Contacts of the helix formed by residues 20 - 40 (chain J) in PDB entry 6NR8
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 ARG 20 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J GLU* 3.8 6.9 + - - +
19J GLU* 1.3 80.4 - - - +
21J ALA* 1.3 80.5 + - + +
22J GLU* 3.2 28.6 + - + +
23J THR* 3.3 5.4 + - - +
24J ALA* 3.0 23.4 + - - +
518J ASP 3.9 18.8 + - - -
519J ASN* 5.0 4.2 - - - -
43M ALA* 3.7 27.3 + - - +
46M ASN* 3.7 22.5 + - - +
47M THR* 4.0 23.3 + - - +
50M THR* 5.1 5.7 - - - +
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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
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19J GLU 4.0 0.2 + - - -
20J ARG* 1.3 90.5 - - + +
22J GLU* 1.3 55.2 + - - +
24J ALA* 4.1 6.1 - - - -
25J ARG* 2.8 36.3 + - - +
518J ASP* 3.2 41.5 + - + +
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Residues in contact with GLU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ARG* 4.1 21.6 - - + +
21J ALA* 1.3 79.3 - - - +
23J THR* 1.3 69.2 + - - +
25J ARG* 3.7 21.2 + - - +
26J LEU* 3.6 17.5 + - - +
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Residues in contact with THR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J GLU* 3.3 23.6 - - + +
20J ARG* 3.3 8.6 + - - +
21J ALA 3.2 0.2 - - - -
22J GLU* 1.3 87.9 + - - +
24J ALA* 1.3 54.2 + - - +
25J ARG 3.3 0.4 - - - -
26J LEU* 3.1 12.2 + - + -
27J THR* 2.6 45.5 + - - +
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Residues in contact with ALA 24 (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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19J GLU* 4.0 4.2 + - + +
20J ARG 3.0 17.3 + - - +
21J ALA* 3.9 7.9 - - - +
23J THR* 1.3 75.8 - - - +
25J ARG* 1.3 60.8 + - - +
27J THR* 3.8 6.8 - - - -
28J SER* 2.8 28.2 + - - -
517J VAL* 4.9 4.8 - - + +
518J ASP* 4.9 1.6 - - - -
519J ASN 4.8 4.0 - - - +
520J ILE* 3.7 45.5 - - + +
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Residues in contact with ARG 25 (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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21J ALA* 2.8 20.9 + - + +
22J GLU* 3.7 25.4 + - - +
24J ALA* 1.3 72.5 - - - +
26J LEU* 1.3 79.7 + - - +
28J SER* 3.3 16.8 + - - -
29J PHE* 3.3 38.4 + - + -
114J GLU* 2.4 39.4 + - - -
117J ILE* 3.6 34.4 - - + +
514J ILE 5.9 0.2 - - - -
515J LEU* 5.1 8.7 - - + -
517J VAL 5.0 5.5 + - - +
518J ASP* 4.6 13.4 + - - +
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Residues in contact with LEU 26 (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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22J GLU 3.6 15.3 + - - +
23J THR* 3.1 16.8 + - + +
25J ARG* 1.3 95.4 - - - +
27J THR* 1.3 60.3 + - - +
29J PHE* 3.2 7.4 + - + +
30J ILE* 3.0 50.7 + - + +
114J GLU* 4.5 7.9 - - - +
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Residues in contact with THR 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J GLU* 3.3 16.6 + - - +
23J THR* 2.6 31.4 + - - +
24J ALA* 3.8 9.0 - - - -
25J ARG 3.3 0.2 - - - -
26J LEU* 1.3 73.1 - - - +
28J SER* 1.3 58.0 + - - +
30J ILE* 3.6 13.2 - - + +
31J GLY* 2.8 28.2 + - - -
78J ASN* 4.3 21.3 - - + +
79J PRO* 4.9 12.3 - - + -
80J ALA* 4.3 4.8 - - + +
520J ILE* 4.6 12.3 - - + -
522J LYS* 5.8 2.5 - - - +
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Residues in contact with SER 28 (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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24J ALA 2.8 19.9 + - - -
25J ARG* 3.4 12.6 - - - -
26J LEU 3.2 0.2 - - - -
27J THR* 1.3 77.5 - - - +
29J PHE* 1.3 67.6 + - - +
31J GLY* 4.2 0.7 - - - -
32J ALA* 3.6 12.5 + - - +
80J ALA* 3.7 23.1 - - - +
84J LEU* 5.4 0.3 - - - +
110J LEU* 3.7 14.1 - - - +
514J ILE* 3.5 35.5 + - - +
515J LEU* 5.9 0.9 - - - -
517J VAL* 4.8 5.5 + - - +
520J ILE* 5.1 0.3 - - - +
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Residues in contact with PHE 29 (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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25J ARG* 3.3 32.5 + - + -
26J LEU* 3.2 10.4 + - + +
27J THR 3.2 0.4 - - - -
28J SER* 1.3 82.4 - - - +
30J ILE* 1.3 63.5 + - + +
31J GLY 3.1 1.3 - - - -
32J ALA* 3.0 4.0 + - - +
33J ILE* 2.9 42.1 + - + +
110J LEU* 3.4 51.1 - - + +
113J ALA* 3.6 23.3 - - + -
114J GLU* 3.2 46.0 - - + -
117J ILE* 4.8 1.3 - - + -
515J LEU* 4.2 15.0 - - + -
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Residues in contact with ILE 30 (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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26J LEU* 3.0 40.8 + - + +
27J THR* 3.6 19.5 - - + +
29J PHE* 1.3 74.6 - - + +
31J GLY* 1.3 66.8 + - - +
32J ALA 3.2 0.2 - - - -
33J ILE* 4.0 12.1 - - + +
34J ALA* 3.3 26.2 + - - +
78J ASN* 4.6 9.6 - - - +
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Residues in contact with GLY 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 THR 2.8 19.0 + - - -
28J SER 4.2 2.5 - - - -
30J ILE* 1.3 79.9 - - - +
32J ALA* 1.3 56.3 + - - +
34J ALA* 4.3 0.7 - - - +
35J ILE* 3.3 29.6 + - - +
78J ASN* 4.0 25.4 - - - -
81J ALA* 3.5 14.3 - - - +
84J LEU* 4.8 1.8 - - - -
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Residues in contact with ALA 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 SER 3.6 4.3 + - - +
29J PHE 3.0 8.7 + - - +
31J GLY* 1.3 79.2 - - - +
33J ILE* 1.3 54.5 + - + +
34J ALA 3.3 0.4 - - - -
35J ILE* 3.3 7.1 + - - +
36J GLY 2.7 31.4 + - - -
84J LEU* 4.0 12.8 - - + -
107J ALA* 3.3 27.6 - - + +
110J LEU* 3.7 31.6 - - + -
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Residues in contact with ILE 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 PHE* 2.9 30.9 + - + +
30J ILE* 4.5 9.2 - - + -
32J ALA* 1.3 77.4 - - + +
34J ALA* 1.3 59.4 + - - +
35J ILE 3.2 0.9 + - - -
37J ASP* 2.9 32.2 + - + +
107J ALA 4.9 1.8 - - - +
110J LEU 5.7 0.2 - - - -
111J ARG* 3.4 55.5 + - + +
27L ARG* 4.7 23.3 - - + +
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Residues in contact with ALA 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 ILE 3.3 18.1 + - - +
31J GLY 4.8 2.5 - - - +
32J ALA 3.3 0.8 - - - -
33J ILE* 1.3 78.2 - - - +
35J ILE* 1.3 62.0 + - + +
37J ASP* 2.9 12.5 - - - +
38J LEU* 3.3 16.3 - - - +
78J ASN* 5.2 6.3 - - - +
27L ARG* 4.1 20.1 + - - +
29L LYS* 6.1 0.4 - - - +
534L ASP* 5.9 0.2 - - - -
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Residues in contact with ILE 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 GLY 3.3 25.1 - - - +
32J ALA* 3.3 9.4 - - - +
34J ALA* 1.3 85.5 - - + +
36J GLY* 1.3 62.9 + - - +
37J ASP* 3.3 3.1 - - - -
38J LEU* 3.3 30.4 + - + +
39J VAL* 3.6 11.6 - - - +
71J LEU* 5.1 8.6 - - + +
76J VAL* 4.2 21.3 - - + -
78J ASN* 5.8 2.2 - - - +
81J ALA* 3.9 12.3 - - + +
84J LEU* 3.8 28.0 - - + -
85J VAL* 5.0 6.5 - - + -
103J THR* 4.1 22.9 - - + +
107J ALA* 5.5 0.2 - - + -
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Residues in contact with GLY 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 ALA 2.7 18.1 + - - -
33J ILE 3.4 1.1 + - - -
35J ILE* 1.3 79.6 - - - +
37J ASP* 1.3 60.3 + - - +
39J VAL* 3.7 8.2 + - - +
40J LYS* 3.3 26.3 + - - +
103J THR* 4.8 5.6 - - - -
104J VAL* 4.1 7.5 - - - +
107J ALA* 3.9 16.2 - - - -
111J ARG* 4.3 6.3 - - - -
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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 ILE* 2.9 20.8 + - + +
34J ALA 2.9 16.7 - - - +
36J GLY* 1.3 71.1 - - - +
38J LEU* 1.3 71.6 + - - +
40J LYS* 3.5 37.2 + - - +
41J SER 4.3 0.3 + - - -
111J ARG* 4.1 5.4 - - - +
27L ARG* 2.4 36.4 + - - +
30L PRO* 5.2 3.3 - - + +
533L ASP* 4.1 12.0 - - - +
534L ASP* 3.0 20.1 - - - +
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Residues in contact with LEU 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 ALA 3.3 24.5 - - - +
35J ILE* 3.4 23.8 - - + +
36J GLY 3.2 0.6 - - - -
37J ASP* 1.3 84.1 + - - +
39J VAL* 1.3 59.3 + - - +
41J SER* 3.4 16.3 + - - -
50J LYS* 3.7 33.9 - - - +
70J ILE* 4.2 26.9 - - + +
71J LEU* 6.0 2.7 - - + -
74J ILE* 5.9 6.1 - - + -
533L ASP* 4.5 1.5 - - - +
534L ASP* 3.7 32.3 - - + +
536L VAL* 4.4 11.4 - - + -
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Residues in contact with VAL 39 (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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35J ILE 3.6 15.5 - - - +
36J GLY* 3.7 3.1 - - - +
38J LEU* 1.3 74.6 - - + +
40J LYS* 1.3 58.0 + - - +
41J SER 3.1 3.1 - - - -
42J THR* 2.6 39.8 + - - +
43J LEU* 2.9 16.1 + - + +
67J GLY* 4.5 10.5 - - - +
70J ILE* 3.7 38.8 - - + -
71J LEU* 5.8 5.2 - - + -
99J THR 5.4 1.8 - - - +
100J THR* 4.6 8.7 - - + +
103J THR* 4.9 10.3 - - + -
104J VAL* 3.6 22.2 - - + -
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Residues in contact with LYS 40 (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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36J GLY 3.3 13.2 + - - +
37J ASP* 3.5 36.3 + - - +
39J VAL* 1.3 74.0 - - - +
41J SER* 1.3 66.1 + - - +
43J LEU* 3.7 7.1 + - - +
104J VAL* 4.5 6.1 - - + -
111J ARG* 5.5 4.9 - - - +
449J ILE* 3.4 67.1 + - + +
452J ASP* 4.5 14.1 + - - -
453J ASN* 3.5 1.6 + - - -
533L ASP* 5.9 0.4 + - - -
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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