Contacts of the helix formed by residues 55 - 64 (chain H) in PDB entry 6L49
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 SER 55 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77G ARG* 3.5 21.9 + - - +
78G ILE 3.5 8.7 + - - -
79G ILE* 4.7 6.6 - - - +
80G PRO* 5.5 4.7 - - - -
54H ILE* 1.3 81.8 - - - +
56H SER* 1.3 63.6 + - - +
57H LYS* 3.4 10.1 - - - -
58H ALA* 4.4 5.2 - - - -
59H MET* 3.1 24.8 + - - +
-54J C 3.7 17.4 - - - +
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Residues in contact with SER 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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55H SER* 1.3 74.0 - - - +
57H LYS* 1.3 62.7 + - - +
59H MET* 3.7 8.4 + - - +
60H GLY* 3.1 22.3 + - - -
-54J C 3.0 34.4 + - - -
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Residues in contact with LYS 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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99B GLY* 5.4 0.5 - - - -
80G PRO* 4.1 17.7 - - + -
104G GLN* 4.8 23.6 - - + +
55H SER* 3.4 5.5 - - - -
56H SER* 1.3 80.2 - - - +
58H ALA* 1.3 56.8 + - - +
60H GLY* 2.9 16.5 + - - -
61H ILE* 2.9 22.1 + - + +
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Residues in contact with ALA 58 (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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78G ILE* 3.6 32.1 - - + +
79G ILE 4.6 0.2 - - - +
80G PRO* 3.9 26.0 - - + +
83G LEU* 4.6 5.9 - - + +
54H ILE* 3.9 13.9 - - + -
55H SER* 4.2 3.3 + - - +
56H SER 3.5 0.2 - - - -
57H LYS* 1.3 74.8 - - - +
59H MET* 1.3 60.3 + - - +
61H ILE* 3.9 7.9 + - - +
62H MET* 2.8 30.4 + - - +
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Residues in contact with MET 59 (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 SER* 3.4 42.5 - - - +
41H VAL* 4.2 13.8 - - + +
42H TYR* 4.0 25.1 - - + +
45H LEU* 4.0 5.8 - - - -
54H ILE* 3.0 40.6 - - + -
55H SER 3.1 19.2 + - - +
56H SER* 3.7 11.6 + - - +
57H LYS 3.2 0.4 - - - -
58H ALA* 1.3 76.0 - - - +
60H GLY* 1.3 52.5 - - - +
62H MET* 2.9 6.9 + - - +
63H ASN* 2.4 36.1 + - - +
-53J A 5.4 2.7 - - - +
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Residues in contact with GLY 60 (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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99B GLY* 5.1 5.2 - - - -
101B GLY 5.2 8.2 + - - +
56H SER 3.1 12.1 + - - -
57H LYS* 2.9 7.7 + - - -
59H MET* 1.3 74.4 - - - +
61H ILE* 1.3 53.1 + - - +
63H ASN* 3.0 12.5 + - - +
64H SER* 2.5 34.7 + - - -
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Residues in contact with ILE 61 (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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98B TYR* 3.7 29.8 - - + -
99B GLY* 3.7 20.6 - - - +
80G PRO* 3.8 28.3 - - + -
83G LEU* 3.7 21.3 - - + -
102G ILE* 4.0 11.2 - - + -
103G ALA 3.7 22.7 - - - +
57H LYS* 2.9 12.6 + - + +
58H ALA* 4.0 7.2 - - - +
60H GLY* 1.3 72.6 - - - +
62H MET* 1.3 51.7 + - - +
64H SER* 2.8 11.9 + - - -
65H PHE* 2.6 34.8 + - + +
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Residues in contact with MET 62 (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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59G THR* 4.0 17.5 - - + +
62G ILE* 3.7 25.6 - - + -
63G LEU* 3.3 39.9 - - + -
83G LEU* 4.7 11.2 - - + -
41H VAL* 3.5 31.7 - - + +
54H ILE* 4.9 2.7 - - + -
58H ALA 2.8 23.3 + - - +
59H MET* 2.9 14.5 + - - +
61H ILE* 1.3 73.9 - - - +
63H ASN* 1.3 56.6 + - - +
65H PHE* 2.9 31.7 + - + +
66H VAL* 3.5 16.3 + - + +
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Residues in contact with ASN 63 (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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101B GLY 5.1 8.2 + - - +
102B GLY* 5.7 4.4 + - - -
36H SER* 3.1 20.6 + - - -
37H TYR* 3.1 19.8 + - - +
38H SER* 2.9 36.8 + - - -
41H VAL* 5.0 4.0 - - - +
59H MET 2.4 26.4 + - - +
60H GLY* 3.0 15.9 + - - +
62H MET* 1.3 68.3 - - - +
64H SER* 1.3 56.7 + - - +
65H PHE 3.4 0.2 - - - -
66H VAL* 4.8 1.3 + - - +
67H ASN* 3.2 16.6 + - - +
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Residues in contact with SER 64 (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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97B LEU 5.5 0.2 - - - -
98B TYR* 3.1 50.5 + - - +
101B GLY* 5.1 9.9 - - - -
60H GLY 2.5 13.6 + - - -
61H ILE* 2.8 13.2 + - - -
63H ASN* 1.3 72.5 - - - +
65H PHE* 1.3 56.9 + - - +
67H ASN* 3.2 13.1 - - - +
68H ASP* 3.3 19.9 - - - +
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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