Contacts of the helix formed by residues 71 - 79 (chain A) in PDB entry 3QFR
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER* 1.3 73.9 - - - +
72A PHE* 1.3 64.3 + - - +
73A VAL* 3.3 18.5 + - - +
74A GLU* 3.2 27.4 + - - +
75A LYS* 3.2 19.4 + - - +
120A TYR* 4.1 1.0 - - - -
124A ASP* 3.5 26.7 + - - -
127A SER* 5.5 1.6 - - - -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER* 1.3 74.0 + - - +
73A VAL* 1.3 68.4 + - + +
75A LYS* 3.4 4.6 + - - +
76A MET* 3.1 29.8 + - - +
84A ILE* 3.4 34.5 - - + +
86A PHE* 3.8 22.4 - + + -
113A MET* 5.1 1.2 - - + +
120A TYR* 3.5 39.9 - - + -
121A ASP 4.0 15.3 - - - -
122A LEU* 4.4 8.3 - - + -
124A ASP* 3.8 18.5 + - + -
125A LEU* 3.9 37.5 - - + -
128A LEU* 3.7 24.5 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.1 9.4 + - - +
72A PHE* 1.3 84.9 - - + +
74A GLU* 1.3 69.1 + - - +
76A MET* 3.1 17.7 + - - +
77A LYS* 3.1 31.9 + - - +
124A ASP* 3.6 24.7 - - + +
127A SER* 3.7 28.7 - - - +
128A LEU* 3.7 26.2 - - + -
130A GLU* 4.3 2.0 - - - +
131A ILE* 3.6 9.3 - - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 6.1 0.2 - - - -
71A SER* 3.2 27.1 + - - +
73A VAL* 1.3 80.7 - - - +
75A LYS* 1.3 63.4 + - - +
77A LYS* 3.1 40.2 + - - +
78A LYS* 3.0 25.7 + - + +
130A GLU* 4.6 2.6 - - - +
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 6.1 3.8 - - - -
71A SER 3.2 10.9 + - - +
72A PHE* 3.7 10.3 - - - +
73A VAL 3.2 0.2 - - - -
74A GLU* 1.3 78.2 - - - +
76A MET* 1.3 61.1 + - - +
78A LYS* 3.1 23.1 - - + +
79A THR* 2.9 41.2 + - + +
113A MET* 4.5 17.8 - - + +
120A TYR* 3.4 26.9 - - + +
357A GLU* 2.9 40.3 + - - +
358A SER* 4.9 1.8 - - - +
359A ASN* 5.5 6.1 - - - +
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.1 27.0 + - - +
73A VAL* 3.1 7.2 + - - +
75A LYS* 1.3 75.3 - - - +
77A LYS* 1.3 65.2 + - - +
79A THR* 3.3 5.7 + - - -
80A GLY 2.9 5.0 + - - -
81A ARG* 2.8 36.1 + - + +
82A ASN* 3.5 38.8 - - - +
83A ILE 3.8 4.3 - - - +
84A ILE* 3.8 32.8 - - + -
113A MET* 4.0 19.3 - - - -
128A LEU* 4.1 11.7 - - + -
131A ILE* 3.4 19.7 - - + -
134A ALA* 5.6 0.2 - - + -
135A LEU 5.0 0.7 - - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.1 20.3 + - - +
74A GLU* 3.2 40.7 + - - +
76A MET* 1.3 79.0 - - - +
78A LYS* 1.3 61.2 + - - +
80A GLY* 3.3 10.1 + - - -
81A ARG 5.0 1.1 - - - -
130A GLU* 3.1 48.9 + - - +
131A ILE* 3.8 18.1 - - + +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 3.0 12.6 + - + +
75A LYS* 3.1 40.4 - - + +
77A LYS* 1.3 76.2 - - - +
79A THR* 1.3 66.7 + - - +
80A GLY 3.3 1.3 + - - -
357A GLU* 3.3 34.2 + - - +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 2.9 36.5 + - - +
76A MET 3.6 0.3 + - - -
78A LYS* 1.3 89.1 - - - +
80A GLY* 1.3 56.2 + - - +
81A ARG* 3.0 47.2 + - - +
111A ARG* 5.4 1.2 - - - +
113A MET* 4.7 3.8 - - - -
357A GLU* 3.6 36.1 - - + +
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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