Contacts of the helix formed by residues 18 - 33 (chain A) in PDB entry 1NN5
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 GLY 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG 3.2 3.4 - - - -
17A ALA* 1.3 78.4 - - - +
19A LYS* 1.3 59.4 + - - +
20A SER 3.3 2.7 - - - -
21A THR 3.4 0.2 + - - -
22A GLN* 2.8 37.8 + - - +
133A LEU* 3.7 6.7 - - - -
303A ANP 2.9 38.3 + - - -
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Residues in contact with LYS 19 (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 LEU* 3.8 14.4 - - + +
12A GLU* 3.7 23.6 - - - +
13A GLY* 3.3 24.3 + - - +
14A VAL 2.8 29.1 + - - -
17A ALA* 3.7 2.2 - - + -
18A GLY* 1.3 77.0 - - - +
20A SER* 1.3 60.0 + - - +
22A GLN 3.8 0.3 - - - -
23A SER* 2.7 34.8 + - - -
96A ASP* 3.3 12.6 - - - +
97A ARG* 3.4 39.0 - - + +
133A LEU* 3.8 11.4 - - + +
303A ANP 2.8 38.9 + - - +
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Residues in contact with SER 20 (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 LYS* 1.3 73.6 - - - +
21A THR* 1.3 68.8 + - - +
23A SER* 3.3 2.3 + - - -
24A ARG* 3.0 46.5 + - - +
96A ASP* 2.6 23.9 + - - -
303A ANP 2.9 13.4 + - - -
401A MG 2.1 30.4 - - - -
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Residues in contact with THR 21 (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 3.9 2.7 - - - -
20A SER* 1.3 78.5 - - - +
22A GLN* 1.3 61.6 + - - +
24A ARG* 3.2 26.4 + - - +
25A LYS* 3.0 36.0 + - + +
184A ILE* 4.0 37.9 - - + -
303A ANP 2.7 45.9 + - - -
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Residues in contact with GLN 22 (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 LEU* 3.7 9.8 - - + +
18A GLY* 2.8 26.6 + - - +
21A THR* 1.3 73.7 - - - +
23A SER* 1.3 60.2 + - - +
25A LYS* 3.8 3.4 - - - +
26A LEU* 2.9 31.7 + - - +
133A LEU* 4.0 4.9 - - + -
184A ILE* 3.0 39.2 + - - +
187A VAL* 3.6 24.2 - - + +
188A HIS* 3.0 31.1 + - - +
191A ILE* 3.6 26.7 - - + +
303A ANP 5.0 4.9 + - - -
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Residues in contact with SER 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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11A LEU* 3.6 18.5 - - - +
19A LYS 2.7 25.1 + - - -
20A SER* 3.3 4.0 + - - -
22A GLN* 1.3 77.1 - - - +
24A ARG* 1.3 63.8 + - - +
26A LEU* 3.3 2.1 + - - +
27A VAL* 3.1 28.2 + - - +
39A LEU* 3.5 23.8 - - - -
94A VAL* 3.9 12.9 - - - +
96A ASP* 3.6 21.9 + - - +
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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
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20A SER* 3.0 41.3 + - - +
21A THR* 3.2 33.1 + - - +
23A SER* 1.3 77.9 - - - +
25A LYS* 1.3 65.1 + - + +
27A VAL* 3.4 4.5 + - - +
28A GLU* 3.1 22.7 + - - +
39A LEU* 4.1 22.9 - - + +
303A ANP 5.5 1.6 + - - -
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Residues in contact with LYS 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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21A THR* 3.0 27.7 + - + +
22A GLN* 4.1 5.4 - - - +
24A ARG* 1.3 75.9 - - + +
26A LEU* 1.3 67.6 + - - +
28A GLU* 3.4 22.0 + - - +
29A ALA* 2.9 19.4 + - - +
184A ILE* 3.6 25.0 - - + +
185A GLU* 2.9 30.1 + - - -
188A HIS* 3.3 45.3 - - + +
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Residues in contact with LEU 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 ILE* 4.4 9.9 - - + -
11A LEU* 4.5 3.8 - - + -
22A GLN 2.9 18.8 + - - +
23A SER 3.7 4.5 - - - +
25A LYS* 1.3 78.1 - - - +
27A VAL* 1.3 58.5 + - - +
29A ALA* 3.2 1.2 + - - -
30A LEU* 2.9 55.1 + - + +
94A VAL* 3.7 27.8 - - + -
188A HIS* 4.1 7.1 - - + -
191A ILE* 3.9 16.2 - - + -
192A ARG* 4.0 22.7 - - + -
195A SER* 3.3 33.9 - - - +
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Residues in contact with VAL 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 SER 3.1 13.1 + - - +
24A ARG* 3.9 4.0 - - - +
26A LEU* 1.3 74.1 - - - +
28A GLU* 1.3 65.6 + - - +
30A LEU* 3.3 5.2 + - - +
31A CYS* 3.0 28.2 + - - -
37A ALA* 3.6 26.9 - - + +
38A GLU* 3.8 18.8 - - - +
39A LEU* 3.9 15.5 - - + +
94A VAL* 3.5 33.2 - - + -
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Residues in contact with GLU 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 ARG 3.1 15.9 + - - +
25A LYS* 3.6 26.0 + - - +
27A VAL* 1.3 79.5 - - - +
29A ALA* 1.3 57.3 + - - +
31A CYS* 3.4 4.2 + - - +
32A ALA* 3.0 30.1 + - + +
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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
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25A LYS 2.9 18.1 + - - +
26A LEU 3.8 2.5 - - - +
28A GLU* 1.3 76.1 - - + +
30A LEU* 1.3 67.5 + - - +
32A ALA* 3.3 7.2 + - - +
33A ALA* 3.1 24.1 + - - +
188A HIS* 3.5 25.6 - - + +
192A ARG* 3.8 18.9 - - + -
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Residues in contact with LEU 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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9A ILE* 4.9 0.4 - - + -
26A LEU* 2.9 47.6 + - + +
27A VAL 3.8 3.1 - - - +
29A ALA* 1.3 76.6 - - - +
31A CYS* 1.3 61.7 + - - +
33A ALA* 3.0 8.7 + - - -
35A HIS* 3.0 48.5 + - + -
37A ALA* 3.9 24.5 - - + -
92A THR* 4.3 3.1 - - + -
94A VAL* 4.2 11.2 - - + -
192A ARG* 5.0 4.3 - - + -
195A SER* 4.7 5.4 - - - -
196A GLU* 4.1 17.5 - - + +
199A ILE* 3.8 26.2 - - + -
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Residues in contact with CYS 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 VAL* 3.0 24.4 + - - +
28A GLU* 3.9 4.9 - - - +
30A LEU* 1.3 76.5 - - - +
32A ALA* 1.3 62.9 + - - +
34A GLY* 3.0 14.6 + - - -
35A HIS 3.4 12.2 - - - +
36A ARG* 5.0 0.4 - - - -
37A ALA* 3.3 38.4 - - - -
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Residues in contact with ALA 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 GLU* 3.0 19.2 + - + +
29A ALA* 3.8 7.9 - - - +
30A LEU 3.2 0.4 - - - -
31A CYS* 1.3 77.7 - - - +
33A ALA* 1.3 56.0 + - - +
34A GLY 3.3 2.6 + - - -
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Residues in contact with ALA 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 ALA 3.1 14.3 + - - +
30A LEU 3.0 6.0 + - - +
32A ALA* 1.3 75.1 - - - +
34A GLY* 1.3 59.1 + - - +
35A HIS* 3.3 10.6 + - + +
192A ARG* 5.8 3.4 - - - +
196A GLU* 4.0 20.6 - - - +
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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