Contacts of the helix formed by residues 38 - 49 (chain H) in PDB entry 1HBX
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 ALA 38 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23H MET 4.3 0.4 + - - -
35H LEU* 3.4 39.7 + - + +
37H GLN* 1.3 75.5 - - - +
39H GLU* 1.3 59.3 + - - +
40H GLU 3.0 1.8 - - - -
41H VAL* 2.5 40.8 + - - +
42H ALA* 2.9 9.6 + - - +
56H TYR* 4.2 11.4 - - + -
80H PHE* 3.5 22.2 - - + -
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Residues in contact with GLU 39 (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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37H GLN* 2.6 14.8 + - + +
38H ALA* 1.3 72.7 - - - +
40H GLU* 1.3 58.4 + - - +
42H ALA* 2.8 27.8 - - - +
43H ARG* 2.9 34.0 + - - +
55H ASN* 3.6 25.1 - - - +
56H TYR* 4.1 17.5 + - - +
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Residues in contact with GLU 40 (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 HIS* 5.0 3.4 - - + +
23H MET* 3.3 33.7 - - + -
37H GLN* 4.5 12.9 + - + +
38H ALA 2.8 4.4 + - - +
39H GLU* 1.3 72.2 - - - +
41H VAL* 1.3 51.9 + - - +
42H ALA 2.8 1.3 - - - -
43H ARG* 2.6 61.5 + - - +
44H LEU* 2.6 51.5 + - + +
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Residues in contact with VAL 41 (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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10H PHE* 4.3 8.8 - - + -
11H LEU* 3.5 32.5 - - + -
14H LEU* 6.0 1.6 - - + -
23H MET* 4.1 15.0 - - + -
24H ILE* 3.6 32.5 - - + -
35H LEU* 4.4 6.1 - - + -
38H ALA* 2.5 32.7 + - - +
40H GLU* 1.3 72.9 - - - +
42H ALA* 1.3 49.2 + - - +
44H LEU* 3.1 16.7 - - + +
45H TRP* 2.7 32.1 + - - +
59H LEU* 4.5 6.3 - - + -
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Residues in contact with ALA 42 (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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38H ALA 2.9 6.0 + - - +
39H GLU* 2.8 20.2 - - - +
40H GLU 2.8 0.6 + - - -
41H VAL* 1.3 73.4 - - - +
43H ARG* 1.3 55.6 + - - +
44H LEU 2.9 1.1 - - - -
45H TRP* 2.4 31.8 + - - +
46H GLY 2.8 10.0 + - - -
54H MET* 3.7 7.1 - - - +
55H ASN* 3.4 14.6 - - - -
56H TYR* 3.3 33.0 - - + +
59H LEU* 4.3 6.6 - - + +
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Residues in contact with ARG 43 (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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39H GLU* 2.9 37.4 + - - +
40H GLU* 2.6 48.8 + - - +
42H ALA* 1.3 71.5 - - - +
44H LEU* 1.3 59.4 + - - +
46H GLY* 3.2 11.2 + - - +
47H ILE* 3.2 20.2 + - - +
54H MET 4.2 5.3 + - - +
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Residues in contact with LEU 44 (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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10H PHE* 3.1 25.6 - - + -
14H LEU* 5.0 11.2 - - + -
20H ASN* 4.4 9.0 - - - +
23H MET* 3.4 33.9 - - + -
24H ILE* 6.0 0.7 - - + -
40H GLU* 2.6 29.4 + - + +
41H VAL* 3.1 23.8 - - + +
43H ARG* 1.3 72.0 - - - +
45H TRP* 1.3 58.6 + - - +
46H GLY 3.4 0.2 - - - -
47H ILE* 3.0 35.2 - - + +
48H ARG* 4.0 1.4 + - - +
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Residues in contact with TRP 45 (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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-8F T 3.1 30.2 + - - -
-7F C 4.3 1.8 - - - -
5H ILE* 5.0 0.9 - - + -
6H THR 3.0 23.6 - - - -
7H LEU* 3.3 36.4 - - + +
10H PHE* 3.7 23.6 - + + -
41H VAL 2.7 10.6 + - - +
42H ALA 2.4 22.6 + - - +
44H LEU* 1.3 71.4 - - - +
46H GLY* 1.3 52.1 + - - +
48H ARG* 2.4 60.1 + - + +
49H LYS* 3.5 21.3 - - + -
51H LYS* 5.3 0.5 - - - +
54H MET* 3.4 27.2 - - + +
59H LEU* 3.3 31.8 - - + +
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Residues in contact with GLY 46 (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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42H ALA 2.8 10.6 + - - -
43H ARG* 3.2 5.7 + - - -
45H TRP* 1.3 72.2 - - - +
47H ILE* 1.3 64.0 + - - +
48H ARG 2.7 17.3 + - - +
50H ASN* 3.5 2.6 - - - -
51H LYS* 3.2 43.0 + - - -
52H PRO* 4.5 5.4 - - - -
54H MET* 3.8 6.4 - - - +
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Residues in contact with ILE 47 (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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10H PHE* 5.4 3.6 - - + -
43H ARG 3.2 13.7 + - - +
44H LEU* 3.0 37.9 - - + +
46H GLY* 1.3 73.6 - - - +
48H ARG* 1.3 68.4 + - + +
49H LYS 3.6 1.6 + - - -
50H ASN* 4.2 5.7 + - - +
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Residues in contact with ARG 48 (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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-8F T 5.1 0.3 + - - -
3H SER* 4.3 17.2 + - - +
5H ILE* 3.6 42.3 - - + +
10H PHE* 4.5 16.4 - - + -
13H GLN* 6.1 0.4 - - - +
44H LEU 4.0 6.5 - - - +
45H TRP* 2.4 54.9 + - + +
46H GLY 2.7 6.9 + - - +
47H ILE* 1.3 83.0 - - + +
49H LYS* 1.3 86.9 + - + +
51H LYS* 4.8 0.5 - - - +
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-8F T 2.6 19.5 + - - -
-7F C 2.6 34.8 + - - -
5H ILE* 4.3 17.0 - - + +
6H THR* 5.4 3.4 + - - +
45H TRP* 3.5 22.4 - - - -
47H ILE 3.6 1.8 + - - -
48H ARG* 1.3 95.4 - - + +
50H ASN* 1.3 74.7 + - - +
51H LYS* 2.6 18.2 + - + +
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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