Contacts of the helix formed by residues 181 - 191 (chain J) in PDB entry 6ALG
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 GLY 181 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J VAL* 3.1 30.7 + - - +
139J LEU* 3.5 13.7 - - - -
141J PHE* 3.5 14.6 - - - -
180J MET* 1.3 72.7 - - - +
182J ALA* 1.3 61.0 + - - -
184J ALA* 2.9 19.2 + - - +
185J ILE* 3.2 13.5 + - - +
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Residues in contact with ALA 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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109J SER* 5.5 0.4 - - - +
110J PRO* 3.3 35.4 - - + +
111J THR* 3.7 11.0 - - - +
112J ALA* 3.9 9.6 - - - +
139J LEU* 3.6 14.4 - - + +
141J PHE* 5.0 1.0 - - - -
180J MET 3.9 0.2 + - - -
181J GLY* 1.3 69.3 - - - -
183J GLU* 1.3 59.9 + - - +
185J ILE* 3.9 3.6 - - - +
186J GLN* 2.9 31.2 + - - +
238J ILE* 4.1 5.6 - - + +
300J GLN* 4.5 3.4 - - - +
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Residues in contact with GLU 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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108J ALA 5.6 0.2 - - - +
109J SER* 5.1 1.2 - - - +
110J PRO* 3.7 32.8 - - + +
179J LYS* 4.5 25.1 + - + +
180J MET 4.4 8.9 - - - +
181J GLY 3.2 0.6 - - - -
182J ALA* 1.3 77.6 - - - +
184J ALA* 1.3 56.4 + - - +
186J GLN* 3.6 4.3 + - - +
187J ALA* 2.9 28.6 + - - +
296J LYS* 3.1 28.5 + - - +
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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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138J VAL* 4.6 1.8 - - + -
145J VAL* 3.7 27.6 - - + -
147J ILE* 4.3 4.2 - - + +
179J LYS* 3.8 23.3 - - + +
180J MET 3.9 9.1 + - - +
181J GLY 2.9 11.2 + - - +
183J GLU* 1.3 78.5 - - - +
185J ILE* 1.3 62.2 + - - +
187J ALA* 3.6 6.9 - - - +
188J LEU* 2.9 33.4 + - - +
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Residues in contact with ILE 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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112J ALA* 6.0 0.2 - - + -
124J ILE* 3.9 23.6 - - + -
128J LEU* 4.0 20.9 - - + -
130J MET* 5.3 4.3 - - + -
135J ILE* 4.2 18.4 - - + -
138J VAL* 4.4 14.4 - - + -
139J LEU* 3.8 20.0 - - + -
145J VAL* 5.7 0.9 - - + -
181J GLY 3.2 11.9 + - - +
182J ALA* 4.1 5.8 - - - +
184J ALA* 1.3 77.2 - - + +
186J GLN* 1.3 58.9 + - - +
188J LEU* 3.2 11.5 + - + +
189J LEU* 2.9 34.9 + - + +
238J ILE* 3.8 22.4 - - + -
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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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110J PRO* 3.5 30.1 - - - +
182J ALA 2.9 16.1 + - - +
183J GLU* 4.0 3.4 - - - +
185J ILE* 1.3 77.1 - - - +
187J ALA* 1.3 58.1 + - - +
189J LEU* 4.2 3.3 - - - +
190J LYS* 2.9 47.0 + - - +
235J GLU* 4.5 21.4 + - + +
238J ILE* 4.0 24.7 + - + +
240J THR* 3.9 18.1 + - - -
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Residues in contact with ALA 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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147J ILE* 3.8 33.3 - - + +
179J LYS* 5.0 5.6 - - - +
183J GLU 2.9 20.7 + - - +
184J ALA 3.6 5.6 - - - +
186J GLN* 1.3 76.4 - - - +
188J LEU* 1.3 51.3 + - - +
190J LYS* 4.9 2.7 - - - -
191J SER* 2.6 40.4 + - - -
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Residues in contact with LEU 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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128J LEU* 4.1 29.8 - - + -
130J MET* 5.1 2.5 - - - -
145J VAL* 4.7 22.4 - - + -
146J VAL 4.2 6.5 - - - +
147J ILE* 3.9 18.8 - - + -
156J ARG* 3.2 43.4 + - + +
157J GLN* 4.5 12.6 - - - +
184J ALA 2.9 20.0 + - - +
185J ILE* 3.2 14.1 + - + +
187J ALA* 1.3 77.1 - - - +
189J LEU* 1.3 58.7 + - - +
191J SER* 3.0 12.6 + - - -
192J MET* 3.1 18.5 + - - +
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Residues in contact with LEU 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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124J ILE* 4.7 10.3 - - + -
127J LEU* 3.8 28.0 - - + -
128J LEU* 3.7 26.0 - - + -
185J ILE* 2.9 36.0 + - + +
186J GLN* 4.2 1.3 - - - +
188J LEU* 1.3 74.6 - - - +
190J LYS* 1.3 64.8 + - - +
192J MET* 3.4 22.2 + - - +
234J PRO* 3.5 31.0 - - + +
235J GLU* 3.8 28.1 - - - +
237J MET* 4.8 6.5 - - + -
238J ILE* 4.5 9.0 - - + -
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Residues in contact with LYS 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* 2.9 31.9 + - - +
187J ALA* 4.4 2.7 - - - +
189J LEU* 1.3 77.5 - - - +
191J SER* 1.3 61.7 + - - +
192J MET 3.2 5.2 + - - +
235J GLU* 4.1 32.4 - - + +
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Residues in contact with SER 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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147J ILE* 5.4 2.3 - - - +
148J GLU* 4.6 17.0 - - - +
156J ARG* 2.5 34.2 + - - -
187J ALA 2.6 23.7 + - - -
188J LEU* 3.0 3.8 + - - +
190J LYS* 1.3 76.0 - - - +
192J MET* 1.3 58.7 + - - +
193J ASP 3.7 2.1 + - - -
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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