Contacts of the helix formed by residues 78 - 86 (chain Y) in PDB entry 5FLX
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 78 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19Y GLN* 4.3 7.9 + - - +
54Y VAL* 3.7 4.0 - - - +
76Y TYR* 3.4 13.9 - - - +
77Y ASP* 1.3 79.7 + - - +
79Y LEU* 1.3 64.4 + - - +
80Y ASP* 4.4 6.7 - - - -
81Y TYR* 3.8 32.0 - - - +
82Y ALA* 3.4 13.9 + - - +
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Residues in contact with LEU 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Y ASP* 4.6 32.5 - - + +
54Y VAL* 4.3 11.1 - - + +
56Y PHE* 6.5 0.7 - - + -
77Y ASP 4.5 0.2 + - - -
78Y SER* 1.3 71.4 - - - +
80Y ASP* 1.3 65.7 + - - +
82Y ALA* 3.1 11.9 + - + +
83Y LYS* 2.9 61.2 + - + +
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Residues in contact with ASP 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Y SER* 3.5 3.7 - - - -
79Y LEU* 1.3 83.6 - - - +
81Y TYR* 1.3 65.3 + - + +
83Y LYS* 3.1 17.8 + - - +
84Y LYS* 2.9 32.3 + - - +
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Residues in contact with TYR 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y LEU 4.2 4.5 - - - +
19Y GLN* 3.7 29.8 - - + +
76Y TYR* 3.9 4.9 - - + -
78Y SER* 3.8 27.2 + - - +
79Y LEU 3.3 0.4 - - - -
80Y ASP* 1.3 83.7 - - + +
82Y ALA* 1.3 58.4 + - - +
84Y LYS* 4.4 19.1 - - + +
85Y ASN* 2.9 56.7 + - - +
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Residues in contact with ALA 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Y VAL* 4.0 14.6 - - + +
56Y PHE* 3.8 16.4 - - + -
76Y TYR* 3.5 35.6 - - + -
78Y SER 3.4 10.1 + - - +
79Y LEU* 3.1 16.2 + - + +
81Y TYR* 1.3 80.1 - - - +
83Y LYS* 1.3 60.3 + - + +
86Y GLU* 3.8 23.9 + - - +
91Y LEU* 4.3 0.3 - - - +
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Residues in contact with LYS 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y PHE* 6.0 1.3 - - + -
79Y LEU* 2.9 51.7 + - + +
80Y ASP* 3.1 16.4 + - - +
82Y ALA* 1.3 79.0 - - + +
84Y LYS* 1.3 62.4 + - - +
86Y GLU 3.9 6.2 - - - +
91Y LEU* 3.3 28.8 - - + +
96Y LEU* 3.7 30.2 - - + +
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Residues in contact with LYS 84 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5021 C 6.4 0.2 - - - +
63E LYS* 4.1 6.2 + - - +
67E GLN* 5.2 11.2 - - - +
80Y ASP* 2.9 17.7 + - - +
81Y TYR* 4.4 17.8 - - + +
83Y LYS* 1.3 77.8 - - - +
85Y ASN* 1.3 72.3 + - - +
86Y GLU 3.6 5.5 - - - +
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Residues in contact with ASN 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU* 3.9 12.4 - - - +
63E LYS* 2.6 31.4 + - - +
67E GLN* 5.0 6.9 + - - -
18Y LEU* 3.0 48.0 + - - +
20Y ARG* 4.6 3.1 + - - +
76Y TYR* 3.3 21.5 - - - +
81Y TYR* 2.9 38.0 + - - +
84Y LYS* 1.3 86.5 - - - +
86Y GLU* 1.3 60.0 + - - +
87Y PRO* 3.6 1.7 - - - +
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Residues in contact with GLU 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LYS* 4.9 0.5 + - - -
20Y ARG* 3.1 14.0 + - - -
56Y PHE* 3.6 27.4 - - + -
74Y MET* 3.3 12.2 - - - +
76Y TYR* 2.3 33.4 + - + +
82Y ALA 3.8 5.1 + - - +
83Y LYS 3.9 2.9 - - - +
84Y LYS 3.5 8.0 - - - +
85Y ASN* 1.3 78.2 - - - +
87Y PRO* 1.3 77.3 - - + +
88Y LYS* 3.8 2.3 + - - +
90Y ARG* 2.4 39.6 + - - -
91Y LEU* 3.6 26.1 - - + +
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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