Contacts of the helix formed by residues 187 - 203 (chain F) 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 187 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176F GLU* 3.7 22.0 - - - -
179F ASN* 3.8 26.3 + - - +
180F ALA* 3.7 13.8 - - - +
184F SER* 4.4 1.8 + - - -
185F SER 3.9 2.8 + - - +
186F ASN* 1.3 80.5 - - - +
188F TYR* 1.3 64.2 + - - +
190F ILE* 3.3 27.7 + - - +
191F LYS* 3.2 23.7 + - - +
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Residues in contact with TYR 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F TRP* 4.8 5.4 - - - -
153F LEU* 3.7 33.0 - - + +
156F THR* 4.1 17.7 - - + +
157F GLY* 3.6 20.9 - - - +
160F GLU* 3.1 31.8 + - - +
176F GLU* 3.0 14.5 + - - +
186F ASN 3.9 1.0 + - - -
187F SER* 1.3 70.6 - - - +
189F ALA* 1.3 66.3 + - - +
191F LYS* 3.0 18.2 + - + +
192F LYS* 2.2 72.4 + - + +
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Residues in contact with ALA 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F SER* 3.9 24.9 - - - +
153F LEU* 4.3 31.1 - - + +
154F LEU* 4.6 8.5 - - + -
176F GLU* 3.1 14.6 + - - +
180F ALA* 4.6 13.7 - - + -
187F SER 3.4 0.2 - - - -
188F TYR* 1.3 78.8 - - - +
190F ILE* 1.3 58.3 + - + +
192F LYS 3.9 0.3 - - - -
193F LYS* 2.9 27.5 + - - +
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Residues in contact with ILE 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASN* 3.4 31.2 - - + +
119F SER* 4.9 0.7 - - - +
180F ALA* 4.2 22.2 - - + +
183F GLY* 4.3 17.0 - - - -
184F SER 5.0 0.9 - - - +
185F SER* 3.5 33.0 - - - +
187F SER* 3.3 21.6 + - - +
188F TYR 3.3 0.2 - - - -
189F ALA* 1.3 76.3 - - + +
191F LYS* 1.3 60.7 + - - +
193F LYS* 3.3 12.9 - - + +
194F ASP* 2.9 37.7 + - - +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F SER* 3.5 20.2 + - - +
186F ASN 4.6 1.3 - - - +
187F SER 3.2 17.9 + - - +
188F TYR* 3.0 24.0 + - + +
190F ILE* 1.3 76.7 - - - +
192F LYS* 1.3 60.5 + - + +
194F ASP* 3.1 10.7 + - - +
195F GLU* 2.9 24.9 + - - +
70z A 4.5 8.9 + - - +
71z G 3.3 47.5 + - - -
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Residues in contact with LYS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F TRP* 5.8 2.8 - - - -
153F LEU* 4.0 21.1 - - + +
188F TYR* 2.2 69.8 + - + +
189F ALA 4.4 1.1 - - - +
191F LYS* 1.3 73.9 - - + +
193F LYS* 1.3 60.1 + - - +
195F GLU* 3.5 20.3 - - + +
196F LEU* 2.9 40.1 + - + +
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Residues in contact with LYS 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ILE 5.1 1.2 + - - -
118F ASN* 3.2 28.6 + - - +
119F SER 3.1 24.9 - - - +
120F GLY* 4.2 14.8 - - - +
121F PRO* 5.8 1.8 - - - -
122F ARG* 5.8 6.5 - - - +
153F LEU* 5.1 2.4 - - - +
189F ALA 2.9 20.3 + - - +
190F ILE* 3.3 18.1 - - + +
191F LYS 3.2 0.2 - - - -
192F LYS* 1.3 76.7 - - - +
194F ASP* 1.3 61.4 + - - +
196F LEU* 3.3 6.8 + - - +
197F GLU* 2.9 57.1 + - - +
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Residues in contact with ASP 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F SER* 4.3 9.0 + - - -
190F ILE* 2.9 29.1 + - - +
191F LYS* 3.1 10.6 + - - +
193F LYS* 1.3 78.8 - - - +
195F GLU* 1.3 56.7 + - - +
197F GLU* 3.3 20.6 + - - +
198F ARG* 2.9 41.1 + - + +
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F LYS 2.9 12.5 + - - +
192F LYS* 3.5 28.7 - - + +
193F LYS 3.2 0.2 - - - -
194F ASP* 1.3 76.6 - - - +
196F LEU* 1.3 62.3 + - + +
198F ARG* 3.1 12.5 + - - +
199F VAL* 2.9 39.8 + - + +
88z G 5.2 5.2 + - - -
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F PRO* 3.9 20.0 - - + -
123F GLU 3.2 23.5 - - - +
124F ASP* 3.5 37.0 - - + +
125F SER 5.2 1.3 - - - +
149F GLN* 3.6 17.0 - - - +
153F LEU* 5.5 2.7 - - + -
192F LYS* 2.9 27.2 + - + +
193F LYS* 3.9 5.2 - - - +
195F GLU* 1.3 80.3 - - + +
197F GLU* 1.3 57.4 + - + +
199F VAL* 3.2 15.4 + - + +
200F ALA* 2.9 22.0 + - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F GLY 5.2 2.4 - - - +
122F ARG* 5.2 18.1 + - + -
123F GLU* 4.9 2.2 - - + +
193F LYS* 2.9 51.2 + - + +
194F ASP* 3.4 21.9 - - - +
195F GLU 3.2 0.2 - - - -
196F LEU* 1.3 77.7 - - + +
198F ARG* 1.3 56.2 + - + +
200F ALA* 3.1 9.9 + - - +
201F LYS* 2.9 34.3 + - + +
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Residues in contact with ARG 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ASP* 2.9 26.2 + - + +
195F GLU* 3.1 14.3 + - - +
197F GLU* 1.3 73.3 - - - +
199F VAL* 1.3 60.6 + - - +
201F LYS* 3.1 13.5 + - - +
202F SER* 2.9 28.9 + - - -
72z A 5.6 3.2 + - - -
73z A 5.5 9.3 - - - -
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Residues in contact with VAL 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP* 5.2 11.9 - - - -
125F SER 5.6 2.0 - - - +
126F THR* 6.1 0.2 - - - +
136F ARG* 3.8 52.1 - - + +
137F GLN 6.3 0.2 - - - -
138F ALA* 4.7 6.2 - - + +
195F GLU* 2.9 31.3 + - + +
196F LEU* 3.2 22.0 + - + +
198F ARG* 1.3 74.9 - - + +
200F ALA* 1.3 61.8 + - - +
202F SER* 3.4 17.6 + - - -
203F ASN 3.9 5.5 + - - +
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Residues in contact with ALA 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F GLU* 3.5 32.3 - - + -
138F ALA* 3.6 15.0 - - + +
196F LEU 2.9 8.5 + - - +
197F GLU* 3.1 10.5 + - - +
199F VAL* 1.3 78.9 - - - +
201F LYS* 1.3 59.0 + - - +
203F ASN 3.1 20.1 - - - +
204F ARG* 3.3 32.0 + - - +
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Residues in contact with LYS 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F GLU* 2.9 23.3 + - + +
198F ARG* 3.1 16.6 + - - +
200F ALA* 1.3 74.8 - - - +
202F SER* 1.3 66.1 + - - +
203F ASN 4.8 1.3 - - - -
204F ARG* 3.2 39.3 + - - +
121O ARG* 5.6 2.6 + - - -
60c GLU* 5.4 2.6 + - - -
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Residues in contact with SER 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ARG 5.6 0.7 - - - -
198F ARG 2.9 13.2 + - - -
199F VAL* 3.6 13.7 - - - -
200F ALA 3.2 0.4 - - - -
201F LYS* 1.3 80.3 - - - +
203F ASN* 1.3 79.3 + - - +
204F ARG 4.3 0.5 + - - -
87z G 5.3 4.3 + - - -
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Residues in contact with ASN 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ARG* 5.0 3.8 - - - +
136F ARG 2.9 35.0 + - - +
137F GLN* 4.4 10.5 - - + +
138F ALA* 3.8 18.9 + - - +
199F VAL 3.9 2.5 + - - +
200F ALA 3.1 11.1 + - - +
202F SER* 1.3 94.1 + - - +
204F ARG* 1.3 60.6 + - - +
63c ARG* 6.0 0.2 - - - -
86z U 5.2 9.1 + - - +
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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