.8 25.6 + - - +
66A ILE* 3.9 15.7 - - - -
99A HIS* 4.1 5.4 - - + +
101A PHE* 3.4 44.6 - - + +
105A GLN* 5.5 1.3 - - + -
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Residues in contact with GLU 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 TRP* 2.8 30.1 + - + +
45A ILE* 4.2 4.9 - - - +
47A CYS* 1.3 74.9 - - - +
49A ASP* 1.3 59.4 + - - +
51A LYS* 2.7 40.6 + - + +
52A LYS* 3.1 30.4 + - - +
99A HIS* 2.6 32.4 + - - +
105A GLN* 4.6 21.8 - - + +
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Residues in contact with ASP 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 ILE* 2.9 21.7 + - + +
46A ALA* 3.3 9.7 - - - +
48A GLU* 1.3 75.8 - - - +
50A PHE* 1.3 60.8 + - - +
52A LYS* 3.2 40.2 + - + +
53A SER 3.9 2.1 + - - -
62A LYS* 2.7 37.3 + - - +
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Residues in contact with PHE 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 ALA 2.9 11.9 + - - +
47A CYS* 3.3 12.6 - - - +
49A ASP* 1.3 74.8 - - - +
51A LYS* 1.3 56.5 + - - +
52A LYS 3.0 1.3 - - - -
53A SER* 2.9 29.0 + - - +
58A GLN 4.7 0.2 - - - -
59A ILE* 3.3 45.3 - - + +
62A LYS* 3.6 38.8 - - + -
63A ALA* 3.6 11.7 - - + -
66A ILE* 4.1 4.3 - - + -
97A THR 2.9 25.6 - - - -
98A LEU 3.2 19.3 - - - +
99A HIS* 3.7 7.0 - - - -
100A SER 4.0 1.1 - - - -
101A PHE* 3.4 35.0 - + - -
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Residues in contact with LYS 51 (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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47A CYS 2.8 13.0 + - - +
48A GLU* 2.7 52.5 + - + +
50A PHE* 1.3 77.1 - - - +
52A LYS* 1.3 58.7 + - + -
53A SER 3.2 8.7 + - - +
98A LEU* 3.2 38.5 + - + +
99A HIS* 3.8 21.9 - - + +
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Residues in contact with LYS 52 (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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48A GLU 3.1 16.8 + - - +
49A ASP* 3.2 28.8 + - - +
50A PHE 3.0 0.6 - - - -
51A LYS* 1.3 77.5 - - + +
53A SER* 1.3 59.6 + - - +
54A LYS* 3.9 2.3 + - - +
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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