Contacts of the helix formed by residues 43 - 50 (chain H) in PDB entry 6ALG
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 LEU 43 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G LEU* 5.3 5.4 - - + -
231G PHE* 3.8 33.7 - - + -
39H LEU* 2.9 39.6 + - + +
40H GLY* 4.9 2.2 - - - +
42H ALA* 1.3 78.8 - - + +
44H ARG* 1.3 64.4 + - - +
46H ILE* 4.0 3.8 - - - +
47H LEU* 3.2 35.3 + - + +
201H LEU* 5.7 2.5 - - + -
203H ILE* 5.0 20.4 - - + -
217H ILE* 3.9 20.9 - - + -
220H ALA* 4.3 17.5 - - + -
221H ALA* 5.2 3.4 - - - +
224H LEU* 5.1 8.3 - - + -
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Residues in contact with ARG 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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40H GLY 3.2 17.2 + - - +
41H ASN* 2.8 24.0 + - - +
43H LEU* 1.3 78.2 - - - +
45H ARG* 1.3 65.0 + - + +
46H ILE 3.2 0.2 + - - -
48H LEU* 2.9 39.4 + - + +
183H ILE* 3.3 34.3 - - + +
184H ALA* 5.5 1.6 - - - +
185H TYR* 4.1 26.2 - - + -
1217I THR* 4.2 23.8 + - - +
1219I GLU* 4.2 12.3 + - - -
538J ARG* 3.1 63.5 + - - +
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Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY* 4.0 26.0 + - - +
37G HIS* 4.4 27.7 - - - +
38G THR* 3.5 30.6 + - - +
41H ASN* 2.9 37.1 + - - +
42H ALA 5.1 0.2 - - - +
44H ARG* 1.3 84.8 - - + +
46H ILE* 1.3 61.3 + - - +
48H LEU* 4.2 5.4 - - - +
49H SER* 3.7 29.2 + - - +
50H SER* 4.1 3.6 + - - -
1217I THR 5.1 3.6 - - - -
1219I GLU* 4.5 13.5 + - - +
538J ARG 4.4 10.0 + - - +
539J SER* 4.3 18.0 + - - +
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Residues in contact with ILE 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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35G PHE* 3.7 26.9 - - + -
38G THR* 4.4 9.0 - - + +
42H ALA 3.3 20.9 + - - +
43H LEU* 4.5 3.1 - - - +
44H ARG 3.2 0.6 - - - -
45H ARG* 1.3 80.9 - - - +
47H LEU* 1.3 63.7 + - - +
48H LEU 3.3 0.4 - - - -
50H SER* 2.8 42.4 + - - +
51H MET* 3.4 1.9 - - - +
220H ALA* 3.9 25.4 - - - +
223H ILE* 4.3 15.0 - - + -
224H LEU* 3.7 40.6 - - + -
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Residues in contact with LEU 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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43H LEU* 3.2 27.6 + - + +
46H ILE* 1.3 76.3 - - - +
48H LEU* 1.3 62.7 + - - +
51H MET* 3.3 29.0 - - + +
178H SER* 4.2 2.1 - - - -
180H VAL* 3.3 33.9 - - + +
183H ILE* 3.8 19.1 - - + -
203H ILE* 5.5 4.0 - - + -
205H MET* 3.7 22.2 - - - -
216H ALA 3.3 28.3 - - - +
217H ILE* 4.5 10.1 - - + -
220H ALA* 3.7 17.7 - - + -
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Residues in contact with LEU 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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44H ARG* 2.9 23.4 + - + +
45H ARG* 4.8 2.0 - - - -
47H LEU* 1.3 79.9 - - - +
49H SER* 1.3 74.3 + - - +
152H TYR* 4.9 8.4 + - + +
178H SER* 3.8 17.0 + - - -
180H VAL* 4.2 5.8 - - + -
181H GLU 5.7 1.1 - - - +
183H ILE* 3.7 24.2 - - + +
535J ARG* 3.5 47.6 - - + +
538J ARG* 3.8 26.2 - - + -
539J SER* 3.7 15.9 - - - +
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Residues in contact with SER 49 (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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33G ARG* 5.4 8.0 + - - -
34G GLY* 5.9 6.5 - - - -
45H ARG* 3.7 24.5 + - - +
48H LEU* 1.3 96.0 - - - +
50H SER* 1.3 60.5 + - - +
51H MET 4.0 1.3 - - - -
150H ARG 3.1 13.1 - - - +
151H GLY* 3.2 12.7 - - - -
152H TYR* 4.3 4.0 + - - +
539J SER* 3.9 13.3 - - - -
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Residues in contact with SER 50 (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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8G PHE* 4.4 14.3 - - - -
33G ARG 5.2 8.1 - - - -
34G GLY* 6.1 1.9 - - - -
35G PHE* 3.5 33.3 - - - -
45H ARG 4.1 2.7 + - - -
46H ILE* 2.8 28.3 + - - +
49H SER* 1.3 80.3 - - - +
51H MET* 1.3 58.9 + - - +
150H ARG 3.4 7.6 - - - -
223H ILE* 3.8 15.4 - - - +
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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