Contacts of the helix formed by residues 85 - 94 (chain W) 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 ASP 85 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81W VAL* 3.6 16.9 - - + +
82W GLN* 3.3 25.8 + - - +
83W LEU 3.0 7.6 - - - +
84W LYS* 1.3 83.1 - - - +
86W LEU* 1.3 60.5 + - - +
87W GLU 3.3 3.5 + - - -
88W LYS* 3.6 18.6 + - - +
89W TRP* 3.9 5.4 - - - -
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Residues in contact with LEU 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W VAL* 3.6 28.3 - - + +
82W GLN 4.3 7.4 - - - +
83W LEU* 3.6 29.8 - - + -
84W LYS 3.4 1.3 - - - +
85W ASP* 1.3 75.1 - - - +
87W GLU* 1.3 65.4 + - - +
88W LYS 3.1 2.9 - - - -
89W TRP* 3.0 9.8 + - + +
90W GLN* 2.9 39.5 + - - +
102W ILE* 6.6 0.2 - - + -
104W LEU* 5.1 13.2 - - + -
113W HIS* 4.6 14.7 - - + +
116W ALA* 4.3 20.2 - - + -
117W ARG* 5.9 0.7 - - + +
123W GLY 5.9 0.7 - - - +
125W ILE* 5.0 10.1 - - + -
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Residues in contact with GLU 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J THR* 3.7 33.1 - - + +
63J LEU* 5.9 2.8 - - - +
84W LYS* 2.8 38.6 + - - +
85W ASP 3.3 0.2 - - - -
86W LEU* 1.3 75.4 + - - +
88W LYS* 1.3 57.2 + - - +
90W GLN* 3.3 24.3 - - - +
91W ASN* 2.9 40.0 + - - +
117W ARG* 5.8 2.0 + - - +
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Residues in contact with LYS 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4191 G 3.6 27.6 - - - +
4201 G 3.4 33.7 + - - -
6601 C 5.5 3.4 + - - -
6611 U 4.0 24.3 + - - -
100L ASN* 5.8 4.4 - - - +
85W ASP* 3.6 13.9 + - - +
87W GLU* 1.3 78.6 - - - +
89W TRP* 1.3 73.3 + - + +
91W ASN* 4.1 3.3 - - - +
92W ASN* 2.9 36.6 + - + +
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Residues in contact with TRP 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6611 U 6.0 0.2 - - - -
11571 G 3.2 30.3 - + - -
100L ASN* 5.2 6.1 - - - +
75W ILE* 3.6 18.6 - - + -
79W PHE* 3.4 40.8 - + + -
81W VAL* 3.3 29.7 - - + +
85W ASP 3.9 15.0 + - - -
86W LEU* 3.0 9.0 + - + +
88W LYS* 1.3 92.3 - - + +
90W GLN* 1.3 59.8 + - - +
92W ASN* 4.4 9.2 - - - +
93W LEU* 2.9 67.4 + - + +
94W LEU 3.8 0.2 + - - -
102W ILE* 4.1 10.9 - - + +
125W ILE* 3.9 16.6 - - + -
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Residues in contact with GLN 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86W LEU* 2.9 24.6 + - - +
87W GLU* 3.2 30.9 + - - +
89W TRP* 1.3 77.6 - - - +
91W ASN* 1.3 65.9 + - - +
94W LEU* 3.3 38.5 + - + +
96W SER 5.3 1.6 - - - +
97W ARG* 3.8 23.8 + - - +
102W ILE* 4.9 0.9 - - - -
113W HIS* 3.0 39.1 + - + +
117W ARG* 4.1 14.3 + - - +
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Residues in contact with ASN 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21 A 4.9 20.9 + - - +
4181 A 6.4 2.2 - - + -
170C TRP* 5.6 6.1 + - - -
183C LYS* 3.4 17.0 + - - +
87W GLU* 2.9 24.6 + - - +
88W LYS* 4.2 3.3 - - - +
90W GLN* 1.3 78.2 - - - +
92W ASN* 1.3 64.0 + - - +
94W LEU 3.5 5.8 - - - +
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Residues in contact with ASN 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4181 A 6.5 0.7 - - + -
6611 U 3.0 37.0 + - - +
6621 G 4.5 7.9 + - - -
11561 U 5.2 6.6 + - - +
11571 G 4.4 17.0 + - - +
183C LYS* 3.2 17.3 + - - +
194C ARG* 4.9 2.6 + - - -
88W LYS* 2.9 25.2 + - + +
89W TRP* 4.4 12.4 - - + -
91W ASN* 1.3 77.9 - - - +
93W LEU* 1.3 66.0 + - + +
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Residues in contact with LEU 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11551 U 5.6 3.6 - - - +
11561 U 5.0 5.8 + - - +
11571 G 4.8 9.9 - - - +
183C LYS* 4.7 1.6 + - - -
75W ILE* 3.7 17.7 - - + -
89W TRP* 2.9 55.7 + - + +
92W ASN* 1.3 86.8 - - - +
94W LEU* 1.3 64.9 + - + +
95W PRO* 3.7 4.0 - - - +
102W ILE* 3.8 25.1 - - + -
125W ILE* 4.8 4.0 - - + -
128W PHE* 3.6 45.8 - - + -
130W PHE* 4.5 11.6 - - - -
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Residues in contact with LEU 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LYS* 3.5 5.1 - - - -
90W GLN* 3.3 32.5 + - + +
91W ASN* 3.5 15.8 - - - +
93W LEU* 1.3 82.2 - - + +
95W PRO* 1.3 72.0 - - + +
96W SER 3.4 17.1 + - - +
97W ARG* 5.4 7.4 - - - +
99W PHE 4.1 0.2 - - - +
100W GLY* 3.7 12.1 - - - -
101W PHE 3.3 43.1 - - - +
102W ILE* 4.2 9.4 - - + -
113W HIS* 4.4 21.1 - - + -
128W PHE* 5.1 4.0 - - + -
130W PHE* 5.4 4.3 - - + -
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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