Contacts of the helix formed by residues 71 - 81 (chain A) in PDB entry 3L73
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 PRO 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY* 4.1 3.4 - - - -
67A THR 3.5 9.7 - - - +
68A LYS 4.4 7.2 - - - +
69A LYS 4.5 1.6 - - - +
70A ARG* 1.3 92.9 - - - +
72A CYS* 1.3 68.5 + - + +
73A ALA* 3.6 2.2 - - + +
74A ALA* 3.2 13.6 + - + +
75A PHE* 2.9 14.9 + - - +
121A ALA* 6.0 1.8 - - + -
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Residues in contact with CYS 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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65A LYS* 3.9 34.1 + - - +
66A GLY* 3.9 8.9 - - - +
71A PRO* 1.3 76.5 - - - +
73A ALA* 1.3 65.6 + - - +
75A PHE* 3.0 9.7 + - - +
76A GLU* 3.0 37.2 + - - +
126A GLN* 4.5 12.8 - - - +
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Residues in contact with ALA 73 (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 PRO* 3.6 1.9 - - + +
72A CYS* 1.3 79.0 - - - +
74A ALA* 1.3 63.9 + - - +
76A GLU* 3.5 8.2 + - - +
77A LYS* 3.0 29.8 + - + +
291B VAL* 4.7 10.1 - - + +
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Residues in contact with ALA 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 ARG* 4.2 19.3 - - + -
71A PRO* 3.2 18.4 + - + +
72A CYS 3.2 0.6 - - - -
73A ALA* 1.3 77.7 - - - +
75A PHE* 1.3 59.3 + - - +
77A LYS* 3.7 5.3 - - - +
78A GLU* 2.8 34.9 + - - +
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Residues in contact with PHE 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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63A ALA 4.8 1.1 - - - -
64A PHE* 3.4 38.1 - + + -
66A GLY* 4.2 10.5 - - - -
67A THR* 4.8 9.6 - - + -
70A ARG* 3.8 23.6 + - + +
71A PRO 2.9 15.9 + - - +
72A CYS 3.4 6.7 - - - +
74A ALA* 1.3 75.2 - - - +
76A GLU* 1.3 68.7 + - + +
78A GLU* 3.1 4.5 + - - +
79A VAL* 3.0 35.1 + - + +
86A PHE* 3.5 38.4 - + - -
112A LEU* 4.0 29.2 - - + -
115A ASP* 5.3 0.2 - - - -
116A VAL* 4.1 17.5 - - + -
285B ILE* 5.2 4.7 - - + -
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Residues in contact with GLU 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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64A PHE 4.5 14.7 - - - +
65A LYS* 5.0 4.3 + - - +
72A CYS* 3.0 36.0 + - - +
73A ALA* 3.9 3.9 + - - +
75A PHE* 1.3 78.9 - - + +
77A LYS* 1.3 57.0 + - - +
79A VAL* 2.9 4.3 + - - +
80A GLU* 2.8 50.6 + - - +
285B ILE* 3.6 19.2 - - + +
288B GLY* 3.8 7.4 - - - -
289B SER* 2.9 47.1 + - - +
291B VAL* 4.2 10.2 - - + +
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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 ALA* 3.0 20.5 + - + +
74A ALA* 3.8 5.4 - - - +
76A GLU* 1.3 75.2 - - - +
78A GLU* 1.3 53.8 + - - +
80A GLU* 4.1 9.4 + - - -
81A SER* 2.5 39.7 + - - +
291B VAL* 4.6 19.0 - - + +
292B THR* 4.7 5.2 - - - +
355B GLU* 5.6 3.0 + - - -
359B LYS* 3.3 28.7 - - - +
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Residues in contact with GLU 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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70A ARG* 3.3 40.1 + - - +
74A ALA* 2.8 22.4 + - - +
75A PHE 3.5 5.2 - - - +
77A LYS* 1.3 74.0 - - - +
79A VAL* 1.3 60.5 + - - +
81A SER* 2.9 15.6 + - - -
82A MET* 3.3 20.3 - - - +
108A LYS* 3.6 26.7 + - + +
112A LEU* 4.1 11.3 - - + +
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Residues in contact with VAL 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 PHE* 3.1 46.0 - - + +
76A GLU* 2.9 5.7 + - - +
78A GLU* 1.3 75.9 - - + +
80A GLU* 1.3 67.5 + - - +
82A MET* 2.9 23.4 - - - +
84A ALA* 3.4 35.4 + - + +
85A HIS 5.2 0.2 - - - -
86A PHE* 4.4 20.9 - - + -
99A ILE* 5.2 4.7 - - + -
112A LEU* 4.3 14.1 - - + -
285B ILE* 4.1 10.8 - - + -
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Residues in contact with GLU 80 (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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76A GLU* 2.8 35.4 + - - +
77A LYS 4.0 1.3 - - - +
79A VAL* 1.3 73.0 - - - +
81A SER* 1.3 53.6 - - - +
82A MET 2.8 0.9 + - - -
83A GLY* 2.6 31.4 + - - -
84A ALA 4.7 0.7 - - - -
284B LEU* 4.2 20.8 - - + +
285B ILE* 4.1 13.5 - - + +
289B SER 3.3 18.7 - - - +
290B SER* 3.7 11.3 - - - -
291B VAL* 3.1 13.5 + - - +
292B THR* 2.7 50.2 + - - +
363B GLN* 3.4 15.9 + - - +
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Residues in contact with SER 81 (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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77A LYS* 2.5 22.9 + - - +
78A GLU* 2.9 18.2 + - - -
80A GLU* 1.3 76.1 - - - +
82A MET* 1.3 56.2 + - - +
83A GLY 3.3 1.5 + - - -
292B THR* 4.0 2.6 + - - -
359B LYS* 3.9 42.8 - - - +
362B ASN* 3.8 21.8 + - - +
363B GLN* 4.9 2.0 - - - +
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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