Contacts of the helix formed by residues 18 - 29 (chain H) in PDB entry 6BCH
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 SER 18 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16H ASN 3.7 2.0 + - - -
17H ILE* 1.3 78.3 - - - +
19H PRO* 1.3 75.3 - - - +
20H TRP* 3.2 16.9 + - - +
21H THR* 3.1 28.2 + - - -
22H ILE* 3.2 14.4 + - - +
70H TYR* 4.8 0.2 - - - -
173H ASP* 5.5 0.2 - - - -
175H ASN* 3.6 24.2 + - - -
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Residues in contact with PRO 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ILE 3.9 0.4 - - - +
18H SER* 1.3 89.4 - - - +
20H TRP* 1.3 60.5 + - + +
22H ILE* 3.2 9.0 + - + +
23H THR* 2.9 29.4 + - - -
70H TYR* 3.2 35.2 - - + +
98H HIS* 3.7 9.9 + - + -
102H TYR* 3.5 44.0 - - + +
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Residues in contact with TRP 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H SER* 3.2 10.4 + - - +
19H PRO* 1.3 78.1 - - + +
21H THR* 1.3 61.1 + - - +
23H THR* 4.1 7.6 - - + -
24H GLY 2.9 22.9 + - - -
101H LYS 4.7 2.0 - - - -
102H TYR* 3.8 32.0 - + + -
103H PRO* 3.2 47.8 - - + -
105H ILE* 5.0 1.6 - - + -
172H PRO* 3.4 43.6 + - + -
173H ASP* 3.7 27.3 - - + +
176H TRP* 3.2 37.3 - + - +
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Residues in contact with THR 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ILE* 3.8 23.5 - - + +
18H SER* 3.1 19.2 + - - -
20H TRP* 1.3 76.9 - - - +
22H ILE* 1.3 57.9 + - - +
24H GLY 3.4 0.7 + - - -
25H PHE* 2.9 29.5 + - - +
175H ASN* 3.2 33.7 + - - +
178H ALA* 4.9 5.0 - - + +
179H GLY* 3.6 19.0 - - - +
269H HIS 5.6 1.1 - - - +
271H ILE* 4.4 18.4 - - + -
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ILE* 3.8 24.0 - - + -
18H SER 3.5 11.2 - - - +
19H PRO* 3.2 9.6 + - + +
21H THR* 1.3 77.1 - - - +
23H THR* 1.3 57.9 + - - +
25H PHE* 3.4 5.4 + - - +
26H ALA* 2.9 32.2 + - + +
54H ILE* 5.7 2.2 - - + +
67H ILE* 4.2 35.4 - - + +
70H TYR* 3.6 46.4 - - + -
71H LEU* 5.2 4.7 - - + -
98H HIS* 3.8 17.5 - - + +
99H PHE* 5.7 1.8 - - + -
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Residues in contact with THR 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H PRO 2.9 13.0 + - - -
20H TRP* 3.8 11.2 - - + -
21H THR 3.3 0.2 - - - -
22H ILE* 1.3 77.2 - - - +
24H GLY* 1.3 57.3 + - - +
26H ALA 3.4 0.3 + - - -
27H ASP* 2.8 31.1 + - - +
98H HIS* 3.3 16.1 + - - -
99H PHE* 4.0 11.3 - - + -
102H TYR* 2.7 24.0 + - - +
103H PRO 3.3 30.3 - - - +
104H LEU* 3.6 16.3 - - + +
176H TRP* 4.0 6.7 - - + -
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Residues in contact with GLY 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TRP 2.9 12.0 + - - -
21H THR 3.8 0.4 - - - -
23H THR* 1.3 77.9 - - - +
25H PHE* 1.3 55.5 + - - +
27H ASP* 3.0 5.9 - - - +
28H ALA 3.0 21.1 + - - -
176H TRP* 3.4 38.7 - - - -
180H PHE* 3.6 17.4 - - - -
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Residues in contact with PHE 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ILE* 6.5 0.4 - - + -
21H THR 2.9 17.9 + - - +
22H ILE* 3.8 4.9 - - - +
24H GLY* 1.3 73.4 - - - +
26H ALA* 1.3 61.1 + - - +
28H ALA* 3.1 4.2 + - - +
29H ASP* 2.9 30.0 + - + -
54H ILE* 4.3 13.5 - - + -
56H LEU* 3.5 49.1 - - + -
60H ASP* 5.8 2.7 - - - -
63H ILE* 5.3 5.2 - - + -
67H ILE* 4.9 14.8 - - + -
179H GLY* 3.3 22.7 - - - +
182H ALA* 3.8 30.1 - - + -
183H GLY* 3.8 8.3 - - - -
271H ILE* 4.4 18.6 - - + -
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ILE* 2.9 19.2 + - + +
23H THR 3.8 3.8 - - - +
25H PHE* 1.3 74.1 - - - +
27H ASP* 1.3 66.6 + - - +
28H ALA 3.0 0.2 - - - -
30H SER* 2.6 51.6 + - - +
52H PHE* 4.3 5.2 - - + -
54H ILE* 4.4 11.2 - - + +
99H PHE* 3.9 24.0 - - + -
104H LEU* 4.3 2.5 - - + -
108H LYS* 5.5 2.3 - - - +
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Residues in contact with ASP 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H THR 2.8 12.2 + - - +
24H GLY* 3.0 15.3 - - - +
26H ALA* 1.3 76.8 - - - +
28H ALA* 1.3 57.9 + - - +
104H LEU* 3.4 21.4 - - - +
105H ILE 2.9 15.7 + - - -
106H THR* 2.4 60.9 + - + +
108H LYS* 4.6 5.6 - - - +
176H TRP* 2.9 25.4 + - + -
180H PHE* 4.1 7.8 - - + -
184H GLU* 4.7 0.9 - - - +
211H GLN* 4.8 3.5 + - - -
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLY 3.0 11.7 + - - +
25H PHE* 3.4 7.9 - - - +
26H ALA 3.0 0.4 - - - -
27H ASP* 1.3 80.6 - - - +
29H ASP* 1.3 62.6 + - - +
30H SER 3.8 1.0 - - - +
180H PHE* 4.1 7.4 - - + +
183H GLY* 3.7 21.8 - - - -
184H GLU* 3.2 44.7 - - + +
211H GLN* 5.8 0.2 + - - -
17K A 3.3 12.5 + - - +
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Residues in contact with ASP 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE* 2.9 23.6 + - + +
28H ALA* 1.3 79.1 - - - +
30H SER* 1.3 63.5 + - - +
31H SER* 4.2 0.3 + - - -
54H ILE* 4.8 4.0 - - + -
55H GLY 4.3 6.0 + - - +
56H LEU* 3.3 31.7 - - + +
183H GLY* 4.0 13.1 - - - +
184H GLU* 3.7 7.3 - - - +
16J G 4.3 1.3 + - - -
16K T 3.7 24.7 + - - -
17K A 2.5 39.5 + - - +
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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