Contacts of the helix formed by residues 20 - 35 (chain E) in PDB entry 1HBS
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 HIS 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E LYS 5.3 4.0 - - - -
17E VAL 2.3 38.5 + - - +
19E ALA* 1.4 80.0 + - + +
21E ALA* 1.3 68.7 - - - +
22E GLY 3.4 1.3 - - - -
23E GLU* 2.9 33.9 + - - +
24E TYR* 3.1 42.2 + - + -
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E TRP* 4.4 23.1 - - + +
17E VAL* 3.7 13.3 + - + +
18E GLY 3.6 18.4 - - - +
19E ALA* 3.0 2.3 - - - -
20E HIS* 1.3 74.7 - - - +
22E GLY* 1.4 53.4 + - - +
23E GLU 3.3 0.4 - - - -
24E TYR* 4.3 4.2 - - - +
25E GLY* 2.9 13.6 + - - -
63E ALA* 2.7 27.3 - - + +
64E ASP* 5.9 1.8 - - - +
67E THR* 4.7 6.1 - - - +
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Residues in contact with GLY 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ALA 5.2 0.4 + - - -
20E HIS 3.0 3.2 + - - -
21E ALA* 1.4 67.5 - - - +
23E GLU* 1.5 54.9 - - - +
25E GLY* 3.0 7.6 - - - -
26E ALA* 2.3 37.4 + - - +
56E LYS* 4.4 4.1 - - - +
59E GLY 3.7 11.1 - - - +
60E LYS* 4.0 20.0 - - - +
63E ALA* 3.6 13.2 - - - +
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Residues in contact with GLU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E HIS* 2.9 22.2 + - - +
22E GLY* 1.5 76.6 - - - +
24E TYR* 1.4 63.6 + - + +
25E GLY 2.8 1.3 - - - -
26E ALA* 3.2 3.0 - - - +
27E GLU* 2.4 47.5 + - + +
56E LYS* 6.1 7.6 - - + -
112E HIS* 4.6 15.4 - - - -
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Residues in contact with TYR 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E TRP* 5.7 1.6 - + + -
17E VAL* 3.4 35.4 - - + -
20E HIS* 3.1 41.3 + - + +
21E ALA* 4.3 4.5 - - - +
23E GLU* 1.4 85.4 - - - +
25E GLY* 1.6 55.9 + - - +
26E ALA 3.0 0.2 + - - -
27E GLU* 3.1 8.7 + - - +
28E ALA* 3.4 14.9 + - - +
108E THR* 4.2 14.1 - - + +
109E LEU* 3.9 29.2 - - + -
112E HIS* 3.7 40.9 + + + +
113E LEU* 3.3 36.3 - - + +
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Residues in contact with GLY 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ALA 2.9 19.7 + - - -
22E GLY* 3.0 8.9 - - - -
23E GLU 2.8 0.6 - - - -
24E TYR* 1.6 65.1 - - - +
26E ALA* 1.3 59.0 - - - +
28E ALA* 3.9 5.4 - - - +
29E LEU* 3.8 14.4 + - - +
59E GLY* 4.0 13.0 - - - -
62E VAL* 3.9 19.4 - - - +
63E ALA* 4.3 4.5 - - - -
101E LEU* 5.4 0.2 - - - +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLY 2.3 24.0 + - - +
23E GLU* 3.0 3.8 + - - +
25E GLY* 1.3 78.2 - - - +
27E GLU* 1.4 61.7 + - - +
28E ALA 3.4 0.2 - - - -
29E LEU* 3.3 11.7 + - - +
30E GLU* 3.4 18.0 + - - +
55E VAL* 3.3 34.1 - - + +
56E LYS* 4.0 15.3 - - + -
59E GLY* 3.9 4.7 - - - -
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLU* 2.4 28.5 + - + +
24E TYR* 3.1 2.1 + - - +
26E ALA* 1.4 65.8 - - - +
28E ALA* 1.3 54.2 + - - +
30E GLU* 2.9 17.2 - - + +
31E ARG* 2.4 72.5 + - + +
108E THR* 3.7 14.4 - - + -
111E ALA* 5.3 0.2 - - - +
112E HIS* 2.5 42.7 + - - -
124F PRO* 5.6 3.4 - - + -
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Residues in contact with ALA 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TYR 3.4 16.6 + - - +
25E GLY* 3.9 7.0 - - - +
27E GLU* 1.3 73.1 - - - +
29E LEU* 1.5 78.0 - - + +
31E ARG* 2.8 7.6 + - - +
32E MET* 2.6 23.7 + - - +
101E LEU* 3.8 10.0 - - + +
104E CYS* 3.9 17.2 - - + -
105E LEU* 4.3 15.3 - - + -
108E THR* 3.9 10.8 - - - +
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLY 3.8 10.0 + - - +
26E ALA* 3.3 7.3 + - - +
27E GLU 3.3 0.6 - - - -
28E ALA* 1.5 63.4 - - - +
30E GLU* 1.3 49.7 + - - +
32E MET* 2.8 14.7 - - + +
33E PHE* 2.7 60.4 + - + -
43E PHE* 4.5 8.1 - - + -
55E VAL* 3.8 21.3 - - + -
58E HIS* 3.1 41.1 - - + -
59E GLY* 5.6 1.8 - - - -
62E VAL* 5.3 4.5 - - + -
101E LEU* 2.9 45.5 - - + -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA* 3.4 13.0 + - - +
27E GLU* 2.9 23.8 - - + +
28E ALA 2.8 0.4 + - - -
29E LEU* 1.3 73.9 - - - +
31E ARG* 1.3 65.7 - - - +
33E PHE* 3.6 13.7 + - - +
34E LEU* 3.2 31.7 + - + +
50E HIS* 2.3 50.6 + - - +
51E GLY* 4.7 5.9 + - - +
55E VAL* 4.7 7.7 - - + +
124F PRO* 4.9 11.0 - - + +
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU* 2.4 51.9 + - + +
28E ALA* 3.4 10.1 - - - +
30E GLU* 1.3 78.5 - - - +
32E MET* 1.3 52.2 + - - +
34E LEU* 3.6 2.1 + - - +
35E SER* 2.7 30.8 + - - -
104E CYS* 4.4 4.9 - - + -
107E VAL* 4.0 15.7 + - - -
108E THR* 4.1 11.5 - - - +
111E ALA* 4.5 13.9 - - - +
119F GLY 4.5 4.6 + - - -
120F LYS* 5.8 1.0 - - - +
122F PHE* 2.0 49.6 + - - +
123F THR* 3.6 14.4 - - - +
124F PRO* 3.1 32.8 - - + +
127F GLN* 3.0 26.3 + - - +
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Residues in contact with MET 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ALA 2.6 16.2 + - - +
29E LEU* 2.8 26.5 - - + +
31E ARG* 1.3 68.6 - - - +
33E PHE* 1.2 55.6 - - + +
35E SER* 3.4 3.0 + - - -
36E PHE* 3.0 33.0 + - + -
39E THR* 3.4 38.5 - - + +
43E PHE* 4.3 12.8 - - + -
97E ASN* 5.0 3.6 - - - +
100E LEU* 4.1 7.9 - - - -
101E LEU* 3.6 45.8 - - + -
104E CYS* 3.5 13.3 - - - -
142E HEM 5.0 8.5 - - + -
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Residues in contact with PHE 33 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E LEU* 2.7 42.5 + - + +
30E GLU* 3.9 9.0 - - - +
31E ARG 3.5 0.6 - - - -
32E MET* 1.2 78.5 - - + +
34E LEU* 1.4 60.2 + - + +
37E PRO* 3.5 23.2 - - - +
39E THR* 3.1 38.8 - - + -
40E LYS* 3.4 26.9 - - + +
43E PHE* 3.3 37.0 - + + -
46E PHE* 6.0 0.9 - + - -
48E LEU* 2.7 36.1 - - + -
55E VAL* 4.9 6.3 - - + -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLU* 3.2 25.5 + - + +
31E ARG 3.6 4.3 + - - +
33E PHE* 1.4 71.4 - - + +
35E SER* 1.4 60.5 + - - +
37E PRO* 3.9 10.5 - - - +
124F PRO* 3.5 30.7 - - + +
125F PRO* 4.5 12.1 - - + -
128F ALA* 3.1 18.9 - - + +
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG 2.7 22.4 + - - -
32E MET 3.4 3.5 + - - -
34E LEU* 1.4 74.6 - - - +
36E PHE* 1.4 88.4 + - - +
37E PRO* 3.4 6.0 - - - +
127F GLN* 4.1 9.7 + - - -
128F ALA* 3.1 22.5 - - - +
131F GLN* 3.4 29.1 - - - +
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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