Contacts of the helix formed by residues 18 - 30 (chain B) in PDB entry 3NA1
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 ASN 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.5 2.0 - - - -
17B ASP* 1.3 75.3 - - - +
19B GLY* 1.3 58.3 + - - +
20B TRP* 2.9 28.7 + - - +
21B LEU* 3.0 31.7 + - + +
22B ASN* 2.9 33.3 + - - +
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Residues in contact with GLY 19 (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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17B ASP 3.4 7.1 + - - -
18B ASN* 1.3 73.2 + - - +
20B TRP* 1.3 57.8 + - - +
22B ASN 3.6 0.2 + - - -
23B LEU* 3.1 19.8 + - - +
53B LYS* 3.5 28.2 - - - +
55B GLY 3.0 38.9 + - - -
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Residues in contact with TRP 20 (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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18B ASN* 2.9 12.6 + - - +
19B GLY* 1.3 76.6 - - - +
21B LEU* 1.3 61.0 + - - +
23B LEU* 3.4 10.9 + - + +
24B TYR* 3.0 27.2 + - - +
55B GLY* 3.7 26.1 + - - -
56B ASN* 3.4 27.3 + - - -
211B LEU* 4.0 22.9 - - + -
212B PRO* 3.9 15.0 - - + -
215B LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 21 (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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18B ASN* 3.0 31.8 + - + +
20B TRP* 1.3 75.0 - - - +
22B ASN* 1.3 67.3 + - - +
24B TYR* 3.2 18.5 + - + +
25B HIS* 3.0 57.1 + - + +
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Residues in contact with ASN 22 (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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15B PRO* 3.9 33.5 - - + +
16B GLY* 3.0 26.4 + - - +
18B ASN* 2.9 23.0 + - - +
19B GLY 3.8 0.2 - - - +
21B LEU* 1.3 78.0 - - - +
23B LEU* 1.3 56.9 + - - +
25B HIS* 3.4 9.7 + - - +
26B PHE* 2.9 30.1 + - - +
52B GLU* 4.4 8.2 - - - +
53B LYS* 3.1 32.5 + - - +
54B LEU* 3.9 8.0 - - + +
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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
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19B GLY 3.1 16.6 + - - +
20B TRP* 3.6 13.9 - - + +
21B LEU 3.2 0.2 - - - -
22B ASN* 1.3 73.3 - - - +
24B TYR* 1.3 61.0 + - - +
26B PHE* 3.3 10.6 + - + +
27B TRP* 2.9 82.9 + - + +
54B LEU* 3.9 10.0 - - + +
55B GLY* 4.2 11.0 - - - +
210B ASN* 3.8 44.4 - - + +
211B LEU* 4.1 11.7 - - + -
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Residues in contact with TYR 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 TRP 3.0 14.1 + - - +
21B LEU* 3.5 19.5 - - + +
23B LEU* 1.3 77.1 - - - +
25B HIS* 1.3 73.0 + + - +
27B TRP* 3.4 9.3 + + + +
28B ARG* 2.9 75.1 + - + +
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Residues in contact with HIS 25 (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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21B LEU* 3.0 50.9 + - + +
22B ASN* 3.9 9.0 - - - +
24B TYR* 1.3 84.5 - + - +
26B PHE* 1.3 57.7 + - - +
28B ARG* 3.3 37.4 + - - -
29B GLU* 2.8 50.8 + - - +
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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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22B ASN 2.9 19.0 + - - +
23B LEU* 3.6 12.8 - - + +
25B HIS* 1.3 76.3 - - - +
27B TRP* 1.3 85.1 + + - +
29B GLU* 5.1 0.7 - - - -
30B THR* 3.0 17.5 + - - +
31B GLY 2.9 47.9 + - - -
32B THR* 4.2 4.9 - - - -
35B VAL* 3.7 28.9 - - + -
38B HIS* 3.5 57.4 - + + +
54B LEU* 4.4 13.5 - - + -
210B ASN* 4.5 13.2 - - - -
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Residues in contact with TRP 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* 2.9 58.9 + - + +
24B TYR* 3.9 7.4 - + + +
26B PHE* 1.3 94.7 - + - +
28B ARG* 1.3 63.6 + - - +
30B THR 4.4 0.2 - - - -
31B GLY* 3.5 19.6 + - - +
32B THR* 3.6 30.2 - - + +
207B PRO 5.2 4.3 - - - -
210B ASN* 5.0 6.2 - - + +
211B LEU* 4.6 18.4 - - + -
220B ARG* 3.4 31.0 - - - -
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Residues in contact with ARG 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 TYR* 2.9 62.3 + - + +
25B HIS* 3.3 20.9 + - - +
27B TRP* 1.3 78.4 - - - +
29B GLU* 1.3 94.1 + - - +
30B THR 5.4 0.2 - - - -
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Residues in contact with GLU 29 (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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25B HIS* 2.8 41.1 + - - +
28B ARG* 1.3 109.4 + - - +
30B THR* 1.3 65.0 + - - +
45B LYS* 4.9 10.0 + - - -
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Residues in contact with THR 30 (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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26B PHE* 3.0 17.0 + - - -
27B TRP 4.4 0.4 - - - -
28B ARG 3.7 0.2 - - - -
29B GLU* 1.3 86.4 + - - +
31B GLY* 1.3 62.2 + - - +
34B LYS* 3.3 48.5 - - + +
37B LEU* 4.6 4.0 - - + -
38B HIS* 4.0 23.3 + - + +
41B GLN* 3.4 21.5 + - - +
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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