Contacts of the strand formed by residues 84 - 92 (chain B) 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 PHE 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B PHE* 5.2 12.3 - + - -
67B PHE 3.7 1.4 - - - +
68B GLU* 3.2 7.2 - - - +
69B VAL* 2.6 42.2 + - + +
70B SER 5.7 0.7 - - - -
71B LEU* 3.5 31.6 - - + -
74B LEU* 5.7 8.3 - - + -
75B GLN* 4.7 12.8 - - - -
82B ARG 3.8 7.0 - - - -
83B LYS* 1.3 81.5 - - - +
85B LYS* 1.3 59.3 + - - +
86B LEU* 3.9 19.2 - - + +
100B PHE* 5.1 12.3 - + + -
102B GLY 3.7 3.1 - - - +
103B MET* 3.5 41.3 - - + -
104B ASP 5.2 0.2 - - - -
185B VAL* 5.7 5.2 - - + -
188B LEU* 5.8 2.5 - - + -
189B ILE* 4.5 16.8 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9761 G 5.0 0.4 - - - -
9771 C 2.8 35.1 + - - -
66B VAL* 3.7 34.2 - - - +
67B PHE 3.3 9.0 - - - +
68B GLU* 3.7 29.2 + - + +
83B LYS 4.3 0.4 - - - -
84B PHE* 1.3 72.8 - - - +
86B LEU* 1.3 62.7 + - - +
100B PHE* 4.5 0.5 - - - -
101B HIS* 3.0 25.8 + - + +
102B GLY* 2.5 52.3 + - - +
103B MET* 4.3 1.1 - - - +
104B ASP* 4.9 13.0 - - + +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA* 4.2 9.6 - - + -
36B PRO* 3.7 17.5 - - + -
44B ILE* 5.5 4.3 - - + -
66B VAL* 3.3 12.1 - - - +
67B PHE* 2.4 52.5 + - + +
69B VAL* 5.2 8.5 - - + -
84B PHE* 3.9 28.5 - - + +
85B LYS* 1.3 79.4 - - - +
87B ILE* 1.3 62.4 + - - +
98B THR* 3.6 30.3 - - + +
99B ASN 3.3 13.2 - - - +
100B PHE* 4.3 9.9 - - + -
101B HIS* 3.5 6.9 - - - +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS 4.6 5.2 - - - +
64B GLY* 5.5 4.5 - - - +
65B ARG 3.2 15.5 - - - +
66B VAL* 4.0 8.5 - - + +
86B LEU* 1.3 76.9 - - - +
88B THR* 1.3 67.3 + - - +
89B GLU* 5.7 1.6 - - - +
98B THR* 2.4 19.5 + - - -
99B ASN* 2.5 40.0 + - + +
100B PHE 4.1 6.3 - - - +
101B HIS* 3.7 24.0 - - + +
220B LYS* 3.3 29.6 - - - +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.1 33.9 - - + +
63B LYS* 2.8 24.0 - - - +
65B ARG* 3.1 21.9 + - - +
66B VAL* 4.6 0.2 - - - +
67B PHE* 3.1 27.1 - - + -
87B ILE* 1.3 79.2 - - - +
89B GLU* 1.3 69.1 + - - +
90B ASP* 4.4 3.6 - - - +
96B CYS* 5.0 8.1 - - + -
97B LEU 3.2 16.6 - - - +
98B THR* 3.6 5.8 - - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 3.3 28.6 - - - +
87B ILE* 5.7 1.9 - - - +
88B THR* 1.3 76.6 - - - +
90B ASP* 1.3 63.5 + - - +
97B LEU* 2.7 26.0 + - + +
98B THR* 3.6 7.0 - - - +
99B ASN* 4.1 19.3 + - + +
223B PHE* 3.1 49.6 - - + +
224B GLU 5.4 0.7 - - - +
225B LEU 5.5 0.2 + - - -
228B LEU* 3.5 30.7 - - + +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER 5.9 2.0 - - - -
63B LYS* 5.6 5.8 - - - +
88B THR* 4.4 4.0 - - - +
89B GLU* 1.3 86.3 - - + +
91B VAL* 1.3 60.9 + - - +
92B GLN* 5.2 9.1 - - - +
96B CYS* 4.7 0.4 - - - -
97B LEU* 2.6 49.4 + - - +
223B PHE* 4.9 13.2 - - + -
225B LEU* 5.3 3.8 - - - +
228B LEU* 3.8 18.4 - - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TYR* 4.0 33.7 - - + -
58B ALA* 5.6 1.8 - - + +
59B SER* 3.8 32.7 + - - +
62B LEU* 5.7 4.5 - - + -
90B ASP* 1.3 78.6 - - - +
92B GLN* 1.3 65.7 + - - +
93B GLY 4.4 0.6 + - - +
94B LYS 4.5 6.1 - - - +
95B ASN 3.5 19.3 - - - +
96B CYS* 4.0 7.4 - - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 4.0 12.5 + - - +
91B VAL* 1.3 77.0 - - - +
93B GLY* 1.3 78.8 + - - +
94B LYS 3.5 1.3 - - - -
95B ASN* 2.7 32.2 + - + +
97B LEU* 5.4 9.6 - - + -
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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