Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 3NDR
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 GLN 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 3.8 5.6 + - - +
15A ALA 3.2 2.2 + - - -
16A ALA* 1.3 81.7 - - - +
18A GLY* 1.3 72.5 + - - +
19A ILE 3.4 1.2 + - - -
20A GLY 3.4 3.6 + - - -
21A LYS* 3.1 22.2 + - - -
40A ASN* 4.9 8.3 + - - -
190A ASP* 3.4 33.2 - - - +
191A GLY* 4.1 4.2 - - - +
251A NAD 3.4 49.7 + - - +
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Residues in contact with GLY 18 (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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17A GLN* 1.3 72.9 - - - +
19A ILE* 1.3 63.9 + - - -
21A LYS* 3.7 2.8 - - - +
22A ALA* 3.0 21.5 + - - +
189A SER* 3.8 16.4 - - - -
190A ASP* 2.8 23.6 + - - -
216A PRO* 4.1 9.0 - - - +
251A NAD 3.6 10.3 - - - -
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Residues in contact with ILE 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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18A GLY* 1.3 68.9 - - - -
20A GLY* 1.3 56.8 + - - +
22A ALA* 3.0 2.4 + - - +
23A ILE* 2.7 51.4 + - + +
88A ASN* 3.7 9.0 - - - +
139A ILE* 4.9 2.0 - - + -
184A PRO* 4.8 7.0 - - + -
187A ILE* 4.1 27.8 - - + -
189A SER* 4.7 1.1 - - - -
216A PRO* 4.1 15.9 - - + +
219A ILE* 3.5 30.7 - - + -
251A NAD 2.9 65.4 + - + +
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Residues in contact with GLY 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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12A VAL* 3.6 13.1 - - - +
14A GLY 3.7 5.4 - - - -
15A ALA* 3.6 10.1 - - - -
17A GLN 3.4 2.0 + - - -
18A GLY 3.4 0.4 - - - -
19A ILE* 1.3 76.9 - - - +
21A LYS* 1.3 57.4 + - - +
23A ILE* 3.3 3.9 + - - +
24A ALA* 2.9 26.3 + - - +
88A ASN* 3.2 34.3 + - - +
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Residues in contact with LYS 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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15A ALA 3.1 21.5 + - - +
16A ALA 3.9 13.8 + - - +
17A GLN* 3.1 25.1 + - - +
18A GLY 3.7 2.0 - - - +
20A GLY* 1.3 73.0 - - - +
22A ALA* 1.3 61.1 + - - +
24A ALA* 3.2 4.4 + - - +
25A ALA* 2.9 31.6 + - + +
46A ALA* 5.4 0.8 - - - +
47A ALA* 4.2 27.1 - - + +
50A SER* 4.2 20.2 + - - -
51A ILE* 4.4 8.7 - - + +
190A ASP* 6.0 0.2 - - - +
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Residues in contact with ALA 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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18A GLY 3.0 7.2 + - - +
19A ILE 3.0 9.1 + - - +
21A LYS* 1.3 76.8 - - - +
23A ILE* 1.3 60.5 + - - +
25A ALA* 3.7 7.3 - - - +
26A ARG* 3.3 14.9 + - - +
216A PRO* 3.5 43.3 - - + +
217A GLU* 4.2 13.4 - - + +
220A ALA* 3.2 14.7 - - + +
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Residues in contact with ILE 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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12A VAL* 4.0 10.3 - - + -
19A ILE* 2.7 38.7 + - + +
20A GLY* 3.5 6.3 - - - +
22A ALA* 1.3 74.0 - - - +
24A ALA* 1.3 67.1 + - - +
25A ALA 3.1 1.1 - - - -
26A ARG* 3.0 3.9 + - - +
27A LEU* 2.8 44.3 + - + +
86A VAL* 4.1 16.8 - - + -
88A ASN* 4.4 4.0 - - - +
139A ILE* 4.2 7.4 - - + -
219A ILE* 4.2 0.2 - - + -
220A ALA* 3.7 25.4 - - - +
223A VAL* 3.6 34.1 - - + -
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Residues in contact with ALA 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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12A VAL* 4.2 9.2 - - + +
15A ALA* 4.5 5.2 - - + +
20A GLY 2.9 16.5 + - - +
21A LYS* 3.7 5.6 - - - +
23A ILE* 1.3 75.6 - - - +
25A ALA* 1.3 62.7 + - - +
27A LEU* 3.4 1.3 + - - -
28A ALA* 3.0 25.6 + - - +
34A VAL* 3.7 30.1 - - + +
36A VAL* 4.1 8.7 - - + -
51A ILE* 3.8 17.3 - - + -
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Residues in contact with ALA 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 LYS* 2.9 18.7 + - + +
22A ALA* 3.7 9.0 - - - +
24A ALA* 1.3 78.8 - - - +
26A ARG* 1.3 56.3 + - - +
28A ALA* 3.3 3.8 + - - +
29A ALA* 3.0 26.8 + - - +
51A ILE* 3.9 23.4 - - + +
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Residues in contact with ARG 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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4A ARG* 3.9 6.5 - - - +
22A ALA 3.3 11.1 + - - +
23A ILE 3.0 8.5 + - - +
25A ALA* 1.3 73.7 - - - +
27A LEU* 1.3 61.8 + - + +
28A ALA 3.1 1.6 - - - -
29A ALA* 3.0 13.6 + - - +
30A ASP* 2.8 44.8 + - - -
220A ALA* 3.9 15.0 - - + +
221A ASP* 3.0 32.5 + - - +
224A SER* 3.1 36.9 + - - -
230C ASP* 3.0 38.8 + - - -
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Residues in contact with LEU 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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5A LEU* 3.7 23.6 - - + -
10A ALA* 3.9 22.4 - - + -
12A VAL* 4.0 8.5 - - + -
23A ILE* 2.8 36.0 + - + +
24A ALA 4.6 0.2 - - - -
26A ARG* 1.3 78.0 - - + +
28A ALA* 1.3 62.5 + - - +
30A ASP* 3.1 15.0 + - - +
32A ALA* 3.1 21.6 + - + +
34A VAL* 3.8 14.8 - - + -
84A ILE* 4.7 2.2 - - + -
86A VAL* 4.0 17.3 - - + -
220A ALA 5.7 0.2 - - - +
223A VAL* 4.7 2.0 - - + -
224A SER* 3.9 28.0 - - - +
227A ALA* 4.0 9.2 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.7 + - - +
25A ALA 3.5 5.4 - - - +
27A LEU* 1.3 75.6 - - - +
29A ALA* 1.3 59.4 + - - +
31A GLY 2.8 16.3 + - - -
32A ALA 3.5 11.4 - - - +
34A VAL* 3.7 6.9 - - + +
51A ILE* 3.6 22.9 - - + +
54A LYS* 3.3 37.0 + - + -
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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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3A GLU* 4.3 13.7 + - - +
25A ALA 3.0 14.0 + - - +
26A ARG* 3.0 18.1 + - - +
28A ALA* 1.3 75.4 - - - +
30A ASP* 1.3 61.8 + - - +
31A GLY 3.0 1.0 + - - -
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Residues in contact with ASP 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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3A GLU* 3.0 17.0 - - - +
4A ARG* 4.3 11.9 + - + +
5A LEU* 2.8 53.5 + - + +
26A ARG* 2.8 36.4 + - - +
27A LEU* 3.3 13.0 - - - +
28A ALA 3.1 0.6 - - - -
29A ALA* 1.3 77.0 - - - +
31A GLY* 1.3 58.0 + - - +
32A ALA 3.4 0.4 - - - -
224A SER* 2.8 31.1 + - - +
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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