Contacts of the helix formed by residues 115 - 130 (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 ASN 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D TRP* 3.7 27.3 - - + +
97D ASP* 3.2 40.5 + - - +
111D ILE* 3.2 17.7 + - - +
112D GLY 3.3 4.2 + - - -
114D ARG* 1.4 78.4 + - - +
116D GLN* 1.4 62.6 + - - +
117D ASP 3.4 2.5 - - - -
118D ASP* 3.3 30.4 + - - +
119D ILE* 3.1 26.9 + - + +
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Residues in contact with GLN 116 (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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112D GLY 3.3 9.7 + - - +
113D THR* 3.1 33.5 - - - +
114D ARG 3.3 3.3 + - - +
115D ASN* 1.4 75.3 - - - +
117D ASP* 1.3 80.8 + - - +
119D ILE* 3.8 3.3 - - - +
120D LEU* 2.9 50.0 + - + +
153D ASN* 5.8 2.0 - - - +
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Residues in contact with ASP 117 (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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114D ARG 5.1 3.6 - - - +
115D ASN 3.4 0.6 - - - -
116D GLN* 1.3 94.7 + - - +
118D ASP* 1.4 53.7 + - - +
120D LEU* 3.1 12.8 + - - +
121D ASN* 2.9 42.4 + - - +
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Residues in contact with ASP 118 (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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93D TRP* 3.2 34.1 + - - -
115D ASN* 3.3 28.9 + - - +
117D ASP* 1.4 75.4 + - - +
119D ILE* 1.3 67.0 + - - +
121D ASN* 3.2 27.8 - - - +
122D LYS* 3.3 24.3 + - - +
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Residues in contact with ILE 119 (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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67D ILE* 4.9 2.9 - - + -
69D MET* 3.8 27.8 - - + -
93D TRP* 4.0 36.3 - - + +
112D GLY* 4.5 8.5 - - - +
115D ASN* 3.1 24.8 + - + +
116D GLN* 3.8 3.8 - - - +
117D ASP 3.2 0.4 - - - -
118D ASP* 1.3 83.0 - - - +
120D LEU* 1.3 64.2 + - + +
121D ASN 3.2 0.2 - - - -
122D LYS* 3.2 11.3 + - + +
123D ILE* 3.2 25.1 + - + +
150D LEU* 4.5 16.8 - - + -
154D LEU* 3.9 19.7 - - + -
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Residues in contact with LEU 120 (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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116D GLN* 2.9 48.4 + - + +
117D ASP* 3.1 11.4 + - - +
119D ILE* 1.3 75.8 - - + +
121D ASN* 1.4 51.4 + - - +
123D ILE* 3.2 10.9 + - + +
124D ASP* 2.7 43.9 + - - +
154D LEU* 5.9 3.8 - - + -
157D ALA* 5.3 10.5 - - + -
158D LEU* 4.8 17.7 - - + -
161D ARG* 3.4 36.8 - - - +
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Residues in contact with ASN 121 (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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117D ASP* 2.9 24.1 + - - +
118D ASP* 3.2 18.6 - - - +
119D ILE 3.2 0.2 - - - -
120D LEU* 1.4 72.1 - - - +
122D LYS* 1.4 62.8 + - + +
124D ASP* 4.0 8.8 - - - +
125D LYS* 3.1 26.0 + - - +
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Residues in contact with LYS 122 (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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67D ILE* 3.1 24.0 - - + -
69D MET* 6.2 0.2 - - + -
90D ARG 3.2 29.4 - - - +
91D ASN* 4.0 13.3 - - - +
92D THR 3.5 15.7 - - - -
93D TRP* 3.8 25.0 - - + +
118D ASP* 3.3 32.8 + - - +
119D ILE* 3.2 9.7 + - + +
121D ASN* 1.4 75.1 - - + +
123D ILE* 1.3 65.7 + - - +
125D LYS* 3.6 7.1 + - - +
126D GLU* 3.3 26.5 + - - +
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Residues in contact with ILE 123 (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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6D ILE* 5.5 4.5 - - + -
8D LEU* 4.9 11.9 - - + -
67D ILE* 3.3 26.7 - - + -
69D MET* 5.7 0.7 - - - -
119D ILE* 3.2 11.0 + - + +
120D LEU* 3.5 13.9 - - + +
122D LYS* 1.3 81.0 - - - +
124D ASP* 1.4 56.7 + - - +
126D GLU* 3.3 8.5 + - - +
127D ILE* 2.8 61.1 + - + +
136D PHE* 4.9 7.0 - - + -
154D LEU* 4.4 19.1 - - + -
158D LEU* 4.0 34.3 - - + -
162D TYR* 5.5 0.9 - - + -
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Residues in contact with ASP 124 (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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120D LEU* 2.7 26.5 + - - +
121D ASN* 4.1 9.8 + - - +
123D ILE* 1.4 77.5 - - - +
125D LYS* 1.3 51.9 + - - +
127D ILE* 3.2 7.1 + - - +
128D ASP* 2.8 45.2 + - - +
161D ARG* 3.0 43.3 + - - -
162D TYR* 3.7 12.3 + - - +
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Residues in contact with LYS 125 (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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88D ASP* 3.1 24.9 + - - -
90D ARG* 4.8 13.0 - - - +
91D ASN* 3.3 7.1 + - - -
121D ASN 3.1 18.9 + - - +
122D LYS* 3.7 7.6 - - - +
123D ILE 3.3 0.2 - - - -
124D ASP* 1.3 73.2 - - - +
126D GLU* 1.3 80.9 + - - +
128D ASP* 3.4 9.0 + - - +
129D SER* 3.2 28.5 + - - +
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Residues in contact with GLU 126 (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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6D ILE* 3.6 23.4 - - + +
65D ARG* 3.9 32.8 + - - +
66D ALA 4.9 4.3 - - - +
67D ILE* 5.3 4.5 - - + -
91D ASN* 2.9 26.2 + - - +
122D LYS 3.3 13.9 + - - +
123D ILE* 3.3 11.6 + - - +
125D LYS* 1.3 105.2 + - - +
127D ILE* 1.3 57.6 + - - +
129D SER* 2.9 21.7 + - - -
130D THR* 2.9 17.0 + - - -
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Residues in contact with ILE 127 (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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6D ILE* 3.8 15.5 - - + -
123D ILE* 2.8 43.5 + - + +
124D ASP* 3.5 8.5 - - - +
126D GLU* 1.3 70.0 - - - +
128D ASP* 1.4 61.8 + - - +
130D THR* 3.0 31.4 + - - +
133D PHE* 5.2 12.6 - - + -
136D PHE* 4.4 12.8 - - + -
162D TYR* 3.6 48.0 - - + +
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Residues in contact with ASP 128 (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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124D ASP* 2.8 27.4 + - - +
125D LYS* 3.7 8.1 - - - +
126D GLU 3.3 0.2 - - - -
127D ILE* 1.4 76.3 - - - +
129D SER* 1.4 63.7 + - - +
130D THR 3.2 7.5 + - - +
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Residues in contact with SER 129 (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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55D ARG* 3.4 38.5 + - - +
65D ARG* 3.3 10.7 + - - -
125D LYS* 3.2 12.2 + - - +
126D GLU* 2.9 26.5 + - - -
128D ASP* 1.4 76.5 - - - +
130D THR* 1.4 58.9 + - - +
131D ASP* 4.9 0.7 - - - +
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Residues in contact with THR 130 (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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4D GLU* 3.5 27.1 - - + -
6D ILE* 4.7 0.3 - - - +
55D ARG* 4.0 6.1 - - - +
65D ARG* 2.8 17.2 + - - -
126D GLU 2.9 11.6 + - - -
127D ILE* 3.0 20.0 + - - +
128D ASP 3.8 5.4 - - - +
129D SER* 1.4 77.7 + - - +
131D ASP* 1.3 69.3 + - - +
132D ASN 3.9 0.2 - - - -
133D PHE* 3.6 37.2 - - + +
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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