Contacts of the helix formed by residues 183 - 192 (chain J) in PDB entry 4GUN
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 VAL 183 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180J TYR* 3.0 27.4 + - + +
181J GLN* 3.2 0.6 - - + -
182J ASN* 1.4 81.7 - - - +
184J ARG* 1.3 62.3 + - - +
185J PRO* 3.4 11.0 - - + -
186J ASP* 3.1 48.4 + - + +
187J TYR 3.7 2.6 + - - -
303L SO4 3.7 35.0 - - - +
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Residues in contact with ARG 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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126J LEU 3.3 13.3 + - - -
127J ALA* 2.7 32.3 + - - +
129J ILE* 2.9 33.1 + - - +
131J GLY 4.1 13.5 + - - +
171J ALA* 4.4 7.3 + - - +
176J TYR* 3.1 48.2 + - + +
182J ASN 2.8 12.8 + - - +
183J VAL* 1.3 71.5 - - - +
185J PRO* 1.4 65.7 - - + +
187J TYR* 3.1 14.3 + - - +
188J PHE* 3.2 37.7 + - + -
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Residues in contact with PRO 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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127J ALA* 6.2 4.7 - - + -
182J ASN 4.6 1.3 - - - +
183J VAL* 3.4 14.4 - - + -
184J ARG* 1.4 93.2 - - + +
186J ASP* 1.3 60.0 + - - +
188J PHE* 3.6 13.0 + - + +
189J LYS* 3.1 29.3 + - - +
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Residues in contact with ASP 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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180J TYR* 3.7 20.0 - - + -
183J VAL* 3.1 34.4 + - + +
185J PRO* 1.3 77.8 - - - +
187J TYR* 1.3 61.3 + - - +
189J LYS* 3.6 6.6 + - - +
190J ALA* 3.0 30.1 + - - +
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Residues in contact with TYR 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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23J TYR 5.1 0.7 - - - -
24J ILE* 4.3 16.6 - - + +
83J PHE* 3.5 11.4 - - - -
169J ILE* 5.0 0.4 - - + -
170J ASP 2.9 29.4 + - - -
175J ALA* 3.6 22.3 + - + +
176J TYR* 3.4 43.7 - + + -
180J TYR* 3.7 29.1 - + + -
183J VAL 3.7 1.8 + - - -
184J ARG 3.1 8.6 + - - +
186J ASP* 1.3 76.7 - - - +
188J PHE* 1.3 87.6 + + - +
190J ALA* 3.1 1.7 + - - +
191J ILE* 3.0 57.1 + - + +
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Residues in contact with PHE 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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123J ASN* 3.9 21.1 - - + +
126J LEU* 3.5 55.9 - - + -
127J ALA* 3.9 7.2 - - + -
169J ILE* 4.6 3.6 - - + -
170J ASP 4.5 0.4 - - - -
171J ALA* 3.8 20.9 - - + -
184J ARG* 3.2 54.0 + - + -
185J PRO* 3.9 11.0 - - + +
187J TYR* 1.3 104.4 - + - +
189J LYS* 1.3 62.5 + - - +
191J ILE* 3.3 9.0 - - - +
192J TRP* 3.0 23.6 + - - -
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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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123J ASN* 4.5 12.9 + - - +
185J PRO 3.1 18.8 + - - +
186J ASP* 3.8 6.7 - - - +
188J PHE* 1.3 75.1 - - - +
190J ALA* 1.4 61.8 + - - +
192J TRP* 3.7 14.6 + - - +
193J ASN* 4.2 5.5 + - - -
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Residues in contact with ALA 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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23J TYR* 3.7 21.1 - - + +
180J TYR* 3.2 24.9 - - + +
186J ASP 3.0 19.5 + - - +
187J TYR* 3.1 4.2 + - + +
189J LYS* 1.4 74.9 - - - +
191J ILE* 1.3 63.3 + - - +
193J ASN* 2.9 32.0 + - - +
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Residues in contact with ILE 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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23J TYR* 5.0 1.8 - - - +
24J ILE* 3.9 15.7 - - + -
83J PHE* 3.5 28.0 - - + -
87J LEU* 4.0 14.8 - - + -
126J LEU* 5.7 0.2 - - + -
169J ILE* 4.2 28.7 - - + -
187J TYR* 3.0 46.1 + - + +
188J PHE* 3.3 22.2 - - - +
190J ALA* 1.3 70.4 - - - +
192J TRP* 1.3 66.9 + - + +
193J ASN 3.1 2.9 - - - -
194J VAL* 2.9 25.1 + - + +
195J ILE* 3.2 12.7 + - + +
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Residues in contact with TRP 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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95J GLY* 3.3 16.8 - - - +
97J HIS* 6.1 0.3 - - - -
119J ILE* 3.7 46.0 - - + -
122J THR* 3.5 38.4 - - + -
123J ASN* 2.8 26.1 + - - -
126J LEU* 4.7 1.3 - - + +
137J ILE* 4.0 13.5 - - + -
167J ILE* 4.3 11.7 - - + -
169J ILE* 4.4 8.5 - - + -
188J PHE 3.0 22.7 + - - -
189J LYS 3.7 11.0 - - - +
190J ALA 3.3 1.6 + - - -
191J ILE* 1.3 82.7 - - + +
193J ASN* 1.3 61.1 + - - +
194J VAL 3.3 1.0 + - - -
195J ILE* 3.4 37.5 + - + +
197J TRP* 3.6 33.2 + + - +
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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