Contacts of the helix formed by residues 15 - 38 (chain J) in PDB entry 4NE1
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 TYR 15 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J SER* 1.3 74.7 + - - +
16J GLN* 1.3 67.9 + - + +
18J ARG* 3.4 45.0 + - - +
19J LEU* 3.6 35.9 + - + +
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Residues in contact with GLN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J SER* 3.3 9.7 + - - +
15J TYR* 1.3 84.4 - - + +
17J GLN* 1.3 62.4 + - + +
19J LEU* 3.5 9.2 + - - +
20J LYS* 3.3 42.6 + - - +
55J PHE* 4.1 12.1 - - + -
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Residues in contact with GLN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J SER* 3.0 41.7 + - - +
15J TYR 3.3 0.2 - - - -
16J GLN* 1.3 74.8 - - + +
18J ARG* 1.3 66.1 + - - +
20J LYS* 3.3 25.7 + - + +
21J ALA* 3.5 10.2 + - - +
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Residues in contact with ARG 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J SER 3.5 7.3 + - - +
15J TYR* 3.4 44.2 + - - +
16J GLN 3.4 0.2 - - - -
17J GLN* 1.3 78.9 - - - +
19J LEU* 1.3 85.2 + - - +
21J ALA* 3.4 19.7 + - - +
22J ALA* 3.7 6.1 + - - +
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Residues in contact with LEU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J TYR* 3.6 34.1 - - + +
16J GLN* 3.5 9.7 + - - +
17J GLN 3.2 0.6 - - - -
18J ARG* 1.3 102.1 - - - +
20J LYS* 1.3 57.5 + - - +
21J ALA 3.2 1.8 - - - -
22J ALA* 3.4 10.7 + - + +
23J VAL* 3.0 33.9 + - + +
55J PHE* 4.5 9.9 - - + -
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Residues in contact with LYS 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLN* 3.3 37.3 + - - +
17J GLN* 3.3 17.3 + - + +
19J LEU* 1.3 77.0 - - - +
21J ALA* 1.3 55.6 + - - +
23J VAL* 3.3 11.2 + - - +
24J HIS* 3.0 26.7 + - - +
51J SER* 4.7 3.8 - - - +
52J GLU* 6.5 0.9 - - - -
55J PHE* 3.6 45.8 - - + -
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J GLN 3.5 7.1 + - - +
18J ARG* 3.4 14.0 + - - +
19J LEU 3.2 0.4 - - - -
20J LYS* 1.3 74.6 - - - +
22J ALA* 1.3 62.8 + - - +
23J VAL 3.2 0.2 - - - -
24J HIS* 3.4 8.1 + - - +
25J TYR* 3.2 20.1 + - - +
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Residues in contact with ALA 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ARG 3.7 6.2 + - - +
19J LEU* 3.4 16.4 + - + +
21J ALA* 1.3 77.1 - - - +
23J VAL* 1.3 62.6 + - - +
25J TYR* 3.2 21.7 - - + +
26J THR* 3.3 13.2 + - - -
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Residues in contact with VAL 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J LEU* 3.0 20.3 + - + +
20J LYS* 3.4 10.3 - - + +
21J ALA 3.2 0.2 - - - -
22J ALA* 1.3 74.3 - - - +
24J HIS* 1.3 61.0 + - - +
26J THR* 3.2 6.2 + - - +
27J VAL* 2.9 31.0 + - + +
51J SER* 3.8 31.0 - - - +
54J THR* 4.1 18.6 - - + -
55J PHE* 3.9 23.8 - - + -
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Residues in contact with HIS 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LYS 3.0 13.6 + - - +
21J ALA* 3.6 12.1 - - - +
22J ALA 3.3 0.2 - - - -
23J VAL* 1.3 74.4 - - - +
25J TYR* 1.3 53.5 + - - +
27J VAL* 3.7 1.0 - - - +
28J GLY* 2.8 32.1 + - - -
44J LYS* 4.6 15.4 + - - +
47J ILE* 3.6 17.5 + - + +
48J ALA* 3.4 39.3 - - + +
51J SER* 3.1 30.3 + - - +
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Residues in contact with TYR 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ALA 3.2 12.3 + - - +
22J ALA* 3.2 15.3 - - + +
24J HIS* 1.3 76.9 - - - +
26J THR* 1.3 69.5 + - - +
28J GLY* 3.1 5.2 + - - -
29J CYS* 3.0 39.5 + - - +
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Residues in contact with THR 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ALA 3.3 9.9 + - - -
23J VAL* 3.2 8.0 + - - -
25J TYR* 1.3 83.8 - - - +
27J VAL* 1.3 67.9 + - + +
28J GLY 3.2 1.1 - - - -
29J CYS* 3.0 29.8 - - + +
30J LEU* 3.3 20.0 + - + +
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Residues in contact with VAL 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J VAL* 2.9 22.6 + - + +
24J HIS 3.7 0.4 - - - +
26J THR* 1.3 79.7 - - + +
28J GLY* 1.3 61.6 + - - +
30J LEU* 3.6 5.8 + - - +
31J CYS* 3.1 27.7 + - - -
47J ILE* 3.6 12.1 - - + +
50J ILE* 3.4 45.5 - - + -
51J SER* 3.3 32.3 - - - +
54J THR* 4.0 10.5 - - + +
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Residues in contact with GLY 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J HIS 2.8 18.7 + - - -
25J TYR 3.1 6.9 + - - -
27J VAL* 1.3 75.5 - - - +
29J CYS* 1.3 62.6 + - - +
31J CYS* 3.7 3.8 + - - +
32J GLU* 3.6 22.5 + - - +
47J ILE* 3.9 17.4 - - - +
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Residues in contact with CYS 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J TYR* 3.0 33.2 + - - -
26J THR* 3.0 23.3 - - + +
28J GLY* 1.3 77.4 - - - +
30J LEU* 1.3 71.2 + - + +
32J GLU* 3.4 16.0 + - - +
33J GLU* 3.9 7.6 + - - +
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Residues in contact with LEU 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J THR* 3.3 24.0 + - + +
27J VAL* 4.5 5.2 - - - +
29J CYS* 1.3 80.3 - - + +
31J CYS* 1.3 64.6 + - - +
32J GLU 3.1 3.4 + - - -
33J GLU* 3.2 33.0 + - - +
34J VAL* 3.5 16.0 + - + +
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Residues in contact with CYS 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J VAL* 3.1 25.5 + - - +
28J GLY 4.0 4.0 - - - +
29J CYS 3.4 0.2 - - - -
30J LEU* 1.3 77.4 - - - +
32J GLU* 1.3 59.1 + - + +
34J VAL* 3.4 12.4 - - - +
35J ALA* 3.1 21.9 + - - +
42J PHE* 3.5 19.5 - - + -
47J ILE* 3.7 28.7 - - + -
50J ILE* 3.3 34.5 - - - -
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLY 3.6 10.9 + - - +
29J CYS* 3.4 12.0 + - - +
30J LEU 3.1 0.6 - - - -
31J CYS* 1.3 76.6 - - + +
33J GLU* 1.3 63.9 + - - +
34J VAL 3.2 0.2 - - - -
35J ALA* 3.1 25.5 + - - +
36J LEU* 3.3 12.3 + - - +
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Residues in contact with GLU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J CYS 3.9 7.1 + - - +
30J LEU* 3.2 29.1 + - - +
32J GLU* 1.3 76.8 - - - +
34J VAL* 1.3 56.0 + - + +
36J LEU* 3.4 6.9 + - - +
37J ASP* 3.2 26.0 + - - +
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Residues in contact with VAL 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J LEU* 3.5 15.9 - - + +
31J CYS* 3.4 12.6 - - - +
32J GLU 3.2 0.4 - - - -
33J GLU* 1.3 74.5 - - + +
35J ALA* 1.3 62.1 + - - +
37J ASP* 3.4 15.2 + - - +
38J LYS* 3.3 30.1 + - + +
42J PHE* 3.5 21.8 - - + -
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J CYS 3.1 12.8 + - - +
32J GLU* 3.1 29.2 + - - +
34J VAL* 1.3 76.3 - - - +
36J LEU* 1.3 59.2 + - - +
39J ALA* 3.3 4.3 + - - -
40J MET 3.2 42.5 + - - +
41J GLN* 5.7 0.7 - - - -
42J PHE* 4.0 12.5 - - + -
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Residues in contact with LEU 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J GLU 3.3 9.9 + - - +
33J GLU* 3.4 7.4 + - - +
34J VAL 3.2 0.2 - - - -
35J ALA* 1.3 77.0 - - - +
37J ASP* 1.3 65.6 + - - +
38J LYS 3.4 0.7 - - - -
39J ALA* 3.6 12.9 + - - +
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Residues in contact with ASP 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J GLU 3.2 14.9 + - - +
34J VAL* 3.5 18.1 - - - +
36J LEU* 1.3 77.8 - - - +
38J LYS* 1.3 78.3 + - - +
39J ALA* 3.9 0.5 + - - +
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Residues in contact with LYS 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J VAL* 3.3 18.6 + - + +
37J ASP* 1.3 96.3 - - - +
39J ALA* 1.3 69.0 + - - +
40J MET* 3.4 18.4 + - + +
42J PHE* 6.0 4.0 - - + -
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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
------------------------------------------------------------
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