Contacts of the helix formed by residues 15 - 39 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F T 5.6 2.1 + - - -
14I SER* 1.3 77.6 + - - +
16I GLN* 1.3 69.6 + - + +
18I ARG* 3.0 57.2 + - - +
19I LEU* 3.2 31.4 + - + +
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Residues in contact with GLN 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I SER* 3.0 16.1 + - - +
15I TYR* 1.3 86.7 - - + +
17I GLN* 1.3 55.1 + - - +
18I ARG 3.1 1.3 - - - -
19I LEU* 3.1 9.6 + - + +
20I LYS* 2.8 56.9 + - + +
55I PHE* 5.2 7.9 - - + -
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Residues in contact with GLN 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I SER* 2.2 43.7 + - - +
16I GLN* 1.3 75.1 - - - +
18I ARG* 1.3 61.3 + - - +
20I LYS* 3.7 21.7 - - + +
21I ALA* 3.2 24.6 + - - +
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Residues in contact with ARG 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I SER 3.8 3.4 - - - +
15I TYR* 3.0 63.8 + - - +
17I GLN* 1.3 82.2 - - + +
19I LEU* 1.3 80.5 + - - +
21I ALA* 3.5 4.0 + - - +
22I ALA* 3.4 18.5 + - - +
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I TYR* 3.2 36.9 + - + +
16I GLN* 3.1 12.1 + - + +
18I ARG* 1.3 93.8 - - - +
20I LYS* 1.3 65.2 + - - +
22I ALA* 3.3 24.3 - - + +
23I VAL* 3.4 14.0 + - - +
55I PHE* 5.7 4.0 - - + -
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Residues in contact with LYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I SER* 6.3 0.2 - - - -
16I GLN* 2.8 35.9 + - - +
17I GLN* 3.7 27.5 - - + +
19I LEU* 1.3 68.9 - - - +
21I ALA* 1.3 64.7 + - - +
23I VAL* 3.2 24.3 + - - +
24I HIS* 3.4 5.7 + - - +
51I SER* 5.3 2.4 - - - -
55I PHE* 3.8 48.1 - - + -
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Residues in contact with ALA 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLN 3.2 16.4 + - - +
18I ARG* 3.5 4.9 + - - +
20I LYS* 1.3 79.9 - - - +
22I ALA* 1.3 61.8 + - - +
24I HIS* 3.2 19.4 + - + +
25I TYR* 3.3 11.8 + - - +
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Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG 3.4 10.8 + - - +
19I LEU* 3.3 22.0 + - + +
20I LYS 3.1 0.6 - - - -
21I ALA* 1.3 75.0 - - - +
23I VAL* 1.3 66.9 + - - +
25I TYR* 3.3 20.8 + - - +
26I THR* 3.7 9.4 + - - -
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU 3.4 15.7 - - - +
20I LYS* 3.2 13.0 + - - +
22I ALA* 1.3 78.6 - - + +
24I HIS* 1.3 62.1 + - - +
25I TYR 3.2 0.9 + - - -
26I THR* 3.2 4.1 + - - -
27I VAL* 3.2 37.7 + - + +
51I SER* 4.2 21.3 - - - +
54I THR* 4.6 15.0 - - + -
55I PHE* 5.1 12.8 - - + +
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Residues in contact with HIS 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LYS 3.4 5.1 + - - +
21I ALA* 3.2 17.1 + - + +
23I VAL* 1.3 78.5 - - - +
25I TYR* 1.3 60.3 + - - +
27I VAL* 3.4 0.7 + - - +
28I GLY* 2.8 28.1 + - - -
44I LYS* 4.7 18.4 + - + +
47I ILE* 3.4 30.8 - - + +
48I ALA* 3.7 20.9 - - + -
51I SER* 3.0 34.9 + - - +
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Residues in contact with TYR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E A 4.8 14.4 + - - -
21I ALA 3.3 7.6 + - - +
22I ALA* 3.3 13.6 + - - +
23I VAL 3.2 0.4 + - - -
24I HIS* 1.3 84.8 - - - +
26I THR* 1.3 90.2 + - + +
28I GLY* 3.2 8.7 + - - -
29I CYS* 3.2 30.0 + - - +
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Residues in contact with THR 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ALA 3.7 7.3 + - - -
23I VAL* 3.2 5.8 + - - -
25I TYR* 1.3 91.4 - - + +
27I VAL* 1.3 67.2 + - - +
29I CYS* 3.2 7.6 + - + -
30I LEU* 3.0 50.8 + - + +
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Residues in contact with VAL 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I VAL* 3.2 27.4 + - + +
24I HIS 3.6 2.5 - - - +
26I THR* 1.3 76.5 - - - +
28I GLY* 1.3 62.8 + - - +
30I LEU* 4.8 2.9 - - - +
31I CYS* 3.1 39.2 + - - +
47I ILE* 4.1 7.9 - - + +
50I ILE* 3.9 29.2 - - + -
51I SER* 3.6 28.3 - - - +
54I THR* 4.9 7.9 - - + +
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Residues in contact with GLY 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I HIS* 2.8 16.8 + - - -
25I TYR* 3.2 6.0 + - - -
27I VAL* 1.3 77.2 - - - +
29I CYS* 1.3 60.5 + - - +
31I CYS* 4.2 1.7 - - - +
32I GLU* 3.3 26.0 + - - +
47I ILE* 4.1 20.7 - - - +
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Residues in contact with CYS 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR* 3.2 36.4 + - - +
26I THR* 3.2 13.2 + - + +
28I GLY* 1.3 76.2 - - - +
30I LEU* 1.3 68.2 + - + +
32I GLU* 3.0 26.7 + - - +
33I GLU* 3.3 7.5 + - - +
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Residues in contact with LEU 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I THR* 3.0 39.7 + - + +
27I VAL* 4.6 2.5 - - - +
29I CYS* 1.3 76.1 - - + +
31I CYS* 1.3 61.0 + - - +
33I GLU* 3.1 45.4 - - + +
34I VAL* 3.6 9.2 + - - +
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Residues in contact with CYS 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I VAL* 3.1 26.4 + - - +
28I GLY 4.2 2.9 - - - +
30I LEU* 1.3 74.8 - - - +
32I GLU* 1.3 61.7 + - - +
34I VAL* 3.3 9.7 + - - +
35I ALA* 3.0 27.2 + - - +
42I PHE* 4.9 15.4 - - + -
47I ILE* 4.3 20.0 - - + -
50I ILE* 3.5 33.0 - - - -
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Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I GLY 3.3 14.5 + - - +
29I CYS* 3.0 16.6 + - - +
31I CYS* 1.3 79.0 - - - +
33I GLU* 1.3 61.2 + - - +
35I ALA* 3.3 18.2 + - - +
36I LEU* 3.0 46.1 + - + +
42I PHE* 5.6 4.0 + - - +
47I ILE* 5.4 7.3 - - - +
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Residues in contact with GLU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I CYS 3.3 3.7 + - - +
30I LEU* 3.1 40.5 + - + +
32I GLU* 1.3 76.8 - - - +
34I VAL* 1.3 57.5 + - + +
36I LEU* 3.4 10.9 - - - +
37I ASP* 3.2 25.3 + - - +
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Residues in contact with VAL 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LEU 3.6 10.0 + - - +
31I CYS* 3.3 11.6 + - - +
33I GLU* 1.3 73.5 - - + +
35I ALA* 1.3 65.6 + - - +
36I LEU 3.2 1.8 - - - -
37I ASP* 3.3 15.9 + - - +
38I LYS* 3.2 33.6 + - + +
42I PHE* 5.0 15.6 - - + -
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I CYS 3.0 16.4 + - - +
32I GLU* 3.3 25.5 + - - +
34I VAL* 1.3 76.5 - - - +
36I LEU* 1.3 62.6 + - - +
39I ALA* 3.6 15.6 + - - -
40I MET 3.5 27.3 + - - +
41I GLN* 4.6 7.6 - - + -
42I PHE* 4.4 13.8 - - + +
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Residues in contact with LEU 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I GLU* 3.0 37.3 + - + +
33I GLU* 3.4 14.1 - - - +
35I ALA* 1.3 77.8 - - - +
37I ASP* 1.3 62.2 + - - +
38I LYS 3.3 0.7 + - - -
39I ALA* 3.8 5.9 + - - +
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Residues in contact with ASP 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I GLU 3.2 14.5 + - - +
34I VAL* 3.3 14.8 + - - +
36I LEU* 1.3 78.8 - - - +
38I LYS* 1.3 73.4 + - - +
39I ALA 3.9 0.3 + - - -
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Residues in contact with LYS 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I VAL* 3.2 23.4 + - + +
36I LEU 3.3 0.4 - - - -
37I ASP* 1.3 93.3 - - - +
39I ALA* 1.3 69.6 + - - +
40I MET* 3.4 15.9 + - + +
42I PHE* 6.3 1.6 - - + -
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Residues in contact with ALA 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I ALA 3.6 7.2 + - - -
36I LEU 3.8 5.0 + - - -
37I ASP 3.6 2.4 + - - -
38I LYS* 1.3 81.3 - - - +
40I MET* 1.3 73.3 + - - +
41I GLN* 4.7 4.7 + - - -
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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
------------------------------------------------------------
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