Contacts of the helix formed by residues 47 - 57 (chain H) in PDB entry 6V96
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 ILE 47 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H VAL* 4.3 13.7 - - + -
19H ALA* 3.9 14.1 - - + -
36H PRO* 2.9 25.1 + - + +
45H ARG* 4.6 2.2 - - + -
46H ILE* 1.3 76.4 - - - +
48H ASP* 1.3 76.8 + - - +
49H PHE 3.1 1.6 + - - -
50H ALA* 3.4 4.4 + - - +
51H LEU* 3.2 32.5 + - + +
64H VAL* 3.8 28.7 - - + -
73H LEU* 4.0 21.5 - - + -
76H HIS* 4.2 11.4 - - + +
77H LEU* 4.1 9.0 - - + -
134H GLY* 3.5 16.8 + - - +
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Residues in contact with ASP 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 ALA* 3.2 9.9 - - + +
45H ARG 2.9 27.9 + - - +
47H ILE* 1.3 79.6 - - - +
49H PHE* 1.3 58.8 + - - +
51H LEU* 4.3 5.4 - - - -
52H SER* 2.9 35.4 + - - -
76H HIS* 2.7 27.8 + - - -
81H TRP* 2.8 18.9 + - - -
299H ILE* 3.9 2.1 - - + +
300H TRP 3.4 16.4 - - - +
301H THR* 2.5 27.9 + - - -
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Residues in contact with PHE 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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40H PHE* 4.0 24.0 - + + -
43H LYS* 4.6 11.4 - - + -
44H ALA* 4.5 11.2 - - + -
45H ARG 3.9 11.7 - - - -
46H ILE 3.1 18.0 + - - +
48H ASP* 1.3 75.4 - - - +
50H ALA* 1.3 61.7 + - - +
52H SER* 3.2 2.4 + - - -
53H ASN* 2.8 35.6 + - - +
136H HIS 3.9 11.2 - - - +
137H ILE* 3.7 35.7 - - + -
138H TYR* 3.7 22.4 - - - +
139H LYS* 4.6 7.0 - - + -
290H LEU* 4.6 13.7 - - + -
299H ILE* 3.7 36.5 - - + +
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Residues in contact with ALA 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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17H VAL* 4.6 10.5 - - + -
46H ILE 4.4 0.4 + - - -
47H ILE 3.4 7.1 + - - +
49H PHE* 1.3 77.9 - - - +
51H LEU* 1.3 58.3 + - - +
53H ASN* 3.2 5.3 + - - +
54H ALA* 2.9 28.6 + - - +
132H LEU* 4.1 16.3 - - + +
133H ALA 3.9 21.3 - - - +
134H GLY* 4.7 3.8 - - - -
136H HIS 4.8 3.5 + - - +
138H TYR* 4.2 13.9 - - + +
142H TYR* 3.9 12.1 + - - +
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Residues in contact with LEU 51 (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 VAL* 3.9 13.0 - - + -
47H ILE* 3.2 29.0 + - + +
48H ASP* 4.0 0.9 - - - +
50H ALA* 1.3 78.6 - - - +
52H SER* 1.3 56.8 + - - +
54H ALA* 3.3 7.2 + - + +
55H LEU* 3.0 27.0 + - - +
62H ILE* 3.8 31.1 - - + +
64H VAL* 3.9 10.1 - - + -
77H LEU* 3.6 25.6 - - + -
81H TRP* 3.4 45.6 - - + +
92H PHE* 3.9 11.7 - - + -
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Residues in contact with SER 52 (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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48H ASP 2.9 24.7 + - - -
49H PHE 3.8 2.2 - - - -
51H LEU* 1.3 73.0 - - - +
53H ASN* 1.3 62.4 + - - +
55H LEU* 4.2 4.3 - - - -
56H ASN* 2.8 38.3 + - - -
81H TRP* 3.6 9.6 - - - -
298H PRO 3.7 18.8 - - - -
299H ILE* 3.5 11.3 - - - -
300H TRP* 2.8 30.9 + - - +
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Residues in contact with ASN 53 (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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49H PHE 2.8 17.3 + - - +
50H ALA 3.5 2.7 - - - +
52H SER* 1.3 76.1 - - - +
54H ALA* 1.3 61.4 + - - +
57H SER* 2.8 31.0 + - - -
138H TYR* 3.0 50.4 + - - +
139H LYS* 3.2 6.8 - - - +
140H MET 3.2 16.4 + - - +
142H TYR* 3.2 23.8 + - + +
297H TRP* 2.8 27.6 + - - +
299H ILE* 5.2 1.2 - - - +
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Residues in contact with ALA 54 (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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15H ALA* 4.0 23.6 - - + -
17H VAL* 6.1 0.7 - - + -
50H ALA 2.9 13.2 + - - +
51H LEU* 3.4 10.5 - - - +
53H ASN* 1.3 77.7 - - - +
55H LEU* 1.3 62.5 + - - +
57H SER* 3.3 4.5 + - - -
59H ILE* 3.0 31.8 + - + +
62H ILE* 3.9 19.3 - - + -
132H LEU* 4.8 0.9 - - + -
142H TYR* 3.5 14.6 - - + -
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Residues in contact with LEU 55 (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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51H LEU 3.0 16.4 + - - +
52H SER* 3.3 5.1 + - - +
54H ALA* 1.3 77.1 - - - +
56H ASN* 1.3 71.4 + - - +
58H GLY* 2.9 21.0 + - - -
59H ILE 4.0 6.4 + - - +
60H ARG* 3.3 35.1 + - - +
62H ILE* 4.7 2.2 - - + +
81H TRP* 4.2 11.9 - - + -
83H PHE* 4.1 31.9 - - + -
84H PHE* 4.3 10.3 - - + -
300H TRP* 4.4 15.7 - - + -
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Residues in contact with ASN 56 (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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52H SER 2.8 21.6 + - - +
55H LEU* 1.3 87.5 - - - +
57H SER* 1.3 58.1 + - - +
58H GLY 3.2 1.5 + - - -
297H TRP* 3.3 56.2 - - + -
298H PRO* 3.0 44.5 + - - +
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Residues in contact with SER 57 (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 ALA* 3.1 19.1 - - - +
53H ASN 2.8 23.1 + - - -
54H ALA 3.6 4.9 - - - -
55H LEU 3.1 0.2 - - - -
56H ASN* 1.3 77.4 - - - +
58H GLY* 1.3 56.8 + - - +
59H ILE* 3.4 4.7 - - - -
140H MET 3.5 1.6 + - - -
141H ASP* 3.4 17.6 - - - +
142H TYR* 2.8 42.8 + - - -
143H GLU* 4.4 7.3 - - - +
297H TRP* 3.6 4.4 - - - -
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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