Contacts of the helix formed by residues 191 - 202 (chain J) in PDB entry 5U0A
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 ASP 191 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J ASP* 5.1 0.7 - - - +
14J VAL* 5.8 1.4 - - - +
136J ARG* 2.2 44.0 + - - +
137J PRO* 4.2 26.2 + - + +
138J ASN 5.6 2.0 + - - -
142J SER* 4.6 1.8 + - - -
189J HIS* 3.9 18.2 + - + -
190J ILE* 1.3 71.6 - - - +
192J TRP* 1.3 64.3 + - - +
193J GLY 3.2 11.3 + - - -
194J ILE* 3.4 12.2 + - + +
195J LEU* 3.4 17.8 + - - +
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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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14J VAL* 3.7 24.0 - - + +
84J VAL* 3.5 27.7 - - + +
87J ILE* 3.7 22.9 - - + -
88J MET* 4.2 29.0 - - + +
91J GLN* 3.3 32.7 - - - +
180J VAL* 3.3 28.0 - - + -
184J ARG* 3.5 21.7 - - + +
190J ILE* 3.4 21.2 + - + -
191J ASP* 1.3 72.3 + - - +
193J GLY* 1.3 61.1 + - - +
195J LEU* 3.3 32.1 + - + +
196J ILE* 2.9 32.6 + - - +
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Residues in contact with GLY 193 (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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7J LEU* 4.9 3.3 - - - +
10J ALA* 4.1 18.4 - - - +
11J ASP* 4.2 12.8 + - - -
14J VAL* 3.7 16.1 - - - +
136J ARG* 4.6 2.5 - - - -
191J ASP* 3.2 8.0 + - - -
192J TRP* 1.3 77.6 - - - +
194J ILE* 1.3 63.7 + - - +
196J ILE* 3.1 3.5 + - - +
197J ARG* 2.9 23.7 + - - +
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Residues in contact with ILE 194 (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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7J LEU* 3.6 26.5 - - + -
136J ARG* 3.6 30.7 - - + +
137J PRO 3.6 22.7 - - - +
138J ASN* 3.3 28.9 - - - +
191J ASP* 3.4 20.5 + - - +
192J TRP 3.3 0.6 - - - -
193J GLY* 1.3 74.6 - - - +
195J LEU* 1.3 63.5 + - - +
197J ARG* 3.3 21.3 + - - +
198J ASP* 2.9 34.4 + - - +
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Residues in contact with LEU 195 (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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84J VAL* 4.4 6.3 - - + -
87J ILE* 5.7 0.4 - - + -
139J LEU* 4.0 27.3 - - + +
176J LEU* 4.0 20.6 - - + -
180J VAL* 4.5 2.2 - - + -
190J ILE* 4.5 7.6 - - + -
191J ASP 3.4 10.2 + - - +
192J TRP* 3.3 41.4 + - + +
193J GLY 3.3 0.4 - - - -
194J ILE* 1.3 77.9 - - - +
196J ILE* 1.3 58.6 + - - +
198J ASP* 3.7 5.5 - - - +
199J LEU* 2.9 43.5 + - + +
213J TRP* 3.7 32.3 - - + -
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Residues in contact with ILE 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 5.1 1.8 - - + -
10J ALA* 3.8 17.0 - - + +
13J LEU* 4.2 17.9 - - + -
14J VAL* 4.0 20.2 - - + -
80J ALA* 3.7 5.9 - - + +
81J PHE* 3.3 38.1 - - + +
84J VAL* 3.4 36.6 - - + -
85J ALA 5.6 0.2 - - - +
192J TRP 2.9 19.3 + - - +
193J GLY 3.1 7.2 + - - +
195J LEU* 1.3 74.1 - - - +
197J ARG* 1.3 67.4 + - - +
199J LEU* 3.1 3.9 + - - -
200J ALA* 2.9 19.9 + - + +
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Residues in contact with ARG 197 (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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5J TYR 5.5 5.2 - - - +
6J ILE* 5.0 11.0 - - + -
7J LEU* 3.5 41.6 - - + +
10J ALA* 5.0 0.2 - - - +
138J ASN* 4.7 3.4 + - - -
193J GLY 2.9 15.0 + - - +
194J ILE* 3.6 33.7 - - - +
196J ILE* 1.3 76.9 - - - +
198J ASP* 1.3 72.0 + - - +
200J ALA* 3.1 7.9 + - - +
201J ARG* 2.5 77.4 + - + +
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Residues in contact with ASP 198 (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 ASN* 3.5 7.0 - - - +
139J LEU 5.2 0.2 + - - -
194J ILE* 2.9 37.0 + - - +
195J LEU* 3.7 7.3 + - - +
197J ARG* 1.3 88.2 + - - +
199J LEU* 1.3 58.3 + - - +
201J ARG* 2.4 40.8 + - - +
202J TRP* 2.8 27.6 + - - +
209J VAL* 3.7 15.6 - - + +
212J GLU* 4.8 0.5 - - - +
213J TRP* 3.3 29.5 + - + +
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Residues in contact with LEU 199 (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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76J ALA 4.1 5.0 - - - +
80J ALA* 3.6 18.6 - - + +
83J ALA* 5.2 2.0 - - + -
84J VAL* 3.6 28.0 - - + -
87J ILE* 5.7 0.2 - - + -
169J LEU* 4.2 10.8 - - + +
172J VAL* 4.0 26.5 - - + -
173J HIS* 3.9 24.6 + - + +
176J LEU* 3.7 25.4 - - + -
195J LEU* 2.9 27.8 + - + +
196J ILE 3.1 0.6 + - - +
198J ASP* 1.3 77.0 - - - +
200J ALA* 1.3 61.2 + - - +
202J TRP* 3.5 18.4 + - + +
213J TRP* 4.9 7.6 - - + -
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Residues in contact with ALA 200 (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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6J ILE* 4.5 16.8 - - + -
76J ALA* 3.9 17.3 - - - +
77J VAL* 4.1 28.1 - - + +
80J ALA* 3.5 13.2 - - + +
81J PHE* 6.2 0.2 - - + -
196J ILE* 2.9 12.4 + - + +
197J ARG* 3.5 10.1 - - - +
198J ASP 3.1 0.2 - - - -
199J LEU* 1.3 81.1 - - - +
201J ARG* 1.3 60.8 + - + +
202J TRP 3.5 0.9 + - - -
203J GLY* 3.7 6.9 + - - -
204J HIS* 4.1 6.1 + - - -
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Residues in contact with ARG 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 5.7 6.1 - - + -
197J ARG* 2.5 42.3 + - + +
198J ASP* 2.4 32.6 + - - +
200J ALA* 1.3 75.5 - - + +
202J TRP* 1.3 54.6 + - - +
203J GLY 3.2 2.5 - - - -
204J HIS* 3.5 25.5 + - + +
205J THR* 2.2 39.8 + - + +
208J HIS* 4.6 14.6 - - - -
209J VAL* 3.5 26.1 - - + +
212J GLU* 3.7 15.4 + - - -
33O T 5.8 1.6 + - - -
34O G 5.2 11.0 + - - -
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Residues in contact with TRP 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J ILE 4.8 0.9 - - - -
165J ALA* 3.7 12.3 - - - -
167J GLN 2.8 23.3 - - - -
168J ASN* 3.0 22.3 - - - +
169J LEU* 3.1 32.2 + - + +
172J VAL* 3.1 25.2 - - + +
198J ASP 2.8 14.3 + - - +
199J LEU* 3.8 16.4 - - + +
200J ALA 3.2 1.4 - - - -
201J ARG* 1.3 77.1 - - - +
203J GLY* 1.3 64.1 + - - +
205J THR* 3.0 23.2 - - - +
206J PRO 3.5 24.7 - - - -
207J ARG* 4.1 4.5 - - - -
209J VAL* 3.1 26.2 - - + -
210J ALA* 3.2 39.7 - - + -
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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