Contacts of the helix formed by residues 19 - 38 (chain F) in PDB entry 3NBN
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 VAL 19 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940E SER* 6.1 0.9 - - - +
1973E ASP 6.1 0.7 - - - +
16F HIS* 3.9 27.4 - - + +
18F ALA* 1.3 78.6 - - + +
20F MET* 1.3 62.0 + - - +
21F GLU 3.2 0.4 - - - -
22F ARG* 2.9 16.1 + - + +
23F LEU* 2.7 37.4 + - + +
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Residues in contact with MET 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F HIS* 3.1 36.3 - - + +
17F SER* 3.3 22.8 - - - +
18F ALA 3.4 0.6 - - - -
19F VAL* 1.3 83.1 - - - +
21F GLU* 1.3 58.9 + - - +
23F LEU* 3.3 22.5 + - + +
24F ARG* 2.8 63.3 + - + +
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Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER* 3.1 24.4 + - - +
18F ALA 4.4 0.9 - - - +
19F VAL 3.2 0.4 - - - -
20F MET* 1.3 78.9 - - - +
22F ARG* 1.3 62.0 + - - +
24F ARG* 2.7 41.9 + - - +
25F ARG* 3.3 50.1 + - - +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1973E ASP* 2.5 50.9 + - - +
1975E GLN* 3.5 28.9 + - - +
2009E GLU* 3.2 56.7 + - + +
2011E MET* 4.0 6.1 - - - +
18F ALA 3.6 11.9 + - - +
19F VAL* 2.9 18.5 + - - +
21F GLU* 1.3 78.6 - - - +
23F LEU* 1.3 57.4 + - - +
25F ARG* 3.2 12.8 + - - +
26F ARG* 3.0 26.2 + - - +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D VAL* 4.4 27.1 - - + -
19F VAL* 2.7 19.3 + - + +
20F MET* 3.9 25.8 - - + +
22F ARG* 1.3 68.1 - - - +
24F ARG* 1.3 67.5 - - + +
25F ARG 3.1 1.1 - - - -
26F ARG* 3.1 33.4 + - - +
27F ILE* 3.0 49.2 + - + +
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Residues in contact with ARG 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER* 5.1 7.7 - - - +
20F MET* 2.8 48.1 + - + +
21F GLU* 2.7 56.5 + - - +
23F LEU* 1.3 75.0 - - + +
25F ARG* 1.3 62.8 + - - +
27F ILE* 4.2 5.6 - - - +
28F GLU* 3.1 24.8 + - - +
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009E GLU* 3.3 35.8 + - + +
21F GLU* 3.3 52.8 + - - +
22F ARG* 3.2 9.5 + - - +
23F LEU 3.1 0.8 - - - -
24F ARG* 1.3 78.6 - - - +
26F ARG* 1.3 65.4 + - - +
28F GLU* 3.5 8.2 - - - +
29F LEU* 3.3 16.6 + - - +
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ASN* 6.4 0.2 - - - +
354D VAL* 5.3 6.7 - - - +
356D MET* 4.9 14.5 - - - -
1971E SER 4.9 6.2 + - - -
1972E ALA* 5.0 2.8 + - - +
1973E ASP* 2.8 56.6 + - - +
2006E LEU* 3.9 10.5 + - - +
2007E ALA 3.4 26.9 - - - +
2008E VAL* 4.0 6.1 - - - +
2009E GLU* 6.2 5.6 - - + +
22F ARG 3.0 13.1 + - - +
23F LEU* 3.1 36.0 + - - +
25F ARG* 1.3 73.0 - - - +
27F ILE* 1.3 63.0 + - + +
29F LEU* 2.5 37.5 + - - +
30F CYS* 3.3 11.5 + - - -
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Residues in contact with ILE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D VAL* 6.1 1.6 - - + -
356D MET* 4.8 20.6 - - - -
380D MET* 5.0 9.4 - - + +
390D VAL* 5.8 4.9 - - + -
23F LEU* 3.0 38.4 + - + +
24F ARG* 4.2 4.7 - - - +
26F ARG* 1.3 84.0 - - + +
28F GLU* 1.3 63.1 + - - +
29F LEU 3.1 0.3 + - - -
30F CYS* 3.2 11.4 + - - +
31F ARG* 2.8 62.3 + - - +
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ARG 3.1 21.4 + - - +
25F ARG* 3.5 9.4 - - - +
27F ILE* 1.3 77.9 - - - +
29F LEU* 1.3 54.3 + - + +
31F ARG* 3.9 14.7 + - - +
32F ARG* 2.6 52.7 + - + +
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Residues in contact with LEU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D ARG* 5.2 5.4 - - - +
2007E ALA* 4.1 25.8 - - + +
2041E ASN* 6.4 1.1 - - - -
25F ARG* 3.3 7.4 + - + +
26F ARG* 2.5 24.3 + - - +
28F GLU* 1.3 74.2 - - + +
30F CYS* 1.3 50.9 + - - +
32F ARG* 3.4 8.4 + - + +
33F HIS* 2.7 37.9 + - + +
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Residues in contact with CYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D MET* 6.1 0.7 - - - -
380D MET* 3.5 30.5 - - + +
381D TYR 5.1 0.3 - - - +
382D ARG* 4.5 20.3 - - - +
388D LEU* 4.6 15.0 - - + -
2006E LEU 5.3 5.2 - - - -
2007E ALA* 5.4 3.1 - - - -
26F ARG* 3.5 26.0 - - - -
27F ILE* 3.5 12.3 - - - +
29F LEU* 1.3 72.8 - - - +
31F ARG* 1.3 58.3 + - - +
33F HIS* 3.0 6.7 + - - +
34F HIS* 2.6 37.4 + - - +
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Residues in contact with ARG 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D GLU* 3.2 40.5 + - - +
380D MET* 3.8 14.3 - - + +
390D VAL* 5.9 0.8 - - - +
27F ILE* 2.8 47.1 + - - +
28F GLU* 3.4 17.7 + - - +
30F CYS* 1.3 74.8 - - - +
32F ARG* 1.3 64.9 + - - +
34F HIS* 3.7 2.7 - - - +
35F SER* 3.0 20.9 + - - -
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Residues in contact with ARG 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLU* 2.6 40.1 + - + +
29F LEU* 3.7 10.8 - - + +
31F ARG* 1.3 72.2 - - - +
33F HIS* 1.3 65.4 + - - +
35F SER* 3.1 26.0 + - - -
36F THR* 2.9 33.4 + - - +
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Residues in contact with HIS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D TYR* 3.4 22.4 - - - -
382D ARG* 3.1 46.0 + - - +
2038E ALA 5.1 1.5 + - - -
2039E VAL* 3.8 22.0 + - - -
2040E ASN* 4.2 15.2 + - + +
2074E SER* 5.5 2.5 - - - -
29F LEU* 2.7 23.6 + - + +
30F CYS 3.4 3.4 - - - +
32F ARG* 1.3 70.4 - - - +
34F HIS* 1.3 58.8 + - - +
36F THR* 2.6 35.4 + - - -
37F CYS* 3.0 32.0 + - - -
40F ARG* 5.8 2.0 - - - -
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Residues in contact with HIS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D PRO* 3.5 19.2 + - + -
369D ARG* 3.7 9.9 + - - -
379D THR* 2.7 33.1 + - - +
380D MET* 3.3 5.6 - - + -
381D TYR* 2.9 39.9 - - + +
30F CYS 2.6 20.8 + - - +
31F ARG* 3.7 3.6 - - - +
33F HIS* 1.3 72.1 - - - +
35F SER* 1.3 65.0 + - - +
37F CYS* 3.1 6.7 + - - +
38F GLU* 2.9 52.6 + - + +
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Residues in contact with SER 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ARG 3.0 13.2 + - - -
32F ARG* 3.1 25.2 + - - -
34F HIS* 1.3 80.8 + - - +
36F THR* 1.3 64.7 + - - -
37F CYS 3.0 0.2 + - - -
38F GLU* 3.3 7.5 + - - +
39F ALA* 3.2 20.2 + - - +
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Residues in contact with THR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ARG* 2.9 40.6 + - - +
33F HIS* 2.6 14.8 + - - -
35F SER* 1.3 74.4 - - - +
37F CYS* 1.3 64.3 + - - +
39F ALA* 3.9 4.3 - - - +
40F ARG* 3.4 26.3 + - - +
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Residues in contact with CYS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D PRO* 3.7 5.6 - - + -
381D TYR* 3.6 33.7 - - + -
2072E GLU* 5.7 2.0 - - - -
33F HIS* 3.0 45.9 + - - -
34F HIS 3.4 7.0 - - - +
36F THR* 1.3 74.6 - - - +
38F GLU* 1.3 53.2 + - - +
39F ALA 2.4 20.2 + - - -
40F ARG* 2.7 37.1 + - - +
41F TYR* 3.1 10.6 + - - +
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D PRO* 2.9 35.2 - - + +
367D ASN* 3.8 4.8 - - + +
369D ARG* 2.8 42.2 + - - -
417D ASN* 3.5 17.7 + - - -
34F HIS* 2.9 27.3 + - + +
35F SER* 3.8 4.0 - - - +
37F CYS* 1.3 72.1 - - - +
39F ALA* 1.3 58.6 + - - +
41F TYR* 4.4 4.3 - - + -
42F GLU* 3.8 24.2 - - - +
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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