Contacts of the helix formed by residues 17 - 35 (chain C) in PDB entry 3EBL
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 PRO 17 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 1.3 91.8 - - + +
18C LEU* 1.3 66.9 + - - +
19C HIS 4.6 0.4 - - - +
20C THR* 3.1 11.5 + - + +
21C TRP* 3.0 18.4 + - - +
333C ASN* 3.5 29.2 - - + +
334C THR* 3.4 33.0 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL 3.5 3.8 + - - -
17C PRO* 1.3 72.0 - - - +
19C HIS* 1.3 57.1 + - - +
21C TRP* 3.2 12.2 + - + +
22C VAL* 2.9 32.8 + - + +
21D TRP* 3.9 29.2 - - + -
25D SER* 6.2 0.7 - - - -
29D LEU* 4.0 30.5 - - + -
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Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 3.2 1.8 - - - +
18C LEU* 1.3 77.6 - - - +
20C THR* 1.3 56.8 + - - +
22C VAL* 4.6 2.2 - - + -
23C LEU* 2.9 33.5 + - + +
331C LEU* 3.8 19.7 - - + +
333C ASN* 4.2 7.9 - - - +
26D ASN* 3.8 21.2 + - - -
29D LEU* 4.0 38.4 - - + +
30D SER* 3.9 18.6 + - - -
33D ILE* 4.5 15.9 - - + +
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.9 11.4 - - + -
17C PRO* 3.1 15.7 + - + +
19C HIS* 1.3 75.5 - - - +
21C TRP* 1.3 67.6 + - - +
23C LEU* 4.5 0.4 - - - +
24C ILE* 2.9 39.1 + - + +
245C PHE* 4.8 0.9 - - + -
325C THR* 4.0 20.6 - - - +
326C VAL 4.7 1.8 - - - +
328C PHE* 5.1 8.3 - - + -
331C LEU* 3.7 20.5 - - + +
333C ASN* 3.0 27.7 + - - +
334C THR* 5.2 0.7 - - - +
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Residues in contact with TRP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.8 18.5 - - + +
17C PRO 3.0 12.0 + - - +
18C LEU* 3.4 16.4 - - + +
20C THR* 1.3 78.4 - - - +
22C VAL* 1.3 62.4 + - + +
25C SER* 2.7 53.0 + - - -
245C PHE* 3.6 27.2 - + - -
18D LEU* 4.1 23.1 - - + -
21D TRP* 3.9 28.0 - + - -
22D VAL* 3.9 12.8 - - + -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 2.9 31.8 + - + +
19C HIS* 3.9 4.7 - - + +
21C TRP* 1.3 76.6 - - + +
23C LEU* 1.3 65.0 + - - +
25C SER* 4.6 1.1 - - - -
26C ASN* 3.0 23.0 + - - +
21D TRP* 3.9 28.0 - - + -
22D VAL* 3.3 29.0 - - - +
25D SER* 4.0 10.5 - - - +
26D ASN* 3.5 28.9 - - + +
29D LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C HIS* 2.9 24.8 + - + +
20C THR* 4.0 2.5 - - - +
22C VAL* 1.3 76.7 - - - +
24C ILE* 1.3 71.1 + - + +
26C ASN* 3.2 13.0 + - - +
27C PHE* 3.2 36.9 + - + -
51C ARG* 4.1 16.8 - - - +
133C ILE* 4.5 15.7 - - + -
330C LEU* 4.9 5.2 - - + -
331C LEU* 3.8 32.5 - - + -
501C MPD 3.7 16.6 - - + -
603C NO3 5.0 4.7 - - - +
26D ASN* 4.0 14.1 - - - +
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR* 2.9 30.9 + - + +
23C LEU* 1.3 90.5 - - + +
25C SER* 1.3 60.4 + - - +
27C PHE* 3.2 5.1 + - + +
28C LYS* 2.8 25.8 + - - +
245C PHE* 3.5 39.0 - - + -
326C VAL* 4.3 8.7 - - + +
327C GLY* 4.2 13.7 - - - +
330C LEU* 4.7 3.1 - - + -
331C LEU* 5.1 0.7 - - + -
401C GA4 3.8 49.8 - - + +
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 2.7 42.5 + - - -
22C VAL 3.9 2.5 - - - -
24C ILE* 1.3 76.7 - - - +
26C ASN* 1.3 63.4 + - - +
28C LYS* 4.0 10.5 - - - +
29C LEU* 2.9 33.1 + - - +
245C PHE* 3.4 18.4 - - - -
18D LEU* 6.4 0.7 - - - -
22D VAL* 4.1 21.1 - - - -
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Residues in contact with ASN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL 3.0 14.1 + - - +
23C LEU 3.3 10.3 - - - +
24C ILE 3.2 0.2 - - - -
25C SER* 1.3 76.9 - - - +
27C PHE* 1.3 57.6 + - - +
29C LEU* 4.2 2.3 - - - +
30C SER* 2.8 33.3 + - - -
501C MPD 3.4 26.1 - - + +
604C NO3 3.0 33.2 + - - -
19D HIS* 3.8 5.2 + - - -
22D VAL* 3.6 14.3 - - + +
23D LEU* 4.1 8.4 - - - +
26D ASN* 3.1 25.5 - - - +
501D MPD 3.9 10.3 - - - +
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Residues in contact with PHE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.2 47.5 + - + -
24C ILE* 3.2 9.3 + - + +
26C ASN* 1.3 77.3 - - - +
28C LYS* 1.3 66.5 + - - +
30C SER* 3.4 3.9 + - - -
31C TYR* 2.9 64.4 + + + -
50C ASP* 4.8 9.0 - - - -
51C ARG* 6.3 0.7 - - + -
127C SER* 5.0 1.8 - - - -
133C ILE* 3.7 33.4 - - + -
330C LEU* 5.7 0.2 - - + -
401C GA4 3.4 35.7 - - + -
501C MPD 4.0 29.6 - - + +
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE 2.8 20.3 + - - +
25C SER* 3.5 9.6 - - - +
27C PHE* 1.3 74.0 - - - +
29C LEU* 1.3 69.5 + - + +
31C TYR* 3.4 3.5 + - - +
32C ASN* 3.0 45.9 + - - +
35C ARG* 5.1 0.7 + - - -
242C GLY 4.8 9.1 + - - -
245C PHE* 3.6 44.6 - - + +
247C THR* 5.0 12.7 - - - +
401C GA4 4.1 18.3 - - + +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C SER* 2.9 25.9 + - - +
26C ASN 4.2 0.9 - - - +
28C LYS* 1.3 83.7 - - + +
30C SER* 1.3 65.0 - - - +
32C ASN* 3.5 29.1 + - - +
33C ILE* 4.0 10.7 + - - +
18D LEU* 4.1 30.7 - - + -
19D HIS* 3.9 50.7 + - + +
22D VAL* 4.1 12.8 - - + -
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASN 2.8 18.1 + - - -
27C PHE 3.6 3.8 - - - -
29C LEU* 1.3 75.8 - - - +
31C TYR* 1.3 66.5 + - - +
33C ILE* 3.1 27.0 + - - +
34C LEU* 3.5 10.9 - - - +
49C LEU* 5.3 6.4 - - - +
501C MPD 3.6 20.7 - - - +
604C NO3 2.5 39.4 + - - -
19D HIS* 4.1 3.5 - - - -
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Residues in contact with TYR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 2.9 57.3 + + - +
28C LYS 3.9 3.1 - - - +
30C SER* 1.3 77.8 - - - +
32C ASN* 1.3 67.1 + - - +
34C LEU* 3.0 25.9 + - + +
35C ARG* 3.3 33.3 + - - +
50C ASP* 4.8 3.5 + - - -
122C GLY* 5.5 0.7 - - - -
126C HIS* 3.4 57.3 - + + +
127C SER* 3.9 9.4 + - - -
401C GA4 4.0 35.8 + - + +
501C MPD 4.0 14.1 - - + -
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS* 3.0 35.0 + - - +
29C LEU* 3.5 30.9 + - - +
31C TYR* 1.3 78.5 - - - +
33C ILE* 1.3 63.9 + - + +
35C ARG* 3.0 35.6 + - - +
601C NO3 4.5 5.9 + - - -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU 4.0 11.4 - - - +
30C SER* 3.1 18.2 + - - +
31C TYR 3.1 0.6 - - - -
32C ASN* 1.3 81.5 - - + +
34C LEU* 1.3 65.6 + - + +
35C ARG 3.5 3.2 - - - +
36C ARG* 5.7 0.3 - - - +
42C GLU* 3.8 11.8 - - - +
45C LEU* 3.8 28.7 - - + -
49C LEU* 5.2 6.3 - - + -
19D HIS* 6.3 2.0 - - + +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER* 3.5 13.5 - - - +
31C TYR* 3.0 34.4 + - + +
33C ILE* 1.3 81.5 - - + +
35C ARG* 1.3 61.6 + - - +
36C ARG 3.4 2.4 + - - -
41C PHE* 3.3 29.2 - - + -
42C GLU* 2.9 37.1 + - + +
45C LEU* 3.6 37.7 - - + -
46C GLY* 3.7 28.5 - - - +
49C LEU* 4.5 9.4 - - + -
126C HIS* 4.2 2.0 - - + +
501C MPD 6.1 0.9 - - + -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS 5.2 0.2 + - - -
31C TYR* 3.3 21.0 + - - +
32C ASN* 3.0 40.1 + - - +
33C ILE 3.5 3.6 - - - +
34C LEU* 1.3 76.7 - - - +
36C ARG* 1.3 60.0 + - - +
37C ALA 4.0 0.7 + - - -
41C PHE* 4.4 4.0 - - + -
247C THR* 5.4 1.2 + - - -
250C ASP* 3.6 18.2 + - - +
253C TRP* 3.6 43.1 - - + +
254C TYR* 2.9 41.2 + - + +
401C GA4 3.7 17.2 - - - +
601C NO3 2.6 39.3 + - - +
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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
------------------------------------------------------------
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