Contacts of the helix formed by residues 168 - 185 (chain J) in PDB entry 5U07
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 168 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G VAL* 5.6 10.3 - - - +
198H THR* 3.4 32.6 + - + +
167J GLN* 1.3 73.4 - - - +
169J LEU* 1.3 68.0 + - - +
170J ASP* 3.5 8.6 - - - +
171J GLY* 2.5 36.2 + - - -
172J VAL* 3.0 25.7 + - - +
202J TRP* 4.5 4.3 - - - -
206J PRO* 5.7 3.1 - - - -
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Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J HIS* 5.7 2.7 - - + +
76J ALA* 3.6 36.6 - - + +
79J ARG* 4.2 17.5 - - + -
168J ASN* 1.3 75.8 - - - +
170J ASP* 1.3 62.3 + - + +
172J VAL* 3.1 7.0 - - - +
173J HIS* 2.9 47.3 - - + +
199J LEU 3.9 9.0 - - - +
202J TRP* 3.6 37.0 + - + +
203J GLY* 4.9 1.1 - - - +
206J PRO* 5.8 1.4 - - - +
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Residues in contact with ASP 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J ARG* 4.7 15.5 + - - +
168J ASN* 3.1 9.0 + - - +
169J LEU* 1.3 84.8 - - + +
171J GLY* 1.3 62.3 + - - +
172J VAL 3.4 0.2 - - - -
173J HIS* 3.8 4.9 + - - +
174J ARG* 3.3 27.5 + - - +
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Residues in contact with GLY 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J GLN* 3.6 13.2 - - - -
168J ASN* 2.5 24.6 + - - -
170J ASP* 1.3 74.5 - - - +
172J VAL* 1.3 65.2 + - - +
174J ARG* 3.0 29.1 - - - +
175J HIS* 3.0 18.0 + - - +
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Residues in contact with VAL 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J ILE* 4.4 11.9 - - + +
167J GLN* 3.8 10.3 - - + -
168J ASN 3.0 13.0 + - - +
169J LEU* 3.1 21.5 - - - +
171J GLY* 1.3 77.8 - - - +
173J HIS* 1.3 67.9 + - + +
175J HIS* 5.1 0.4 - - - -
176J LEU* 2.5 43.4 + - + +
199J LEU* 4.3 7.4 - - + -
202J TRP* 3.3 57.7 - - + +
213J TRP* 6.1 0.4 - - + -
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Residues in contact with HIS 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J GLY* 3.7 16.8 - - - -
79J ARG* 3.4 40.7 + - + +
80J ALA* 3.5 22.0 - - - -
83J ALA* 2.8 37.8 - - + +
87J ILE* 5.9 0.2 - - - +
169J LEU* 2.9 41.1 - - - +
170J ASP 3.8 5.1 + - - +
171J GLY 3.2 0.8 - - - -
172J VAL* 1.3 85.1 - - + +
174J ARG* 1.3 56.4 + - - +
176J LEU* 4.4 5.1 - - - +
177J PRO* 3.2 15.6 - - - +
199J LEU* 3.6 19.6 - - + +
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Residues in contact with ARG 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 5.3 8.0 - - - +
27G THR* 2.8 32.9 + - - -
29G VAL* 4.1 23.5 - - - +
34G GLU* 4.7 11.5 + - - +
200H GLU* 6.1 2.8 - - - +
36J GLY* 5.3 7.4 - - - +
79J ARG* 6.1 0.4 - - - +
170J ASP* 3.3 24.7 + - - +
171J GLY* 3.0 25.4 - - - +
173J HIS* 1.3 79.6 - - - +
175J HIS* 1.3 79.7 + - + +
176J LEU 3.5 0.2 - - - -
177J PRO* 3.6 12.2 - - - +
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Residues in contact with HIS 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H GLU* 6.3 0.2 - - - -
201H VAL* 5.2 21.6 + - + +
160J ARG* 4.9 0.2 - - - -
163J LEU* 3.6 34.6 - - + +
164J ILE* 4.0 15.8 - - + +
167J GLN* 4.7 9.2 - - + -
171J GLY* 3.0 26.3 + - - +
172J VAL* 4.5 1.1 - - - +
174J ARG* 1.3 99.0 + - + +
176J LEU* 1.3 65.1 + - - +
177J PRO* 3.5 1.3 - - - -
178J ARG* 3.3 40.7 + - - +
179J LEU* 4.3 0.9 + - - +
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J ILE* 3.8 13.2 - - + -
139J LEU* 4.8 0.4 - - + -
164J ILE* 4.1 14.6 - - + +
172J VAL* 2.5 23.8 + - + +
173J HIS* 4.4 2.9 - - - -
175J HIS* 1.3 76.3 - - - +
177J PRO* 1.3 68.7 - - + +
178J ARG 3.1 1.2 + - - -
179J LEU* 3.2 14.0 + - + +
180J VAL* 2.9 67.8 + - + +
195J LEU* 4.8 9.9 - - + -
199J LEU* 4.7 21.3 - - + -
213J TRP* 4.3 25.8 - - + -
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Residues in contact with PRO 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 5.9 2.9 - - + -
35J VAL* 4.1 17.3 - - + -
36J GLY* 5.0 4.0 - - - -
87J ILE* 3.3 27.3 - - + -
173J HIS 3.2 25.6 - - - +
174J ARG* 3.6 11.9 - - - +
175J HIS 3.5 3.1 - - - -
176J LEU* 1.3 91.6 - - + +
178J ARG* 1.3 63.7 + - + +
181J LEU* 2.9 35.0 + - + +
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Residues in contact with ARG 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 2.5 41.9 + - - -
22G LEU* 3.6 44.1 - - + +
201H VAL* 6.3 0.4 - - - +
160J ARG* 3.4 27.4 - - - +
163J LEU* 3.2 41.2 - - - +
175J HIS* 3.3 34.1 + - - +
177J PRO* 1.3 79.5 - - + +
179J LEU* 1.3 72.1 + - - +
181J LEU* 4.9 2.9 - - - -
182J TYR* 2.9 43.3 + - + +
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Residues in contact with LEU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J LEU* 4.3 7.0 - - + -
143J LEU* 4.2 22.3 - - + +
157J THR* 5.5 2.7 - - + -
160J ARG* 3.4 34.1 - - + +
161J LEU* 3.8 24.7 - - + -
164J ILE* 3.3 30.5 - - + -
175J HIS 4.7 0.4 - - - +
176J LEU* 3.2 12.3 + - + +
178J ARG* 1.3 83.8 - - - +
180J VAL* 1.3 92.2 + - + +
182J TYR* 3.8 3.3 - - - +
183J LEU* 2.8 31.1 + - + +
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Residues in contact with VAL 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J ILE* 3.3 31.9 - - + -
91J GLN* 3.9 0.6 + - - -
139J LEU* 3.7 19.5 - - + -
176J LEU* 2.9 40.1 + - + +
177J PRO 3.5 0.7 - - - +
179J LEU* 1.3 93.7 - - + +
181J LEU* 1.3 60.4 + - - +
183J LEU* 3.4 11.2 - - + +
184J ARG* 2.9 28.1 + - - +
190J ILE* 4.9 3.8 - - + +
195J LEU* 4.1 9.4 - - + -
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Residues in contact with LEU 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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35J VAL* 6.2 2.7 - - + -
87J ILE* 4.9 7.4 - - + -
90J ALA* 4.7 9.9 - - + +
91J GLN* 3.0 38.4 + - - +
92J PRO* 4.4 15.0 - - + -
177J PRO* 2.9 26.6 + - + +
178J ARG* 4.9 1.1 - - - -
180J VAL* 1.3 78.2 - - + +
182J TYR* 1.3 86.1 + - + +
185J SER* 3.0 24.7 + - - +
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Residues in contact with TYR 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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22G LEU* 4.1 27.8 - - + +
152J LEU* 5.3 4.1 - - - +
178J ARG* 2.9 31.6 + - + +
179J LEU* 4.2 3.4 - - - +
181J LEU* 1.3 102.5 - - + +
183J LEU* 1.3 60.2 + - - +
185J SER* 2.9 34.1 - - - +
186J ASP* 5.3 0.9 - - - +
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Residues in contact with LEU 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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139J LEU* 5.6 0.9 - - + -
142J SER* 4.4 4.7 - - - +
143J LEU* 3.6 40.8 - - + +
146J ALA* 4.5 3.1 - - + -
152J LEU* 5.1 9.2 - - + -
179J LEU* 2.8 22.6 + - + +
180J VAL* 3.4 20.4 - - + +
182J TYR* 1.3 73.5 - - - +
184J ARG* 1.3 63.3 + - - +
185J SER 2.7 17.9 - - - +
188J VAL* 3.0 46.4 - - + +
190J ILE* 3.9 40.8 - - + -
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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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91J GLN* 3.0 28.4 - - + +
95J ALA* 2.6 52.8 + - + +
96J ARG* 4.4 1.6 - - - +
97J ASP* 4.1 10.1 - - - +
180J VAL 2.9 11.0 + - - +
183J LEU* 1.3 75.8 - - + +
185J SER* 1.3 64.5 + - - +
187J GLN* 3.1 31.8 + - - +
188J VAL 3.7 14.6 + - - +
189J HIS* 4.5 7.9 - - - +
190J ILE* 3.6 35.0 + - + +
192J TRP* 3.1 41.5 - - - +
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Residues in contact with SER 185 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J GLN* 4.5 0.2 - - - +
92J PRO* 4.5 15.1 - - - +
95J ALA* 5.2 2.5 - - - -
152J LEU* 5.7 1.2 - - - +
181J LEU* 3.0 22.0 + - - +
182J TYR* 2.9 31.7 - - - +
183J LEU* 2.7 21.4 - - - +
184J ARG* 1.3 75.7 - - - +
186J ASP* 1.3 70.2 + - - +
188J VAL* 4.3 0.3 - - - +
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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
------------------------------------------------------------
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