Contacts of the helix formed by residues 71 - 81 (chain D) in PDB entry 5FLZ
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ASP* 1.3 97.6 + - - +
72D GLU* 1.4 66.7 + - - +
73D PRO* 3.7 10.1 - - - -
74D SER 4.4 0.2 + - - -
75D VAL* 4.1 7.4 - - - +
94D VAL* 3.9 11.1 - - - +
95D ALA* 3.1 35.8 + - - +
146D THR* 5.8 0.2 - - - +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D SER* 1.4 80.5 + - - +
73D PRO* 1.3 69.5 - - + +
74D SER 3.3 0.7 + - - -
75D VAL* 3.1 26.7 - - - +
76D ILE* 3.1 54.7 + - + +
94D VAL* 3.6 29.7 - - + +
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Residues in contact with PRO 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN* 6.5 0.7 - - + -
16D HIS* 5.6 2.5 - - + -
70D ASP* 4.7 4.5 - - - +
71D SER* 3.6 10.3 - - - +
72D GLU* 1.3 94.2 - - + +
74D SER* 1.4 62.8 + - - +
76D ILE* 3.4 13.7 - - + +
77D ALA* 3.3 20.3 + - - +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN* 3.5 8.0 + - - +
15D ASN* 3.3 36.6 - - - +
16D HIS* 3.1 34.4 + - - -
19D LYS* 4.8 6.8 + - - +
68D MET* 5.9 0.7 - - - -
70D ASP* 3.7 13.5 + - - -
72D GLU 3.5 0.4 - - - -
73D PRO* 1.4 74.5 - - - +
75D VAL* 1.3 67.0 + - - +
77D ALA* 3.2 16.6 + - - +
78D ASP* 3.4 10.9 + - - +
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASN* 3.7 23.6 - - - +
68D MET* 4.5 11.4 - - + -
70D ASP* 5.2 0.2 - - + -
71D SER 4.1 10.5 - - - +
72D GLU* 3.1 29.4 - - - +
74D SER* 1.3 76.0 - - - +
76D ILE* 1.4 61.8 + - - +
78D ASP* 3.3 6.1 + - - +
79D VAL* 3.2 26.3 + - + +
87D PHE* 4.0 11.6 - - + -
92D THR* 3.7 34.3 - - + -
93D TRP 5.0 3.4 - - - +
94D VAL* 3.8 11.2 - - + -
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLU* 3.1 46.5 + - + +
73D PRO* 3.4 13.5 - - + +
74D SER 3.2 0.2 - - - -
75D VAL* 1.4 74.9 - - - +
77D ALA* 1.4 60.1 + - + +
79D VAL* 3.3 12.2 + - + +
80D GLU* 2.8 36.5 + - + +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D HIS* 6.2 2.0 - - + -
19D LYS* 4.3 14.8 - - - +
73D PRO 3.3 7.6 + - - +
74D SER* 3.2 12.6 + - - +
76D ILE* 1.4 79.9 - - + +
78D ASP* 1.4 60.8 + - - +
80D GLU* 3.2 11.3 + - - +
81D ASN* 2.9 31.6 - - - +
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Residues in contact with ASP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LYS* 3.3 33.1 - - + +
22D TRP* 4.7 8.7 - - - -
68D MET* 5.8 5.7 - - + +
74D SER 3.4 6.8 + - - +
75D VAL* 3.3 9.7 + - - +
76D ILE 3.3 0.8 - - - -
77D ALA* 1.4 74.0 - - - +
79D VAL* 1.4 57.3 + - - +
81D ASN* 3.1 30.0 + - - +
83D PHE* 3.3 22.5 - - - +
84D ARG 3.5 16.6 + - - -
86D PHE 5.4 1.0 - - - +
87D PHE* 3.2 31.9 - - + +
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 3.2 12.7 + - + +
76D ILE* 3.6 12.8 - - + +
78D ASP* 1.4 71.7 - - - +
80D GLU* 1.4 65.8 + - - +
81D ASN 3.4 5.5 - - - +
84D ARG* 3.7 30.0 - - - +
87D PHE* 3.2 44.2 - - + -
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ILE* 2.8 18.6 + - + +
77D ALA* 3.2 8.9 + - - +
79D VAL* 1.4 77.9 - - - +
81D ASN* 1.3 68.6 + - - +
82D THR 3.9 0.2 + - - -
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LYS* 4.2 8.7 - - - +
77D ALA* 2.9 24.6 + - - +
78D ASP 3.1 17.1 + - - +
79D VAL 3.4 6.4 - - - +
80D GLU* 1.3 89.9 - - - +
82D THR* 1.3 61.9 - - + +
83D PHE* 3.0 45.0 + - + +
84D ARG* 3.4 8.1 + - - +
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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