Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 1NWW
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA 3.7 0.4 - - - -
21A SER* 1.3 87.0 - - - +
23A PRO* 1.3 76.7 - - - +
24A ASP* 3.4 7.4 + - - +
25A GLU* 3.1 28.0 + - - +
26A LYS* 2.9 30.4 + - - +
90A SER* 3.9 18.8 + - - +
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Residues in contact with PRO 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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22A THR* 1.3 90.1 - - - +
24A ASP* 1.3 65.7 + - - +
26A LYS* 3.2 21.6 + - + +
27A ILE* 3.1 29.6 + - + +
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Residues in contact with ASP 24 (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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22A THR* 3.3 7.1 + - - +
23A PRO* 1.3 78.4 - - - +
25A GLU* 1.3 67.2 + - - +
27A ILE* 3.3 13.3 + - - +
28A VAL* 3.0 26.2 + - - +
90A SER* 5.9 0.9 - - - -
93A GLY* 4.7 14.0 - - - +
95A VAL* 3.8 17.4 - - + +
122A LEU* 3.9 35.9 - - + +
125A GLY* 4.7 6.1 + - - -
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Residues in contact with GLU 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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19A ALA 3.9 4.0 - - - +
20A ALA* 3.5 15.8 - - + -
21A SER* 2.9 27.9 + - - -
22A THR* 3.1 25.5 + - - +
24A ASP* 1.3 76.8 - - - +
26A LYS* 1.3 63.4 + - - +
28A VAL* 3.2 2.3 + - - +
29A LEU* 3.0 28.2 + - - +
88A ILE* 3.8 22.0 - - + +
89A GLY* 3.3 11.6 - - - -
90A SER* 2.6 43.4 + - - +
95A VAL* 4.1 8.7 - - + -
91B SER* 3.8 5.0 + - - -
92B ASN* 5.6 1.0 + - - -
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Residues in contact with LYS 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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20A ALA* 3.5 22.7 - - + -
21A SER 5.4 1.8 - - - -
22A THR 2.9 24.9 + - - +
23A PRO* 3.4 22.5 - - + +
24A ASP 3.1 0.2 - - - -
25A GLU* 1.3 77.6 - - - +
27A ILE* 1.3 62.9 + - + +
29A LEU* 3.3 5.2 + - - +
30A GLU* 3.0 34.2 + - - +
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Residues in contact with ILE 27 (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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23A PRO* 3.1 17.2 + - + +
24A ASP* 3.3 11.0 + - - +
26A LYS* 1.3 77.5 - - + +
28A VAL* 1.3 58.0 + - + +
30A GLU* 3.1 17.1 + - - +
31A PHE* 2.9 27.0 + - + +
46A TYR* 4.2 20.5 - - + +
122A LEU* 3.7 21.5 - - + -
125A GLY* 3.3 41.5 - - - +
127A ILE* 5.5 4.7 - - + -
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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
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24A ASP 3.0 17.1 + - - +
25A GLU 3.2 4.5 + - - +
27A ILE* 1.3 74.9 - - + +
29A LEU* 1.3 58.9 + - - +
31A PHE* 3.2 8.5 + - - +
32A MET* 2.9 28.8 + - + +
88A ILE* 4.3 2.7 - - + -
95A VAL* 3.9 19.1 - - + -
97A THR* 3.6 30.1 - - + -
120A PHE* 3.8 31.4 - - + -
122A LEU* 3.9 25.4 - - + -
127A ILE* 5.9 2.2 - - + -
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Residues in contact with LEU 29 (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 GLY 3.4 26.0 - - - +
19A ALA* 4.2 1.6 - - - -
20A ALA* 3.6 29.8 - - + +
25A GLU 3.0 15.1 + - - +
26A LYS* 3.9 4.3 - - - +
28A VAL* 1.3 74.9 - - + +
30A GLU* 1.3 64.2 + - - +
32A MET* 3.3 9.5 + - + +
33A ASP* 3.1 29.1 + - - +
85A THR* 4.2 25.6 - - + +
88A ILE* 3.8 17.5 - - + -
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Residues in contact with GLU 30 (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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26A LYS* 3.0 26.5 + - - +
27A ILE* 3.1 15.7 + - - +
29A LEU* 1.3 76.5 - - - +
31A PHE* 1.3 63.7 + - - +
33A ASP* 3.2 11.9 + - - +
34A ALA* 3.0 21.8 + - - +
46A TYR* 3.6 19.1 + - + +
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Residues in contact with PHE 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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27A ILE* 2.9 13.4 + - + +
28A VAL* 3.2 11.2 + - - +
30A GLU* 1.3 74.2 - - - +
32A MET* 1.3 86.0 + - + +
34A ALA* 3.0 12.5 + - - +
35A LEU* 3.1 21.5 + - + +
43A LEU* 3.7 38.1 - - + -
46A TYR* 3.4 35.8 - + + -
47A PHE* 3.7 17.7 - + - -
71A LEU* 5.6 0.2 - - + -
120A PHE* 4.0 8.7 - + - -
127A ILE* 4.0 13.0 - - + -
130A TRP* 3.6 46.4 - + - -
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Residues in contact with MET 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* 2.9 23.4 + - + +
29A LEU* 3.6 14.1 - - + +
30A GLU 3.3 0.2 - - - -
31A PHE* 1.3 103.9 - - + +
33A ASP* 1.3 64.4 + - - +
35A LEU* 3.3 35.2 + - + +
36A THR* 4.4 1.4 + - - +
83A VAL* 3.9 22.8 - - + +
85A THR* 3.9 15.9 - - - +
97A THR* 4.8 2.9 - - + -
99A ARG* 3.4 38.8 - - - -
120A PHE* 3.6 21.8 - - + -
130A TRP* 4.7 1.1 - - + -
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Residues in contact with ASP 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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29A LEU* 3.1 20.0 + - - +
30A GLU* 3.2 12.8 + - - +
32A MET* 1.3 77.8 - - - +
34A ALA* 1.3 58.7 + - - +
36A THR* 3.1 23.4 + - - +
37A SER 4.8 0.2 + - - -
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Residues in contact with ALA 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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30A GLU 3.0 11.8 + - - +
31A PHE 3.0 9.9 + - - +
33A ASP* 1.3 78.0 - - - +
35A LEU* 1.3 60.2 + - - +
36A THR 3.2 0.2 - - - -
37A SER* 2.8 32.1 + - - +
42A LYS* 4.2 21.5 - - - +
43A LEU* 3.6 18.0 - - + +
46A TYR* 4.0 16.8 - - + +
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Residues in contact with LEU 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 PHE* 3.1 23.7 + - + +
32A MET* 3.6 35.4 - - + +
33A ASP 3.3 1.4 - - - -
34A ALA* 1.3 75.1 - - - +
36A THR* 1.3 56.7 + - - +
37A SER 3.0 0.2 - - - -
38A ASN* 3.1 25.6 + - - +
43A LEU* 4.0 24.2 - - + -
75A PHE* 4.2 3.9 - - + -
80A ILE* 3.9 28.5 - - + +
83A VAL* 4.2 12.3 - - + -
99A ARG* 4.4 4.9 - - - +
101A ASP* 4.2 17.7 - - - +
130A TRP* 4.0 24.5 - - + -
900A HPN 4.7 0.7 - - - +
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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
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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