Contacts of the helix formed by residues 16 - 29 (chain A) in PDB entry 3N3B
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 ASP 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.3 11.5 - - - +
15A SER* 1.3 76.2 - - - +
17A ASP* 1.3 67.0 + - - +
18A LYS* 3.3 13.4 + - - +
19A ASP* 3.0 33.6 + - - +
84A THR* 4.7 5.8 - - + -
201A TYR* 2.7 40.7 + - - -
202A LYS* 3.9 10.6 + - - +
205A LYS* 3.9 14.9 - - - -
10D SER* 4.6 1.9 + - - -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.9 18.1 - - - +
15A SER 4.0 2.1 + - - -
16A ASP* 1.3 73.5 + - - +
18A LYS* 1.3 64.9 + - + +
19A ASP 3.4 0.2 + - - -
20A LEU* 3.4 10.5 + - - +
21A GLU* 3.1 27.7 + - - +
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Residues in contact with LYS 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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16A ASP* 3.1 12.9 + - - +
17A ASP* 1.3 79.9 - - + +
19A ASP* 1.3 59.8 + - - +
21A GLU* 2.9 34.9 + - + +
22A VAL* 2.9 36.7 + - + +
197A TYR* 2.8 37.3 + - + +
198A TYR* 4.3 4.5 - - + -
201A TYR* 3.8 27.1 - - + -
9D SER* 3.7 18.8 + - - -
10D SER* 3.3 27.8 - - - +
11D SER* 4.1 5.2 - - - +
49D TYR* 3.7 10.7 + - - -
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 5.0 1.3 - - - -
14A ILE* 5.2 1.5 - - + +
16A ASP* 3.0 27.7 + - - +
18A LYS* 1.3 77.5 - - - +
20A LEU* 1.3 57.8 + - - +
22A VAL* 4.0 0.2 - - - -
23A TRP* 3.0 29.4 + - - +
84A THR* 2.6 32.3 + - - +
86A HIS* 3.8 23.0 + - + +
87A GLU 4.2 2.0 - - - -
90A VAL* 3.4 7.6 - - - +
198A TYR* 2.6 31.6 + - - +
202A LYS* 2.9 19.0 + - - -
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Residues in contact with LEU 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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11A TRP* 3.7 31.8 - - + +
14A ILE* 4.4 30.7 - - + +
16A ASP 4.1 0.8 + - - -
17A ASP* 3.4 10.3 + - - +
18A LYS 3.4 0.2 - - - -
19A ASP* 1.3 75.6 - - - +
21A GLU* 1.3 60.4 + - - +
23A TRP* 3.6 6.4 - - + +
24A ASN* 2.9 50.4 + - - +
103B ARG* 3.9 20.4 - - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 3.1 22.2 + - - +
18A LYS* 2.9 41.3 + - + +
19A ASP 3.3 0.2 - - - -
20A LEU* 1.3 78.7 - - - +
22A VAL* 1.3 57.9 + - + +
24A ASN* 3.7 5.4 + - - +
25A ARG* 3.2 27.2 + - - +
9D SER* 5.1 0.2 + - - -
49D TYR* 3.3 22.9 - - - -
134D FMN 4.1 18.7 - - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 2.9 21.5 + - + +
19A ASP 4.2 1.1 - - - +
21A GLU* 1.3 76.6 - - + +
23A TRP* 1.3 66.2 + - - +
25A ARG* 3.8 4.9 - - - +
26A LEU* 2.9 46.2 + - + +
90A VAL* 3.9 9.4 - - + -
194A VAL* 3.9 18.2 - - + -
197A TYR* 4.5 16.4 - - + -
198A TYR* 3.4 40.2 - - + -
134D FMN 4.7 6.5 - - + -
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Residues in contact with TRP 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 TRP* 3.7 28.7 - + + -
19A ASP 3.0 20.3 + - - +
20A LEU* 3.4 6.3 + - + +
22A VAL* 1.3 76.2 - - - +
24A ASN* 1.3 70.6 + - - +
26A LEU* 4.0 1.7 - - - -
27A THR* 2.7 59.2 + - + +
89A ALA* 3.7 34.1 - - + -
90A VAL* 3.8 14.1 - - + +
93A ASN* 4.7 2.7 - - + -
32B LEU* 4.9 7.1 - - + +
33B PRO* 6.2 0.2 - - + -
34B GLU* 5.4 2.6 + - - -
96B PHE* 3.9 27.4 - + - -
99B ALA* 4.2 13.0 - - + -
100B VAL* 4.0 17.9 - - + -
103B ARG* 3.8 39.7 - - + +
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Residues in contact with ASN 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 LEU* 2.9 39.4 + - - +
21A GLU* 4.0 5.3 - - - +
23A TRP* 1.3 93.0 + - - +
25A ARG* 1.3 53.9 + - - +
27A THR* 3.7 4.5 + - - -
28A SER* 2.6 37.8 + - - -
34B GLU* 4.1 17.3 + - - +
103B ARG* 5.1 1.7 + - - +
51D GLY* 6.3 0.2 - - - -
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Residues in contact with ARG 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 GLU 3.2 19.0 + - - +
22A VAL* 3.8 6.5 - - - +
23A TRP 3.3 0.4 - - - -
24A ASN* 1.3 77.0 - - - +
26A LEU* 1.3 61.1 + - + +
28A SER* 3.5 3.1 + - - -
29A ASN* 2.8 59.0 + - - +
190A ARG* 3.7 14.5 - - - +
194A VAL* 4.1 19.7 - - + -
50D GLY 3.0 22.3 + - - -
51D GLY* 3.2 25.5 + - - -
86D PHE* 3.2 41.2 - - - +
134D FMN 3.3 37.8 + - + -
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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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22A VAL* 2.9 36.3 + - + +
23A TRP* 4.1 2.2 - - - +
25A ARG* 1.3 76.3 - - - +
27A THR* 1.3 64.7 + - - +
29A ASN* 3.4 14.0 + - + +
30A PHE* 3.6 9.0 + - - -
90A VAL* 4.3 6.3 - - + -
93A ASN* 3.2 27.8 + - - +
94A ILE* 3.8 25.4 - - + -
97A MET* 5.5 6.0 - - + +
191A ASP* 4.2 16.9 - - - +
194A VAL* 3.8 26.2 - - + -
195A HIS* 3.7 25.6 - - + +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 2.7 52.5 + - + +
24A ASN* 3.7 7.4 + - - -
26A LEU* 1.3 75.5 - - - +
28A SER* 1.3 63.0 + - - +
30A PHE* 3.3 20.9 - - - +
93A ASN* 3.7 22.4 - - - +
30B PHE* 3.4 13.2 - - - -
32B LEU* 3.7 25.8 - - + +
96B PHE* 3.9 17.9 - - + -
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Residues in contact with SER 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 ASN 2.6 22.0 + - - -
25A ARG* 3.5 6.4 + - - -
27A THR* 1.3 79.0 + - - +
29A ASN* 1.3 67.3 + - - +
30A PHE* 3.2 6.4 + - - +
32B LEU* 4.4 10.5 - - - -
51D GLY 4.5 1.9 + - - -
52D GLY* 4.4 17.2 + - - -
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Residues in contact with ASN 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 ARG* 2.8 51.5 + - - +
26A LEU* 3.4 9.2 + - + +
27A THR 3.2 1.0 - - - -
28A SER* 1.3 83.1 + - - +
30A PHE* 1.3 64.6 + - - +
31A TRP* 3.2 12.0 - - - -
97A MET* 5.0 0.4 - - - +
190A ARG* 3.2 45.0 + - - +
191A ASP* 4.4 10.3 - - - +
194A VAL* 5.6 1.4 - - - +
51D GLY 3.9 15.6 + - - -
52D GLY* 4.6 5.9 - - - -
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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