Contacts of the helix formed by residues 21 - 35 (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 HIS 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A MET 5.2 1.6 - - - -
3A VAL* 4.7 2.5 - - + -
7A GLU* 3.1 41.8 + - + +
11A TRP* 3.2 23.3 - + - +
17A LYS* 2.9 22.8 + - + +
18A LEU 3.1 5.1 + - - +
20A SER* 1.3 76.8 - - - +
22A ARG* 1.3 58.3 + - - +
23A ASP* 3.5 30.8 + - + +
24A GLY 2.8 3.2 + - - +
25A LEU* 2.7 33.8 + - - +
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Residues in contact with ARG 22 (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 5.3 0.4 + - - -
20A SER* 2.8 33.0 + - - +
21A HIS* 1.3 73.5 - - - +
23A ASP* 1.3 65.2 + - - +
25A LEU* 3.3 21.9 - - + +
26A GLU* 3.1 23.9 + - - +
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Residues in contact with ASP 23 (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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1A SER* 3.0 19.0 + - - -
2A MET* 2.8 40.8 + - - +
3A VAL* 4.3 5.8 - - + +
11A TRP* 3.5 15.2 - - + -
21A HIS* 3.2 25.3 + - + +
22A ARG* 1.3 80.2 - - - +
24A GLY* 1.3 58.4 + - - +
26A GLU* 3.4 6.8 - - - +
27A ALA* 3.0 21.1 + - - +
129A LEU* 6.0 0.2 - - - +
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Residues in contact with GLY 24 (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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11A TRP* 3.4 21.6 - - - -
18A LEU* 3.2 34.5 - - - +
21A HIS 2.8 5.2 + - - -
23A ASP* 1.3 77.2 - - - +
25A LEU* 1.3 60.3 + - - +
26A GLU 3.0 1.1 - - - -
27A ALA* 2.9 1.0 + - - -
28A PHE* 2.8 27.9 + - - +
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Residues in contact with LEU 25 (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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18A LEU 3.0 3.9 + - - -
19A LEU* 3.2 29.2 - - + +
21A HIS 2.7 12.2 + - - +
22A ARG* 3.3 26.2 - - + +
24A GLY* 1.3 70.9 - - - -
26A GLU* 1.3 66.9 + - + +
28A PHE* 4.5 4.3 - - - -
29A THR* 2.8 41.2 + - + -
41A ILE* 3.8 14.7 - - + +
44A TRP* 5.1 6.5 - - + -
45A ILE* 4.2 24.9 - - + -
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Residues in contact with GLU 26 (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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1A SER* 3.4 20.9 - - - +
22A ARG 3.1 18.5 + - - +
23A ASP* 3.4 9.2 - - - +
24A GLY 3.0 0.2 - - - -
25A LEU* 1.3 85.5 - - - +
27A ALA* 1.3 64.3 + - - +
29A THR* 3.2 15.6 - - - +
30A ARG* 3.1 42.0 + - - +
33A LYS* 5.4 3.5 - - - -
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Residues in contact with ALA 27 (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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1A SER* 5.4 0.6 + - - -
11A TRP* 4.0 2.9 - - + -
23A ASP 3.0 13.7 + - - +
24A GLY 2.9 8.5 + - - +
26A GLU* 1.3 74.8 - - - +
28A PHE* 1.3 62.1 + - - +
30A ARG* 3.3 7.7 + - - +
31A PHE 3.3 15.8 + - - -
120A PHE* 3.5 24.6 - - + -
125A ILE* 3.7 30.7 - - + +
129A LEU* 3.8 15.7 - - + -
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Residues in contact with PHE 28 (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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15A PHE* 3.7 24.9 - + - -
18A LEU* 4.0 12.6 - - + -
19A LEU* 4.2 2.5 - - + -
24A GLY 2.8 15.3 + - - +
25A LEU* 4.0 5.2 - - - +
27A ALA* 1.3 75.8 - - - +
29A THR* 1.3 59.1 + - - +
31A PHE* 3.2 6.1 + + - +
32A LEU* 2.9 37.4 + - + +
41A ILE* 3.7 17.5 - - + -
112A MET* 3.6 40.8 - - + -
116A SER* 3.6 25.4 - - - -
117A TYR* 3.7 24.0 - - - -
120A PHE* 3.6 26.9 - + + -
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Residues in contact with THR 29 (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* 2.8 31.7 + - + +
26A GLU* 3.2 31.4 - - - +
28A PHE* 1.3 73.6 - - - +
30A ARG* 1.3 51.7 + - - +
32A LEU* 3.5 7.0 - - - +
33A LYS* 2.7 63.7 + - + +
38A GLU* 4.5 3.6 - - - +
41A ILE* 3.6 27.8 - - - +
42A GLU* 4.7 3.1 + - - -
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Residues in contact with ARG 30 (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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1A SER* 5.2 9.9 + - - -
26A GLU* 3.1 34.0 + - - +
27A ALA* 3.5 7.6 - - - +
28A PHE 3.1 0.2 - - - -
29A THR* 1.3 77.0 - - + +
31A PHE* 1.3 56.4 - - - +
33A LYS* 3.1 12.2 + - + +
34A THR* 2.9 33.0 + - - -
125A ILE* 3.5 38.3 - - + +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA 3.3 4.0 + - - +
28A PHE* 3.2 10.2 + + - +
30A ARG* 1.3 78.3 - - - +
32A LEU* 1.3 60.7 + - - +
34A THR* 3.1 28.1 - - + +
35A GLU* 3.8 13.6 - - - +
116A SER* 3.4 32.5 - - - -
119A ARG* 3.5 51.4 - - + -
120A PHE* 3.8 26.9 - + + -
123A SER* 3.4 31.2 - - - -
125A ILE* 4.3 6.2 - - + +
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Residues in contact with LEU 32 (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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28A PHE* 2.9 24.5 + - + +
29A THR* 3.5 5.6 - - - +
31A PHE* 1.3 79.2 - - + +
33A LYS* 1.3 61.0 + - - +
35A GLU* 3.9 5.1 + - - +
36A PHE 3.5 2.9 + - - -
37A SER* 2.9 69.7 + - - +
38A GLU* 3.3 8.5 + - - -
40A ASN* 4.9 2.0 - - - +
41A ILE* 3.5 34.5 - - + +
112A MET* 3.6 20.0 - - + -
116A SER* 3.9 28.0 - - - +
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Residues in contact with LYS 33 (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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26A GLU* 5.4 3.6 - - - -
29A THR* 2.7 50.0 + - + +
30A ARG* 3.1 11.4 + - + +
32A LEU* 1.3 71.9 - - - +
34A THR* 1.3 60.3 + - - +
35A GLU 3.2 0.2 - - - -
36A PHE* 2.9 31.2 + - - +
38A GLU* 2.6 49.9 + - + +
42A GLU* 4.2 8.9 + - - -
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Residues in contact with THR 34 (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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30A ARG 2.9 15.0 + - - +
31A PHE* 3.1 31.9 - - + +
33A LYS* 1.3 77.5 - - - +
35A GLU* 1.3 60.7 + - + +
36A PHE* 3.8 12.0 + - - -
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Residues in contact with GLU 35 (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* 3.8 21.5 - - - +
32A LEU* 4.1 7.5 - - - +
34A THR* 1.3 80.7 - - + +
36A PHE* 1.3 74.8 + - - +
37A SER* 3.9 17.4 + - - +
119A ARG* 2.6 46.9 + - - -
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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