Contacts of the helix formed by residues 176 - 192 (chain J) in PDB entry 6FGA
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 176 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172J GLN* 2.8 27.4 + - + +
175J THR* 1.3 77.0 - - + +
177J ARG* 1.3 62.9 + - - +
178J ALA* 4.0 7.4 + - - +
179J GLU* 3.3 31.7 + - + +
180J HIS* 3.1 17.7 + - - +
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Residues in contact with ARG 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J VAL* 5.7 0.2 - - - +
158J ASP* 5.8 1.2 + - - -
172J GLN 3.6 1.1 + - - -
173J TYR* 3.0 71.3 + - - +
174J MET 5.5 1.8 - - - +
175J THR 3.8 3.0 + - - -
176J ASN* 1.3 73.5 + - - +
178J ALA* 1.3 57.3 + - - +
180J HIS* 3.4 2.3 + - - +
181J ASP* 2.7 78.1 + - - +
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Residues in contact with ALA 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ASN* 3.3 7.3 + - - +
177J ARG* 1.3 78.5 - - - +
179J GLU* 1.3 59.2 + - - +
181J ASP* 3.5 6.8 + - - +
182J ARG* 3.0 28.5 + - - +
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Residues in contact with GLU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J GLN* 3.5 19.1 - - - +
176J ASN* 3.3 31.7 + - + +
177J ARG 3.3 0.8 - - - -
178J ALA* 1.3 76.0 - - - +
180J HIS* 1.3 65.2 + - - +
182J ARG* 2.8 42.5 + - - +
183J MET* 3.1 30.1 + - - +
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Residues in contact with HIS 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J VAL* 5.4 3.4 - - + -
91J TYR* 4.7 9.8 + - - -
120J TYR* 3.8 10.8 + + - -
121J HIS* 5.7 0.2 - - - -
122J CYS* 5.0 3.6 + - - -
159J CYS* 5.3 4.9 - - - -
169J ILE* 3.3 46.3 + - + +
172J GLN* 3.4 19.9 - - + +
173J TYR* 3.7 34.7 - + + +
176J ASN 3.1 13.4 + - - +
177J ARG 3.5 8.3 - - - +
178J ALA 3.3 0.2 - - - -
179J GLU* 1.3 75.8 - - - +
181J ASP* 1.3 65.8 + - - +
183J MET* 3.1 5.5 + - - +
184J ALA* 2.8 47.3 + - + +
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Residues in contact with ASP 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J VAL* 3.7 27.8 - - + +
177J ARG* 2.7 51.7 + - - +
178J ALA* 3.8 5.6 - - - +
180J HIS* 1.3 87.0 + - - +
182J ARG* 1.3 60.1 + - - +
184J ALA* 3.6 0.6 + - - -
185J ARG* 3.2 44.1 + - - +
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Residues in contact with ARG 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J ALA 3.0 18.9 + - - +
179J GLU* 2.8 36.5 + - - +
180J HIS 3.2 0.2 - - - -
181J ASP* 1.3 76.4 - - - +
183J MET* 1.3 83.1 + - - +
185J ARG* 3.2 10.2 + - - +
186J GLN* 3.1 60.9 + - - +
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Residues in contact with MET 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J TYR* 3.2 38.1 - - + +
172J GLN* 3.4 26.9 - - - -
179J GLU* 3.1 19.5 + - - +
180J HIS 3.1 3.3 + - - +
182J ARG* 1.3 99.7 - - - +
184J ALA* 1.3 57.3 + - - +
186J GLN* 3.4 9.2 + - - +
187J TRP* 3.2 43.5 + - + +
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Residues in contact with ALA 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J VAL* 3.4 28.7 - - + -
91J TYR* 4.4 3.1 - - + -
120J TYR* 3.8 30.2 - - + +
180J HIS* 2.8 22.0 + - + +
181J ASP* 3.8 5.4 - - - +
182J ARG 3.2 0.2 - - - -
183J MET* 1.3 75.5 - - - +
185J ARG* 1.3 52.1 + - - +
187J TRP* 3.9 2.6 + - - +
188J THR* 2.7 35.2 + - - -
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Residues in contact with ARG 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J GLY 4.7 6.1 + - - -
89J SER 4.4 7.7 + - - -
90J VAL* 3.5 39.9 + - + +
181J ASP* 3.2 41.9 + - - +
182J ARG* 3.2 7.5 + - - +
184J ALA* 1.3 74.8 - - - +
186J GLN* 1.3 59.4 + - - +
188J THR* 3.4 3.3 + - - +
189J LYS* 3.0 29.3 + - - +
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Residues in contact with GLN 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J ARG* 3.1 50.3 + - - +
183J MET* 3.6 12.1 - - - +
184J ALA 3.4 0.4 - - - -
185J ARG* 1.3 77.1 - - - +
187J TRP* 1.3 62.6 + - + +
189J LYS* 3.5 5.6 + - - +
190J ARG* 3.1 29.3 + - - +
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Residues in contact with TRP 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J ARG* 4.3 30.0 - - - +
119J ILE* 3.7 19.7 - - - -
120J TYR* 3.7 54.4 - + + +
126J SER* 6.1 5.2 - - - -
183J MET* 3.2 31.5 + - + +
184J ALA 4.0 2.0 - - - +
185J ARG 3.4 0.2 - - - -
186J GLN* 1.3 81.6 - - + +
188J THR* 1.3 60.2 + - - +
190J ARG* 4.7 0.2 - - - -
191J TYR* 2.9 67.4 + + + +
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Residues in contact with THR 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J VAL 3.6 6.6 + - - +
91J TYR* 3.5 45.6 - - - +
92J GLU 3.8 13.0 - - - +
93J GLY 4.7 0.7 - - - -
94J GLY* 3.9 13.2 - - - +
96J PHE* 4.3 4.6 - - + -
118J ARG 6.0 0.2 - - - -
119J ILE* 5.7 0.2 - - - +
184J ALA 2.7 21.7 + - - -
185J ARG* 3.5 6.5 - - - +
186J GLN 3.3 0.2 - - - -
187J TRP* 1.3 77.7 - - - +
189J LYS* 1.3 58.2 + - - +
192J ALA* 3.0 37.3 + - + +
193J THR* 3.5 5.2 + - - +
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Residues in contact with LYS 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J ARG 3.0 17.0 + - - +
186J GLN* 3.9 6.7 - - - +
187J TRP 3.4 0.2 - - - -
188J THR* 1.3 77.3 - - - +
190J ARG* 1.3 60.8 + - - +
193J THR* 3.4 32.7 + - + +
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Residues in contact with ARG 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J GLN 3.1 17.8 + - - +
187J TRP* 4.2 1.8 - - - +
188J THR 3.4 0.2 - - - -
189J LYS* 1.3 78.5 - - - +
191J TYR* 1.3 88.9 + - + +
193J THR 4.6 5.3 - - - +
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Residues in contact with TYR 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J THR* 3.8 10.3 - - - +
118J ARG* 3.8 52.8 + - + +
187J TRP* 2.9 66.2 + + + +
190J ARG* 1.3 102.2 - - + +
192J ALA* 1.3 61.2 + - - +
193J THR 3.5 5.3 + - - +
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Residues in contact with ALA 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J GLY 4.4 0.9 - - - +
94J GLY* 3.5 19.5 - - - -
95J VAL* 2.9 39.9 + - - +
96J PHE* 3.7 26.5 - - + -
117J THR* 4.2 2.7 - - + -
118J ARG 5.3 0.4 - - - +
187J TRP 3.9 0.4 + - - -
188J THR* 3.0 17.2 + - - +
191J TYR* 1.3 76.4 - - + +
193J THR* 1.3 62.3 + - - +
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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