Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 6ABP
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 TRP 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.7 12.8 - - + +
15A PRO* 1.4 73.0 - - - +
17A PHE* 1.3 89.1 + + - +
19A THR* 3.4 4.2 + - - -
20A GLU* 3.2 28.7 + - - +
89A ASP* 3.2 34.6 + - - -
108A LEU* 4.2 6.5 - - + -
232A ASN* 3.6 26.2 - - + +
234A VAL* 3.5 10.0 - - - +
235A ASP* 2.7 19.3 + - - +
254A PRO* 3.7 31.9 - - + -
256A PRO* 3.5 46.9 - - + +
259A HIS* 3.8 18.4 - + - -
307A ARA 3.4 25.0 - - - -
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Residues in contact with PHE 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 VAL* 3.7 29.0 - - + +
10A LYS* 3.8 24.9 - - + -
11A GLN* 3.2 33.4 - - + +
12A PRO* 4.7 1.8 - - + -
14A GLU* 3.0 23.7 + - + +
16A TRP* 1.3 89.6 - + - +
18A GLN* 1.3 66.7 + - - +
19A THR 3.1 2.0 - - - -
20A GLU* 3.1 19.6 + - - +
21A TRP* 3.0 28.6 + - - +
64A CYS* 3.6 32.5 - - + -
89A ASP* 3.3 22.9 - - - -
307A ARA 4.3 7.0 - - - -
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Residues in contact with GLN 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 PRO 3.0 26.6 + - - +
13A GLU* 3.6 18.0 + - - +
14A GLU 3.1 11.0 + - - +
15A PRO* 3.1 20.6 + - - +
17A PHE* 1.3 77.4 - - - +
19A THR* 1.4 57.6 + - - +
21A TRP* 3.4 18.7 + - + +
22A LYS* 2.9 31.9 + - - +
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Residues in contact with THR 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 PRO* 2.8 23.2 + - - +
16A TRP 3.6 5.4 - - - -
18A GLN* 1.4 75.6 - - - +
20A GLU* 1.4 64.2 + - - +
22A LYS* 3.2 10.3 + - + +
23A PHE* 3.1 28.9 + - + +
234A VAL* 4.2 12.4 - - + +
256A PRO* 4.0 21.0 - - + +
257A ASP 4.0 7.0 - - - +
303A LEU* 3.6 31.6 - - + +
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Residues in contact with GLU 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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7A PHE* 3.7 26.9 - - + -
16A TRP* 3.2 25.5 + - - +
17A PHE* 3.1 27.9 + - - +
19A THR* 1.4 75.7 - - - +
21A TRP* 1.4 57.7 + - - +
23A PHE 3.2 1.6 + - - -
24A ALA* 2.9 27.0 + - - +
88A VAL* 3.8 7.7 - - - +
89A ASP* 2.6 31.8 - - - +
256A PRO* 3.5 22.2 - - + +
259A HIS* 3.5 15.4 + - - +
260A GLY* 3.4 14.1 - - - +
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Residues in contact with TRP 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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7A PHE* 2.9 46.2 + + + -
9A VAL* 3.6 16.5 - - + +
12A PRO* 3.8 32.8 - - + -
17A PHE 3.0 13.7 + - - +
18A GLN* 3.4 19.5 - - + +
20A GLU* 1.4 76.2 - - - +
22A LYS* 1.3 63.8 + - - +
24A ALA* 3.3 5.0 + - - +
25A ASP* 3.1 27.3 + - - +
35A VAL* 5.4 0.2 - - + -
37A LYS* 3.6 37.7 - - + +
38A ILE* 3.6 35.7 - - - -
39A ALA* 4.4 2.7 - - + -
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Residues in contact with LYS 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 GLN* 2.9 19.1 + - - -
19A THR* 3.2 13.4 + - + +
21A TRP* 1.3 78.1 - - - +
23A PHE* 1.3 78.3 + - + +
25A ASP* 3.5 11.1 + - - +
26A LYS* 3.2 33.8 + - + +
303A LEU* 6.2 0.4 - - + -
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Residues in contact with PHE 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 THR* 3.1 25.0 + - + +
20A GLU 4.0 1.3 - - - +
22A LYS* 1.3 92.8 - - + +
24A ALA* 1.3 64.9 + - - +
26A LYS* 3.2 35.3 + - + +
27A ALA 3.0 17.5 + - - -
257A ASP* 3.4 48.7 - - + +
260A GLY* 4.2 0.4 - - - -
261A TYR* 3.5 27.9 - + + +
301A LYS 5.2 1.8 - - - -
302A GLY* 4.5 13.0 - - - -
303A LEU* 3.6 26.5 - - + -
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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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7A PHE* 3.5 20.9 - - + -
20A GLU 2.9 15.9 + - - +
21A TRP* 3.3 6.3 + - - +
23A PHE* 1.3 74.7 - - - +
25A ASP* 1.3 64.6 + - - +
27A ALA* 3.1 4.2 + - - +
28A GLY 2.9 19.4 + - - -
33A PHE* 4.4 1.0 - - - -
35A VAL* 3.6 19.0 - - + +
260A GLY 3.6 5.3 + - - +
264A SER* 3.3 26.5 - - - +
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Residues in contact with ASP 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 TRP 3.1 16.0 + - - +
22A LYS* 3.5 13.0 - - - +
24A ALA* 1.3 75.9 - - - +
26A LYS* 1.3 61.4 + - - +
28A GLY* 3.1 1.9 + - - -
29A LYS* 2.9 49.6 + - - +
35A VAL* 3.5 15.8 + - - +
37A LYS* 2.7 40.2 + - - +
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Residues in contact with LYS 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 LYS* 3.2 25.1 + - + +
23A PHE* 3.5 48.5 - - + +
24A ALA 3.2 0.6 - - - -
25A ASP* 1.3 75.7 - - - +
27A ALA* 1.3 58.3 - - - +
29A LYS* 3.2 17.6 + - + +
30A ASP* 2.9 34.7 + - - +
261A TYR* 3.9 12.6 - - + -
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Residues in contact with ALA 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 PHE 3.0 8.4 + - - +
24A ALA 3.6 6.7 - - - +
26A LYS* 1.3 75.9 - - - +
28A GLY* 1.3 54.5 - - - +
30A ASP* 3.3 1.6 + - - +
31A LEU* 2.9 40.5 + - + +
33A PHE* 3.7 7.2 - - + -
261A TYR* 3.6 47.7 - - + +
264A SER* 3.8 13.5 - - - -
265A GLU* 4.3 4.9 - - - +
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Residues in contact with GLY 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 2.9 12.0 + - - -
25A ASP 3.1 4.0 + - - -
27A ALA* 1.3 76.1 - - - +
29A LYS* 1.3 59.2 + - - +
32A GLY* 2.8 26.5 + - - -
33A PHE* 3.0 47.5 + - - +
35A VAL* 4.6 2.9 - - - -
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Residues in contact with LYS 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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22A LYS 5.4 0.2 - - - -
25A ASP* 2.9 48.8 + - - +
26A LYS* 3.2 19.0 + - + +
28A GLY* 1.3 76.7 - - - +
30A ASP* 1.3 67.3 + - - +
32A GLY* 3.9 4.2 + - - -
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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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26A LYS* 2.9 19.1 + - - +
27A ALA 3.6 4.0 - - - +
28A GLY 3.3 0.2 - - - -
29A LYS* 1.3 81.2 - - - +
31A LEU* 1.3 65.8 + - + +
261A TYR* 2.6 34.9 + - - +
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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