Contacts of the helix formed by residues 67 - 79 (chain F) in PDB entry 5MG3
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 GLU 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F LEU* 4.6 0.8 - - - +
65F PRO 5.2 3.2 - - - +
66F ALA* 1.3 70.5 - - - +
68F ILE* 1.4 65.2 + - - +
69F ASP* 4.4 19.6 - - - +
70F VAL* 3.7 27.5 - - + +
71F MET* 3.8 8.0 - - - +
123F ASN* 3.0 36.1 + - + +
124F GLN* 3.6 19.1 - - - +
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Residues in contact with ILE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C TRP* 4.2 12.6 - - + +
349C SER* 3.9 28.7 - - - +
350C PHE* 4.0 25.1 - - + -
62F LEU* 3.7 27.1 - - + -
66F ALA 3.1 7.5 + - - +
67F GLU* 1.4 71.9 + - - +
69F ASP* 1.4 75.1 + - - +
70F VAL 3.2 0.7 - - - -
71F MET* 2.9 25.5 + - + +
72F ARG* 3.0 12.1 + - - +
87F ASN* 5.8 0.2 - - - +
94F ILE* 4.0 15.3 - - + -
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Residues in contact with ASP 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 3.4 21.0 - - - +
68F ILE* 1.4 84.5 - - - +
70F VAL* 1.4 55.7 + - + +
72F ARG* 3.0 39.4 + - - +
73F ASP* 3.2 26.2 + - - +
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 3.7 28.0 - - + +
69F ASP* 1.4 74.8 - - + +
71F MET* 1.4 65.8 + - + +
73F ASP* 3.3 16.7 + - + +
74F ALA* 3.4 12.3 + - - +
123F ASN* 4.2 9.2 - - - +
124F GLN* 3.8 40.8 - - + +
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C PHE* 5.6 1.8 - - + -
60F ILE* 4.2 18.8 - - + -
62F LEU* 4.2 14.8 - - + -
67F GLU 3.8 10.8 - - - +
68F ILE* 2.9 19.7 + - + +
70F VAL* 1.4 76.1 - - + +
72F ARG* 1.4 62.4 + - - +
73F ASP 3.4 1.0 + - - -
74F ALA* 3.4 16.0 + - - +
75F LEU* 3.5 21.9 + - + +
94F ILE* 5.3 4.0 - - + -
117F VAL 6.0 0.4 - - - +
118F ILE* 3.8 29.7 - - + +
124F GLN* 3.5 42.0 - - + +
126F ALA* 3.5 20.4 - - + -
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 4.0 36.1 - - + +
68F ILE* 3.0 10.9 + - - +
69F ASP* 3.0 47.4 + - - +
70F VAL 3.3 0.2 - - - -
71F MET* 1.4 75.6 - - - +
73F ASP* 1.3 61.1 + - - +
75F LEU* 4.0 5.6 - - - +
76F GLN* 3.0 34.6 + - + +
82F GLU* 3.6 42.0 + - + -
85F LEU* 5.1 7.8 - - + +
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Residues in contact with ASP 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASP 3.2 13.5 + - - +
70F VAL* 3.3 15.3 + - + +
72F ARG* 1.3 77.9 - - - +
74F ALA* 1.3 59.7 + - - +
76F GLN* 3.5 10.0 + - - +
77F LYS* 2.7 61.4 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F VAL 3.4 7.5 + - - +
71F MET 3.4 10.6 + - - +
73F ASP* 1.3 77.6 - - - +
75F LEU* 1.4 55.5 + - + +
77F LYS* 3.4 11.8 + - - +
78F ALA* 3.0 27.0 + - - +
114F VAL* 3.7 26.3 - - - +
115F LEU* 4.0 12.3 - - + +
117F VAL* 4.1 13.9 - - + -
118F ILE* 4.7 10.5 - - + -
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 5.2 8.3 - - + -
58F ILE* 4.1 33.0 - - + -
60F ILE* 5.7 5.8 - - + -
71F MET* 3.5 18.6 + - + +
72F ARG* 4.2 3.4 - - - +
74F ALA* 1.4 71.8 - - + +
76F GLN* 1.4 54.4 + - - +
78F ALA* 3.4 3.6 + - - +
79F GLY 3.0 8.1 + - - -
80F PHE* 2.7 55.1 + - + +
85F LEU* 3.9 32.8 - - + -
96F VAL* 4.7 7.2 - - + -
98F MET* 4.3 3.1 - - + -
115F LEU* 3.7 22.2 - - + -
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Residues in contact with GLN 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ARG* 3.0 27.6 + - + +
73F ASP* 3.5 12.6 - - - +
75F LEU* 1.4 72.7 - - - +
77F LYS* 1.4 59.1 + - + +
79F GLY* 3.0 22.7 + - - -
80F PHE 3.5 16.3 + - - +
81F GLU* 4.9 8.0 - - - +
82F GLU* 5.9 4.3 - - - +
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Residues in contact with LYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ASP* 2.7 46.5 + - - +
74F ALA* 3.5 11.2 - - - +
75F LEU 3.3 0.2 - - - -
76F GLN* 1.4 74.8 - - + +
78F ALA* 1.3 62.8 + - - +
79F GLY* 3.1 2.2 + - - -
112F SER* 5.2 0.9 + - - -
114F VAL* 3.6 31.2 - - + +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ALA 3.0 15.6 + - - +
75F LEU 3.4 7.4 + - - +
77F LYS* 1.3 73.0 - - - +
79F GLY* 1.3 55.6 + - - +
80F PHE* 3.7 24.1 - - + -
105F THR* 5.7 6.9 - - - +
114F VAL* 3.7 17.4 - - + +
115F LEU* 4.3 15.3 - - + -
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU 3.6 0.2 - - - -
76F GLN* 3.0 17.0 + - - -
77F LYS 4.2 1.3 - - - -
78F ALA* 1.3 78.8 - - - +
80F PHE* 1.4 65.9 + - - +
81F GLU* 3.7 14.9 + - - +
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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