Contacts of the helix formed by residues 15 - 38 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G SER* 1.3 71.9 + - - +
16G GLN* 1.3 59.9 + - - +
18G ARG* 3.3 35.2 + - - +
19G LEU* 3.0 55.8 + - + +
17H ARG* 2.9 30.5 + - - -
21H LEU* 5.0 7.9 - - + -
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Residues in contact with GLN 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G SER* 4.0 9.4 + - - +
15G TYR* 1.3 77.4 - - + +
17G GLN* 1.3 56.4 + - + +
19G LEU* 3.3 8.6 + - - +
20G LYS* 2.9 47.4 + - - +
55G PHE* 4.0 31.0 - - + -
21H LEU* 5.1 11.2 - - + +
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Residues in contact with GLN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER* 2.6 43.7 + - - +
16G GLN* 1.3 77.4 - - + +
18G ARG* 1.3 57.6 + - - +
20G LYS* 3.3 24.3 + - + +
21G ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER 2.8 18.8 + - - +
15G TYR* 3.3 46.7 + - - +
17G GLN* 1.3 74.0 - - - +
19G LEU* 1.3 82.5 + - - +
21G ALA* 3.3 6.1 + - - +
22G ALA* 3.1 21.8 + - - +
17H ARG* 4.9 6.7 - - - +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G TYR* 3.0 32.0 + - + +
16G GLN* 3.7 4.5 - - - +
18G ARG* 1.3 94.2 - - - +
20G LYS* 1.3 59.5 + - - +
22G ALA* 3.3 9.1 + - + +
23G VAL* 2.9 36.6 + - - +
55G PHE* 4.6 2.5 - - + -
14H LEU* 5.0 1.7 - - + +
17H ARG* 4.3 28.9 - - + +
18H LEU* 4.5 14.6 - - + -
21H LEU* 3.2 45.8 - - + -
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Residues in contact with LYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLN* 2.9 34.1 + - - +
17G GLN* 3.4 25.7 - - + +
19G LEU* 1.3 77.0 - - - +
21G ALA* 1.3 55.2 + - - +
23G VAL* 3.7 7.2 - - - +
24G HIS* 2.9 28.2 + - - +
51G SER* 5.0 4.5 - - - +
52G GLU* 6.0 9.0 - - + -
55G PHE* 3.9 45.1 - - + -
56G ARG* 5.6 9.5 - - - +
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLN 2.9 15.9 + - - +
18G ARG* 3.3 6.3 + - - +
19G LEU 3.3 0.2 - - - -
20G LYS* 1.3 75.5 - - - +
22G ALA* 1.3 61.0 + - - +
24G HIS* 3.3 12.2 - - + +
25G TYR* 3.3 19.2 + - - +
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Residues in contact with ALA 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG 3.1 13.3 + - - +
19G LEU* 3.7 13.9 - - + +
21G ALA* 1.3 73.9 - - - +
23G VAL* 1.3 59.3 + - - +
25G TYR* 3.2 24.3 - - - +
26G THR* 3.5 9.5 + - - -
11H ARG* 3.8 6.1 + - - +
14H LEU* 4.0 9.9 - - + -
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Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 2.9 25.7 + - + +
20G LYS* 3.7 7.2 - - - +
22G ALA* 1.3 69.0 - - - +
24G HIS* 1.3 55.4 + - - +
25G TYR 3.2 0.2 - - - -
26G THR* 3.0 3.6 + - - -
27G VAL* 2.9 48.0 + - + +
51G SER* 4.0 18.6 - - - +
54G THR* 4.3 15.0 - - + -
55G PHE* 5.1 7.4 - - + +
10H PHE* 5.7 0.7 - - + -
14H LEU* 3.5 16.2 - - + -
18H LEU* 3.4 40.8 - - + -
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Residues in contact with HIS 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LYS 2.9 18.6 + - - +
21G ALA* 3.3 13.9 - - + +
23G VAL* 1.3 72.6 - - - +
25G TYR* 1.3 66.8 + - - +
28G GLY* 2.9 22.9 + - - -
44G LYS* 5.5 2.5 - - + +
47G ILE* 4.0 15.3 - - + +
48G ALA* 3.8 33.4 - - + -
51G SER* 2.9 30.6 + - - +
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Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA 3.3 8.8 + - - +
22G ALA* 3.2 13.2 - - - +
24G HIS* 1.3 78.6 - - - +
26G THR* 1.3 76.6 + - - +
28G GLY* 3.7 1.2 - - - -
29G CYS* 3.1 44.7 + - - -
11H ARG* 2.9 34.6 - - - -
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Residues in contact with THR 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ALA 3.5 1.9 + - - -
23G VAL 3.0 3.6 + - - -
25G TYR* 1.3 75.1 - - - +
27G VAL* 1.3 62.5 + - - +
29G CYS* 3.1 23.8 - - - +
30G LEU* 3.4 11.4 + - - +
9H GLY 3.8 4.3 - - - +
10H PHE* 3.5 40.4 - - + +
11H ARG* 2.2 53.9 + - - +
14H LEU* 3.2 17.9 - - + +
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G VAL* 2.9 27.0 + - + +
26G THR* 1.3 74.6 - - - +
28G GLY* 1.3 61.4 + - - +
30G LEU 3.4 1.2 + - - -
31G CYS* 3.1 33.0 + - - -
47G ILE 4.0 4.9 - - - +
50G ILE* 3.6 33.2 - - + -
51G SER* 3.2 26.7 - - - +
54G THR* 3.9 20.9 - - - +
10H PHE* 4.5 6.5 - - + -
46H VAL* 3.9 21.5 - - + +
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Residues in contact with GLY 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G HIS 2.9 16.7 + - - -
25G TYR 3.7 1.8 - - - -
27G VAL* 1.3 76.2 - - - +
29G CYS* 1.3 55.7 + - - +
31G CYS* 3.9 2.0 - - - +
32G GLU* 2.9 33.6 + - - +
47G ILE* 3.5 26.5 - - - +
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Residues in contact with CYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G TYR* 3.1 47.8 + - - -
26G THR* 3.1 23.1 - - + +
28G GLY* 1.3 71.7 - - - +
30G LEU* 1.3 67.9 + - + +
32G GLU* 3.2 6.8 + - - +
33G GLU* 2.9 35.6 + - - +
9H GLY* 4.9 10.5 - - - -
11H ARG* 4.9 0.7 - - - -
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G THR 3.7 11.4 - - - +
27G VAL 3.4 1.8 + - - +
29G CYS* 1.3 78.8 - - - +
31G CYS* 1.3 58.0 + - - +
33G GLU* 3.3 12.6 + - - +
34G VAL* 3.0 34.5 + - - +
8H SER 4.3 6.3 - - - +
9H GLY* 3.8 29.2 - - - -
10H PHE* 3.5 18.6 - - + +
43H LYS* 3.5 38.4 - - + +
46H VAL* 3.4 35.7 - - + -
47H VAL* 4.6 10.8 - - + +
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Residues in contact with CYS 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G VAL* 3.1 30.2 + - - +
28G GLY 3.9 0.4 - - - +
30G LEU* 1.3 76.3 - - - +
32G GLU* 1.3 54.6 + - - +
34G VAL* 3.4 5.4 + - - +
35G ALA* 3.1 22.7 + - - +
42G PHE* 3.5 32.6 - - + -
47G ILE* 3.1 37.0 - - + -
50G ILE* 4.1 14.1 - - - -
46H VAL* 3.7 17.7 - - - -
50H ALA* 4.7 0.7 - - - -
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Residues in contact with GLU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G GLY 2.9 20.2 + - - +
29G CYS* 3.2 6.3 + - - +
31G CYS* 1.3 72.4 - - - +
33G GLU* 1.3 62.2 + - - +
35G ALA* 3.0 36.5 + - - +
36G LEU* 3.2 24.4 + - - +
44G LYS* 5.5 9.5 + - - +
47G ILE* 4.8 2.4 - - + +
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Residues in contact with GLU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G CYS* 2.9 22.6 + - - +
30G LEU* 3.3 13.0 + - - +
32G GLU* 1.3 73.7 - - + +
34G VAL* 1.3 58.8 + - + +
36G LEU* 3.2 39.5 - - + +
37G ASP* 3.7 8.1 + - - +
8H SER* 2.5 40.8 + - - +
9H GLY* 4.2 4.7 + - - -
43H LYS* 5.8 0.2 + - - -
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU 3.0 21.1 + - - +
31G CYS 3.7 7.4 - - - +
32G GLU 3.2 0.4 - - - -
33G GLU* 1.3 73.9 - - + +
35G ALA* 1.3 63.3 + - - +
36G LEU 3.5 0.2 + - - -
37G ASP* 3.7 14.8 + - + +
38G LYS* 3.9 15.3 + - + +
40G MET* 4.1 5.6 - - + +
42G PHE* 3.7 22.7 - - + -
47H VAL* 4.1 26.7 - - + +
50H ALA* 4.4 15.0 - - + -
51H VAL* 4.9 12.1 - - + -
54H VAL* 4.7 9.2 - - + -
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G CYS 3.1 13.2 + - - +
32G GLU* 3.0 31.7 + - - +
34G VAL* 1.3 77.6 - - - +
36G LEU* 1.3 56.8 + - + +
39G ALA* 3.8 5.4 - - - -
40G MET 3.3 34.8 + - - +
41G GLN* 4.5 12.3 - - + -
42G PHE* 4.6 4.4 - - + +
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Residues in contact with LEU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G GLU* 3.2 35.0 + - - +
33G GLU* 3.2 27.1 - - + +
34G VAL 3.3 0.2 - - - -
35G ALA* 1.3 77.0 - - + +
37G ASP* 1.3 63.7 + - + +
38G LYS 3.8 0.2 + - - -
39G ALA* 3.9 6.9 + - - +
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Residues in contact with ASP 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G GLU 3.7 10.2 + - - +
34G VAL* 3.7 9.0 + - - +
35G ALA 3.7 0.6 - - - -
36G LEU* 1.3 79.7 - - + +
38G LYS* 1.3 79.2 + - - +
39G ALA 3.4 1.2 + - - -
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Residues in contact with LYS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL* 3.9 11.9 + - + +
37G ASP* 1.3 94.9 + - - +
39G ALA* 1.3 69.5 + - - +
40G MET* 3.1 21.3 + - + +
54H VAL* 5.5 5.4 - - + -
58H GLN* 5.2 10.2 + - - +
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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