Contacts of the helix formed by residues 14 - 27 (chain A) in PDB entry 2B69
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY 3.2 7.8 + - - -
12A GLY 3.4 0.2 - - - -
13A ALA* 1.3 79.1 - - - +
15A PHE* 1.3 62.9 + - - -
16A VAL 3.7 1.1 - - - -
17A GLY 4.2 1.3 - - - -
18A SER* 3.0 30.1 + - - -
40A GLY* 4.2 2.9 - - - -
44A ASN* 3.8 6.4 + - - -
800A NAD 3.1 33.1 + - - -
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Residues in contact with PHE 15 (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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14A GLY* 1.3 74.3 - - - +
16A VAL* 1.3 78.9 + - + +
18A SER* 3.1 13.2 + - - -
19A HIS* 3.2 15.6 - + - -
44A ASN* 4.4 4.5 - - - +
177A THR* 3.5 22.2 - - + -
178A PHE* 3.4 27.4 - - - -
179A GLY* 3.4 14.6 - - - -
180A PRO 3.3 28.0 - - - -
181A ARG* 4.7 4.5 - - - +
182A MSE 3.8 28.3 - - + -
188A ARG* 4.6 7.2 - - - +
218A VAL* 3.9 22.0 - - + -
800A NAD 3.0 38.9 + - - +
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Residues in contact with VAL 16 (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 PHE* 1.3 93.6 - - + +
17A GLY* 1.3 64.6 + - - +
19A HIS* 3.1 7.1 + - - +
20A LEU* 3.1 19.0 + - + +
75A LEU* 3.9 18.6 - - + -
174A ILE* 5.8 1.1 - - + -
177A THR* 4.8 0.4 - - + -
218A VAL* 4.4 9.2 - - + -
221A LEU* 3.8 31.0 - - + -
222A VAL* 4.8 8.5 - - + -
225A LEU* 4.3 13.0 - - + -
800A NAD 2.9 41.9 + - + +
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Residues in contact with GLY 17 (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* 4.5 3.6 - - - +
11A GLY 4.0 12.2 + - - -
12A GLY* 3.2 15.6 - - - +
14A GLY 3.9 2.8 + - - -
15A PHE 3.4 1.0 - - - -
16A VAL* 1.3 78.1 - - - +
18A SER* 1.3 57.0 + - - +
20A LEU* 3.4 4.7 + - - +
21A THR* 2.9 32.1 + - - -
75A LEU* 3.9 19.8 - - - +
800A NAD 4.4 1.6 + - - -
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Residues in contact with SER 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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12A GLY 3.2 12.4 + - - -
14A GLY 3.0 23.3 + - - -
15A PHE* 3.1 9.5 + - - -
16A VAL 3.2 0.2 - - - -
17A GLY* 1.3 75.9 - - - +
19A HIS* 1.3 55.2 + - - +
21A THR* 3.5 3.2 - - - -
22A ASP* 3.2 31.4 + - - +
44A ASN* 3.5 30.5 - - - +
45A VAL* 3.9 6.7 - - - +
181A ARG* 3.1 25.5 + - - -
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Residues in contact with HIS 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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15A PHE* 3.2 24.2 - + - -
16A VAL 3.1 6.8 + - - +
18A SER* 1.3 78.9 + - - +
20A LEU* 1.3 63.9 + - - +
22A ASP* 3.4 11.6 + - - +
23A LYS* 3.3 19.8 + - - +
180A PRO* 3.0 39.5 + - + -
181A ARG* 3.9 24.8 + - - +
217A TYR* 5.7 0.4 - - - -
218A VAL* 3.8 33.8 - - + +
219A SER* 6.3 0.4 - - - -
222A VAL* 4.0 19.2 - - + +
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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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9A ILE* 4.1 16.8 - - + -
16A VAL* 3.1 15.6 + - + +
17A GLY* 3.7 7.0 - - - +
19A HIS* 1.3 72.2 - - - +
21A THR* 1.3 65.9 + - - +
23A LYS* 3.2 3.5 + - - +
24A LEU* 3.1 39.0 + - + +
73A TYR* 3.7 41.7 - - + -
75A LEU* 4.5 12.3 - - + -
222A VAL* 3.9 22.3 - - + +
225A LEU* 4.7 11.7 - - + -
226A VAL* 3.9 27.6 - - + -
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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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9A ILE* 3.5 20.6 - - - +
12A GLY* 3.7 3.6 + - - -
17A GLY 2.9 22.3 + - - -
18A SER* 3.5 9.6 - - - -
20A LEU* 1.3 76.5 - - - +
22A ASP* 1.3 62.4 + - - +
24A LEU* 3.4 1.7 + - - +
25A MSE 3.0 34.7 + - + +
31A VAL* 4.4 5.2 - - + -
33A VAL* 3.6 14.8 - - + +
45A VAL* 4.5 5.8 - - + -
48A TRP* 3.9 17.3 - - + -
54A PHE* 3.8 28.9 - - + -
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Residues in contact with ASP 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 SER 3.2 11.4 + - - +
19A HIS* 3.5 13.3 + - - +
20A LEU 3.3 0.4 - - - -
21A THR* 1.3 77.8 - - - +
23A LYS* 1.3 55.9 + - - +
25A MSE 4.0 1.2 - - - +
26A MSE 2.6 42.0 + - + +
45A VAL* 6.1 0.2 - - - +
47A HIS* 2.9 15.5 + - - -
48A TRP* 2.8 36.6 + - + +
181A ARG* 3.0 30.0 + - - -
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Residues in contact with LYS 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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19A HIS 3.3 3.3 + - - +
20A LEU 3.2 8.5 + - - +
22A ASP* 1.3 78.0 - - - +
24A LEU* 1.3 64.2 + - + +
26A MSE 3.4 9.0 + - - +
27A ASP* 3.2 43.6 + - - +
222A VAL* 3.6 31.4 - - + -
223A ASN* 3.1 24.3 + - - +
226A VAL* 3.9 32.8 - - + -
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Residues in contact with LEU 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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7A ILE* 4.0 20.6 - - + -
9A ILE* 4.2 8.5 - - + -
20A LEU* 3.1 32.9 + - + +
21A THR* 4.1 0.9 - - - +
23A LYS* 1.3 75.2 - - + +
25A MSE 1.3 65.7 + - - +
27A ASP* 3.4 12.1 + - - +
28A GLY 3.4 0.3 + - - -
29A HIS* 3.3 47.4 + - + +
31A VAL* 3.9 17.0 - - + -
73A TYR* 3.7 30.3 - - + +
226A VAL* 4.2 22.9 - - + -
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Residues in contact with MSE 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 28.9 + - + +
24A LEU* 1.3 74.1 - - - +
26A MSE 1.3 64.8 + - - +
28A GLY* 3.2 14.0 + - - -
29A HIS 4.0 6.7 - - - +
31A VAL* 3.8 21.1 - - + -
48A TRP* 3.7 43.0 - - + -
51A HIS* 3.4 42.6 + - + +
53A ASN* 3.5 28.2 + - + +
54A PHE* 3.9 15.0 - - + -
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Residues in contact with MSE 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 ASP* 2.6 32.3 + - - +
23A LYS* 3.6 8.3 - - - +
25A MSE 1.3 77.0 - - - +
27A ASP* 1.3 65.0 + - - +
28A GLY* 3.3 1.6 + - - -
48A TRP* 4.0 22.2 - - + -
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Residues in contact with ASP 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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4A ARG* 6.1 0.3 - - - +
23A LYS* 3.2 38.7 + - - +
24A LEU* 3.8 10.7 - - - +
25A MSE 3.2 0.6 - - - -
26A MSE 1.3 80.9 - - - +
28A GLY* 1.3 59.4 + - - +
29A HIS* 3.6 22.8 + - + +
226A VAL* 5.7 1.9 - - - +
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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