Contacts of the helix formed by residues 19 - 37 (chain B) in PDB entry 1NUR
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 THR 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.3 17.7 - - + +
18B ILE* 1.3 72.3 - - - +
20B ASN* 1.3 64.6 + - - +
21B MET* 3.2 18.6 + - - +
22B HIS* 2.9 33.7 + - + +
23B LEU* 3.2 20.8 + - - +
200B ILE* 4.4 11.6 + - + +
202B ALA* 4.3 10.5 - - - +
205B ILE* 4.1 16.4 - - + -
218B LEU 4.0 2.9 - - - -
219B ILE* 3.8 21.8 - - + -
220B PRO* 4.6 1.1 - - - -
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 1.3 71.9 - - - +
21B MET* 1.3 57.0 + - - +
23B LEU* 3.4 9.8 + - - +
24B ARG* 2.8 30.8 + - - +
198B ASN* 4.3 8.9 + - - +
200B ILE* 4.2 8.1 - - + -
217B TYR* 3.2 28.9 + - - +
218B LEU 3.0 25.9 + - - +
219B ILE* 3.8 3.2 + - - +
220B PRO* 3.3 27.7 - - - +
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Residues in contact with MET 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.1 10.6 + - - +
20B ASN* 1.3 76.8 - - - +
22B HIS* 1.3 72.0 + - - +
24B ARG* 3.7 3.7 - - + +
25B MET* 2.9 32.0 + - + +
166B GLY 5.5 1.8 - - - +
167B ARG* 3.2 41.5 - - + +
194B GLU* 6.4 1.8 - - + -
198B ASN* 3.4 24.9 + - - +
199B GLU* 3.2 41.5 - - + +
200B ILE* 3.4 25.4 - - + +
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Residues in contact with HIS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.0 31.7 - + + -
17B PRO 3.8 9.9 + - - -
18B ILE* 3.4 22.2 - - + -
19B THR* 2.9 44.6 + - + +
21B MET* 1.3 82.4 - - + +
23B LEU* 1.3 62.8 + - - +
25B MET* 3.2 32.1 - - - +
26B PHE* 3.6 15.3 - - + -
46B ILE* 6.2 0.4 - - + -
200B ILE 6.0 1.1 - - - -
202B ALA* 4.6 10.6 - - + +
304B SO4 5.4 6.1 - - - -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.5 20.2 - - + -
19B THR 3.2 15.5 + - - +
20B ASN* 3.6 12.3 - - - +
21B MET 3.1 0.6 - - - -
22B HIS* 1.3 71.7 - - - +
24B ARG* 1.3 65.1 + - - +
25B MET 3.0 1.6 - - - -
26B PHE* 3.0 24.3 + - + +
27B GLU* 3.6 9.4 + - - +
46B ILE* 4.5 2.9 - - + -
71B ALA* 4.1 14.1 - - + +
72B LEU* 3.5 32.3 - - + -
78B ILE* 4.8 4.8 - - + +
220B PRO* 3.5 33.7 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN 2.8 20.8 + - - +
21B MET* 3.7 8.5 - - + +
23B LEU* 1.3 72.8 - - - +
25B MET* 1.3 63.2 + - - +
27B GLU* 3.1 31.4 + - - +
28B VAL* 3.0 42.6 + - + +
31B ASP* 5.3 6.9 + - - -
194B GLU* 3.5 25.2 + - - +
195B PRO* 6.3 1.0 - - - +
196B VAL* 5.8 8.9 - - + +
198B ASN* 4.7 13.0 - - + +
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Residues in contact with MET 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 5.5 4.9 - - - -
21B MET* 2.9 28.0 + - + +
22B HIS* 3.2 27.4 - - - +
23B LEU 3.0 0.4 - - - -
24B ARG* 1.3 77.7 - - - +
26B PHE* 1.3 59.6 + - - +
28B VAL* 3.6 0.8 + - - +
29B ALA* 3.1 23.0 + - - +
133B LEU* 3.7 27.1 - - + +
134B CYS* 4.0 20.6 - - - +
135B GLY* 4.6 12.6 - - - +
165B VAL* 3.5 32.5 - - + +
167B ARG* 5.5 7.9 - - - +
194B GLU* 6.0 0.2 - - - -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.9 11.4 - - + +
11B ALA* 3.5 31.2 - - + -
15B PHE* 5.6 2.5 - + - -
22B HIS 3.6 17.7 - - - -
23B LEU* 3.0 7.5 + - + +
25B MET* 1.3 77.9 - - + +
27B GLU* 1.3 59.2 + - - +
29B ALA* 3.4 1.6 + - - +
30B ARG 2.9 25.6 + - - -
44B GLY* 3.7 9.2 - - - -
45B ILE 3.6 26.0 - - - -
46B ILE* 3.5 33.7 - - + -
77B TRP* 3.4 26.6 - + + -
78B ILE* 3.4 29.6 - - + -
133B LEU* 3.7 20.2 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU 4.0 11.9 - - - +
24B ARG* 3.1 34.1 + - - +
26B PHE* 1.3 77.8 - - - +
28B VAL* 1.3 61.1 + - - +
30B ARG* 3.5 18.4 + - - +
31B ASP* 3.1 33.9 + - - +
75B SER* 5.1 0.9 + - - -
77B TRP* 3.0 33.6 + - - -
78B ILE* 4.1 6.6 - - + +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 3.0 46.3 + - + +
25B MET 4.0 2.9 - - - +
27B GLU* 1.3 72.8 - - - +
29B ALA* 1.3 66.9 + - - +
31B ASP* 3.4 5.4 + - - +
32B HIS* 3.0 22.9 + - + +
165B VAL* 4.3 15.0 - - + -
192B ALA* 3.9 16.2 - - + -
193B LYS 3.6 23.1 - - - +
194B GLU* 3.8 23.1 - - - +
195B PRO* 5.5 1.3 - - + -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 11.7 - - + -
25B MET 3.1 16.1 + - - +
26B PHE 3.7 4.3 - - - +
28B VAL* 1.3 80.9 - - - +
30B ARG* 1.3 56.8 + - - +
32B HIS* 3.3 3.5 + - - +
33B LEU* 2.9 32.6 + - - +
133B LEU* 3.4 26.5 - - + -
163B VAL* 3.7 17.4 - - + +
165B VAL* 4.3 2.0 - - + +
192B ALA* 4.3 7.2 - - - -
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.3 1.1 - - - +
26B PHE 2.9 18.9 + - - +
27B GLU* 3.6 19.3 + - - +
29B ALA* 1.3 73.7 - - - +
31B ASP* 1.3 75.1 + - - +
33B LEU* 3.3 1.7 + - - +
34B HIS* 3.0 44.9 + - + +
41B VAL* 3.6 37.8 + - + -
76B ASP* 4.7 3.4 + - - -
77B TRP* 3.1 65.0 - - + +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 5.3 6.9 + - - -
27B GLU* 3.1 24.0 + - - +
28B VAL* 3.9 5.1 - - - +
30B ARG* 1.3 86.3 + - - +
32B HIS* 1.3 58.2 + - - +
34B HIS* 3.4 8.8 + - - +
35B GLN* 2.9 30.8 + - - +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.0 18.8 + - + +
29B ALA 3.4 4.5 - - - +
31B ASP* 1.3 77.9 - - - +
33B LEU* 1.3 70.2 + - + +
35B GLN* 3.1 20.3 + - + +
36B THR* 3.2 26.5 + - + +
163B VAL* 5.3 1.1 - - + -
190B HIS* 4.1 27.6 + - + +
191B LEU 3.2 25.4 + - - -
192B ALA* 3.7 22.0 - - + -
193B LYS* 5.0 8.9 + - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.1 8.5 - - + -
9B LEU* 3.8 29.8 - - + -
29B ALA 2.9 16.8 + - - +
30B ARG 3.3 4.2 + - - +
32B HIS* 1.3 81.5 - - + +
34B HIS* 1.3 60.4 + - - +
36B THR* 2.7 27.2 + - + -
37B GLY 3.7 0.9 + - - -
39B TYR* 3.9 29.5 - - + +
41B VAL* 3.9 19.7 - - + -
131B LYS* 4.8 1.3 - - + -
163B VAL* 3.9 11.0 - - + -
190B HIS* 3.7 45.3 - - + +
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Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 2.8 28.8 + - - +
30B ARG* 3.0 44.6 + - + +
31B ASP* 3.9 8.8 + - - +
33B LEU* 1.3 72.4 - - - +
35B GLN* 1.3 62.1 + - - +
37B GLY* 2.9 11.6 + - - -
39B TYR 3.3 21.5 - - - -
40B GLN* 3.6 7.0 - - + +
41B VAL* 2.9 38.0 + - + +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP 2.9 18.6 + - - +
32B HIS* 3.1 13.9 + - + +
34B HIS* 1.3 79.4 - - - +
36B THR* 1.3 61.8 + - + +
37B GLY* 3.1 1.6 + - - -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B HIS* 3.2 34.0 + - + +
33B LEU* 2.7 24.1 + - + +
35B GLN* 1.3 76.5 - - + +
37B GLY* 1.3 57.3 + - - +
38B MET* 3.2 26.3 + - - +
39B TYR* 3.4 14.0 - - + -
190B HIS* 5.0 5.6 - - - +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.4 30.9 + - - +
34B HIS 2.9 18.4 + - - -
35B GLN 3.0 2.2 - - - -
36B THR* 1.3 78.7 + - - +
38B MET* 1.3 55.4 + - - +
39B TYR 3.3 5.2 - - - -
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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