Contacts of the helix formed by residues 19 - 36 (chain A) in PDB entry 1NUP
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.4 17.3 - - + +
18A ILE* 1.3 73.7 - - - +
20A ASN* 1.3 66.6 + - - +
21A MET* 3.2 11.0 + - - +
22A HIS* 2.9 38.4 + - + +
23A LEU* 3.2 27.7 + - - +
200A ILE* 4.5 9.8 + - + +
202A ALA* 4.4 11.2 - - + +
205A ILE* 4.2 15.3 - - + -
218A LEU 4.0 2.2 - - - -
219A ILE* 3.8 21.3 - - + -
220A PRO* 4.3 1.3 - - - -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 1.3 75.1 - - - +
21A MET* 1.3 56.3 + - - +
23A LEU* 3.4 8.8 + - - +
24A ARG* 2.8 30.6 + - - +
198A ASN* 5.0 2.5 - - - +
200A ILE* 4.6 7.0 - - + -
217A TYR* 3.2 30.1 + - - +
218A LEU 3.0 23.3 + - - +
219A ILE* 3.7 3.0 - - - +
220A PRO* 3.3 26.5 - - - +
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 3.0 9.2 + - - +
20A ASN* 1.3 76.9 - - - +
22A HIS* 1.3 72.0 + - + +
24A ARG* 3.2 2.1 + - - +
25A MET* 3.1 34.5 + - + +
167A ARG* 3.7 23.3 - - + +
197A GLN 4.1 0.7 - - - +
198A ASN* 2.9 37.5 + - + +
199A GLU* 3.0 50.3 - - - +
200A ILE* 3.3 28.1 - - + +
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.8 37.7 + + + -
17A PRO 3.5 19.3 - - - -
18A ILE* 3.4 12.2 - - + -
19A THR* 2.9 36.4 + - + +
21A MET* 1.3 82.8 - - + +
23A LEU* 1.3 63.6 + - - +
25A MET* 3.5 29.6 + - - +
26A PHE* 3.6 14.7 - - - -
46A ILE* 5.6 0.4 - - + -
202A ALA* 4.5 12.6 + - + +
302A SO4 5.3 4.4 + - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.8 20.0 - - + -
19A THR 3.2 16.5 + - - +
20A ASN* 3.7 9.9 - - - +
21A MET 3.2 0.4 - - - -
22A HIS* 1.3 76.3 - - - +
24A ARG* 1.3 66.5 + - - +
26A PHE* 3.1 25.1 + - + +
27A GLU* 3.5 10.4 + - - +
46A ILE* 5.5 1.3 - - + -
71A ALA* 4.3 12.6 - - + +
72A LEU* 3.5 31.6 - - + -
78A ILE* 4.7 8.0 - - + +
220A PRO* 3.6 30.3 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN 2.8 18.8 + - - +
21A MET* 3.2 9.6 + - + +
23A LEU* 1.3 76.4 - - - +
25A MET* 1.3 58.1 + - + +
27A GLU* 3.1 29.1 + - - +
28A VAL* 2.9 42.9 + - + +
31A ASP* 5.3 7.1 + - - -
194A GLU* 2.5 46.6 + - + +
198A ASN* 4.2 13.9 - - - +
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.6 4.7 - - + -
21A MET* 3.1 31.4 + - + +
22A HIS* 3.5 23.3 - - - +
24A ARG* 1.3 77.4 - - + +
26A PHE* 1.3 63.0 + - + +
28A VAL* 4.6 2.5 - - - +
29A ALA* 2.9 26.3 + - - +
133A LEU* 4.0 22.8 - - + +
134A CYS* 3.9 31.4 - - - +
135A GLY* 4.0 8.5 - - - +
165A VAL* 3.8 27.1 - - + +
167A ARG* 6.0 5.8 - - - -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 11.0 - - + -
11A ALA* 3.6 22.9 - - + -
15A PHE* 5.5 0.4 - + - -
22A HIS 3.6 16.4 - - - -
23A LEU* 3.1 9.4 + - + +
25A MET* 1.3 79.8 - - + +
27A GLU* 1.3 58.7 + - - +
29A ALA* 3.8 1.6 - - - +
30A ARG* 2.9 23.7 + - - +
44A GLY* 3.7 23.6 - - - -
45A ILE 3.6 11.0 - - - -
46A ILE* 3.0 40.8 - - + -
77A TRP* 3.4 28.5 - + + -
78A ILE* 3.4 31.0 - - + -
133A LEU* 3.6 18.6 - - + -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.9 11.9 - - - +
24A ARG* 3.1 32.9 + - - +
26A PHE* 1.3 77.8 - - - +
28A VAL* 1.3 62.4 + - - +
30A ARG* 3.3 21.7 + - - +
31A ASP* 3.0 30.1 + - - +
75A SER* 5.1 1.4 + - - -
77A TRP* 2.9 33.5 + - - -
78A ILE* 4.2 5.9 - - + +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.9 46.8 + - + +
25A MET* 3.9 3.8 - - - +
27A GLU* 1.3 76.0 - - - +
29A ALA* 1.3 58.8 + - - +
31A ASP* 3.4 5.0 + - - +
32A HIS* 3.0 27.8 + - + +
165A VAL* 4.2 12.6 - - + -
192A ALA* 3.9 19.5 - - + -
193A LYS 4.2 9.9 - - - +
194A GLU* 3.5 36.3 - - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 12.3 - - + -
25A MET 2.9 18.5 + - - +
26A PHE 3.8 3.8 - - - +
28A VAL* 1.3 75.9 - - - +
30A ARG* 1.3 64.5 + - - +
32A HIS* 3.4 5.2 + - - +
33A LEU* 3.0 27.7 + - - +
133A LEU* 3.5 24.9 - - + -
163A VAL* 3.6 18.7 - - + +
165A VAL* 4.4 2.2 - - + +
192A ALA* 4.6 3.4 - - - -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.3 1.3 - - - +
26A PHE 2.9 17.6 + - - +
27A GLU* 3.3 26.8 + - - +
29A ALA* 1.3 77.7 - - - +
31A ASP* 1.3 71.1 + - - +
33A LEU* 3.3 1.2 + - - -
34A HIS* 2.9 54.9 + - + +
41A VAL* 3.8 28.0 + - + -
76A ASP* 4.7 3.2 + - - -
77A TRP* 3.2 56.0 - - + +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 5.3 7.1 + - - -
27A GLU* 3.0 21.6 + - - +
28A VAL* 3.9 5.3 - - - +
30A ARG* 1.3 84.9 + - - +
32A HIS* 1.3 59.2 + - - +
34A HIS* 3.3 9.2 + - - +
35A GLN* 2.9 46.2 + - + +
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.0 18.7 + - + +
29A ALA* 3.6 4.3 - - - +
31A ASP* 1.3 77.6 - - - +
33A LEU* 1.3 70.2 + - + +
35A GLN* 3.2 24.0 + - - +
36A THR* 3.3 24.9 + - + +
163A VAL* 5.1 2.0 - - + -
190A HIS* 4.1 26.7 + - + +
191A LEU 3.1 28.4 + - - -
192A ALA* 3.6 22.0 - - + -
193A LYS 5.2 0.6 + - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.0 16.4 - - + -
9A LEU* 4.0 23.6 - - + -
29A ALA 3.0 19.3 + - - +
30A ARG 3.9 2.7 - - - +
32A HIS* 1.3 79.7 - - + +
34A HIS* 1.3 63.1 + - - +
36A THR* 2.8 28.0 + - + -
37A GLY 3.9 0.5 + - - -
39A TYR* 3.9 31.5 + - + +
41A VAL* 3.8 24.7 - - + -
131A LYS* 4.9 2.5 - - + -
163A VAL* 4.1 11.7 - - + -
190A HIS* 3.9 36.8 - - + +
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Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.0 22.6 + - - +
30A ARG* 2.9 43.2 + - + +
31A ASP* 3.7 10.0 + - - +
33A LEU* 1.3 77.1 - - - +
35A GLN* 1.3 58.1 + - + +
37A GLY* 2.9 18.0 + - - -
39A TYR 3.6 11.9 - - - -
40A GLN* 3.7 7.7 - - + +
41A VAL* 2.9 41.8 + - + +
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 2.9 38.7 + - + +
32A HIS* 3.2 15.4 + - - +
34A HIS* 1.3 72.8 - - + +
36A THR* 1.3 59.1 + - - +
37A GLY* 3.0 6.9 + - - -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.4 31.6 - - + +
33A LEU* 2.8 21.5 + - + +
35A GLN* 1.3 76.7 - - - +
37A GLY* 1.3 56.9 + - - +
38A MET* 3.2 27.0 + - - +
39A TYR* 3.3 17.9 - - + -
190A HIS* 5.4 3.8 - - - +
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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