Contacts of the helix formed by residues 36 - 42 (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 PHE 36 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E MET* 3.0 21.6 + - + +
33E PHE 3.7 1.9 - - - +
34E LEU 3.3 0.2 - - - -
35E SER* 1.4 97.5 - - - +
37E PRO* 1.3 71.8 - - - +
38E THR* 2.4 24.2 + - + +
39E THR* 2.6 26.2 - - + +
100E LEU* 4.1 45.5 - - + -
103E HIS* 4.0 23.8 - + + -
104E CYS* 4.7 6.3 - - - -
108F ASN* 5.5 2.0 - - - -
127F GLN* 5.6 1.1 - - - -
131F GLN* 3.9 28.5 - - + -
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Residues in contact with PRO 37 (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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33E PHE 3.5 12.1 - - - +
34E LEU* 3.9 11.2 - - - +
35E SER 3.4 7.9 - - - +
36E PHE* 1.3 90.0 - - - +
38E THR* 1.4 66.3 + - - +
39E THR 3.3 0.2 - - - -
40E LYS* 2.8 27.0 + - + +
41E THR* 4.3 0.5 + - - +
145H TYR* 4.4 16.1 - - - +
146H HIS* 3.0 38.0 - - - +
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Residues in contact with THR 38 (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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36E PHE* 2.4 26.4 + - + +
37E PRO* 1.4 86.8 - - - +
39E THR* 1.3 74.7 - - + +
40E LYS 2.9 3.4 + - - -
41E THR* 3.3 24.3 - - - +
97E ASN* 4.1 13.9 - - - +
100E LEU* 5.1 10.5 - - + -
99H ASP* 2.8 23.3 + - - +
100H PRO* 3.3 19.8 - - - +
145H TYR* 5.1 11.2 - - - +
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Residues in contact with THR 39 (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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32E MET* 3.4 39.3 - - + +
33E PHE* 3.1 11.5 - - + -
36E PHE* 2.6 30.7 - - + +
38E THR* 1.3 82.2 - - + +
40E LYS* 1.3 64.5 + - - +
41E THR 3.3 1.8 - - - -
42E TYR* 4.3 11.7 - - - -
43E PHE* 2.4 46.3 - - - -
97E ASN* 4.6 7.6 - - - +
100E LEU* 6.6 0.2 - - - -
142E HEM 3.8 2.4 - - - +
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Residues in contact with LYS 40 (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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33E PHE* 3.4 44.0 - - + +
37E PRO* 2.8 19.3 + - - +
39E THR* 1.3 80.7 - - - +
41E THR* 1.3 52.4 + - - +
43E PHE* 2.5 39.7 + - - +
44E PRO* 3.6 1.4 - - - +
48E LEU* 4.9 13.7 - - + -
146H HIS* 3.0 34.6 + - - -
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Residues in contact with THR 41 (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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38E THR 3.3 19.9 + - - +
39E THR 3.3 0.4 - - - -
40E LYS* 1.3 75.3 - - - +
42E TYR* 1.2 67.9 + - + +
44E PRO* 3.3 15.3 - - - +
40H ARG* 5.0 2.6 + - - -
93H CYS* 5.8 0.2 - - - -
97H HIS* 2.6 48.0 + - - +
98H VAL 3.5 26.6 - - - +
99H ASP* 4.1 9.2 + - + -
100H PRO* 4.2 0.9 - - + -
145H TYR* 3.8 21.1 - - + -
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Residues in contact with TYR 42 (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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38E THR 5.2 0.4 - - - -
39E THR* 4.5 9.6 - - - -
40E LYS 2.9 1.8 + - - -
41E THR* 1.2 84.0 + - - +
43E PHE* 1.3 71.3 + + + +
44E PRO* 3.0 9.5 - - - +
45E HIS* 4.4 2.6 - - - -
92E ARG 3.9 3.5 + - - -
93E VAL* 3.7 16.6 - - + -
94E ASP* 2.6 34.7 + - - +
97E ASN* 3.2 14.6 - - - -
142E HEM 3.3 41.9 - - + +
37H TRP* 5.2 1.0 - - - -
40H ARG* 3.1 48.8 + - - +
41H PHE* 5.8 1.8 - + - -
99H ASP* 2.9 42.7 + - + +
102H ASN* 5.5 2.1 + - - -
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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