Contacts of the helix formed by residues 168 - 184 (chain B) in PDB entry 5BZZ
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 ILE 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B HIS* 3.5 61.2 - - + +
128B LYS* 6.1 0.4 - - - +
167B THR* 1.3 83.0 - - - +
169B PRO* 1.3 64.2 - - + +
170B SER* 4.0 4.7 - - - +
171B GLN* 3.1 35.0 + - + +
172B ARG* 3.1 11.1 + - - +
272B HIS* 5.8 0.4 - - + -
326B ASP* 3.7 27.1 - - + +
330B LYS* 5.9 8.5 - - - +
401B TLA 4.1 7.9 - - - +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR 3.4 8.5 - - - +
168B ILE* 1.3 84.0 - - + +
170B SER* 1.3 51.4 + - - +
172B ARG* 3.7 12.3 - - + +
173B ARG* 2.8 38.0 + - - +
323B ASN 3.7 20.2 - - - +
324B ASP* 3.6 23.1 - - - +
325B LEU 3.7 9.0 - - - +
326B ASP* 3.4 17.3 - - - +
329B ASN* 3.7 26.0 - - - +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS 5.7 0.2 - - - -
95B PRO* 3.9 13.7 - - - -
168B ILE* 3.3 2.4 - - - -
169B PRO* 1.3 72.5 - - - +
171B GLN* 1.3 65.7 + - - +
173B ARG* 3.2 13.6 + - - +
174B TYR* 3.1 30.3 + - - -
274B TRP* 3.1 37.0 + - - +
326B ASP* 2.6 36.4 + - - -
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 3.7 8.5 - - - +
94B ASN 3.1 33.7 + - - +
95B PRO* 4.0 4.9 - - - -
129B GLY* 3.4 24.7 - - - -
130B ARG* 3.9 13.3 - - - +
133B VAL* 3.6 15.6 - - + +
166B VAL* 3.5 15.6 - - + +
167B THR 4.9 0.5 + - - -
168B ILE* 3.1 30.9 + - + +
170B SER* 1.3 78.3 - - - +
172B ARG* 1.3 60.1 + - - +
174B TYR* 3.4 9.4 + - - +
175B VAL* 3.5 17.5 + - - +
401B TLA 2.9 23.7 + - - +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 4.4 20.4 - - - +
152B LEU* 3.8 43.8 + - + +
153B ASP* 4.7 6.7 + - - -
166B VAL* 2.7 48.0 + - + +
167B THR* 4.0 15.8 - - - +
168B ILE 3.1 9.7 + - - +
169B PRO* 3.7 11.9 - - + +
171B GLN* 1.3 72.7 - - - +
173B ARG* 1.3 65.3 + - - +
175B VAL* 3.2 7.1 + - - +
176B TYR* 3.1 37.6 + - + -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PRO* 2.8 19.7 + - - +
170B SER* 3.2 35.2 + - - +
172B ARG* 1.3 76.8 - - - +
174B TYR* 1.3 51.4 + - + +
176B TYR* 2.9 13.8 + - + +
177B TYR* 2.7 68.9 + - + -
273B PHE* 4.2 3.8 - - - +
274B TRP 2.7 39.6 + - - +
275B VAL* 4.3 4.0 - - - -
318B LEU* 6.0 0.4 - - - -
320B LEU* 3.7 18.9 - - - +
324B ASP* 2.7 44.7 + - - +
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PRO* 3.3 28.3 - - + -
96B PRO* 3.3 36.3 - - + -
98B LEU* 4.1 25.1 - - + -
101B ILE* 3.9 9.8 - - + +
133B VAL* 4.7 1.8 - - + -
170B SER 3.1 23.1 + - - +
171B GLN 3.4 4.7 + - - +
172B ARG 3.3 0.4 - - - -
173B ARG* 1.3 79.4 - - + +
175B VAL* 1.3 60.7 + - - +
177B TYR* 3.5 27.0 - + - +
178B TYR* 3.0 27.9 + - - +
252B ASP* 3.0 33.6 + - - +
274B TRP* 4.0 22.9 - + + +
275B VAL 3.8 14.9 + - - -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.8 33.4 - - + +
136B CYS* 4.0 14.8 - - + -
137B ALA* 4.6 4.9 - - - +
140B LEU* 3.5 24.9 - - + +
148B ALA* 4.0 16.8 - - + +
152B LEU* 4.1 18.6 - - + -
171B GLN 3.5 15.5 - - - +
172B ARG 3.2 6.9 + - - +
174B TYR* 1.3 75.0 - - - +
176B TYR* 1.3 58.1 + - - +
178B TYR* 3.6 3.9 + - - +
179B SER* 2.9 30.1 + - - -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS* 6.3 0.2 - - + -
148B ALA* 3.3 24.0 - - + -
149B GLN* 3.3 36.8 + - + +
152B LEU* 4.1 14.6 - - + -
172B ARG* 3.1 37.5 + - + -
173B ARG* 2.9 13.2 + - + +
175B VAL* 1.3 73.8 - - - +
177B TYR* 1.3 62.8 + - + +
179B SER* 3.5 2.8 + - - -
180B TYR* 2.9 28.4 + - - +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.1 5.4 - - + -
173B ARG* 2.7 45.9 + - + +
174B TYR* 3.5 37.9 - + - +
176B TYR* 1.3 72.2 - - + +
178B TYR* 1.3 66.2 + - - +
180B TYR* 3.0 14.6 + - + +
181B LEU* 3.0 17.0 + - - +
275B VAL* 3.6 6.6 - - - +
276B ASN* 3.1 42.8 + - + -
279B PHE* 3.3 54.7 + + + +
280B ILE* 5.8 0.5 - - - +
318B LEU* 5.2 3.3 - - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.7 4.0 - - + +
101B ILE* 3.5 36.6 - - + -
102B LYS* 3.6 37.0 + - + +
105B CYS* 3.9 9.8 - - - -
137B ALA* 3.8 27.8 - - + -
140B LEU* 5.2 0.7 - - + -
141B HIS* 3.0 25.3 + - + -
174B TYR 3.0 15.7 + - - +
175B VAL 4.0 3.1 - - - +
177B TYR* 1.3 78.7 - - - +
179B SER* 1.3 63.0 + - - +
181B LEU* 3.2 24.3 + - + +
182B LEU* 3.0 57.5 + - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.0 20.1 - - - +
146B LEU 4.7 3.5 + - - -
147B LYS* 4.6 3.5 - - - -
148B ALA* 3.9 21.1 + - - -
175B VAL 2.9 19.5 + - - -
176B TYR* 3.6 6.1 - - - -
178B TYR* 1.3 77.6 - - - +
180B TYR* 1.3 56.5 + - - +
182B LEU* 3.5 12.9 + - - +
183B LYS* 3.0 32.1 + - - +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR 2.9 14.5 + - - +
177B TYR* 3.1 11.0 - - - +
179B SER* 1.3 74.9 - - - +
181B LEU* 1.3 64.4 + - - +
183B LYS* 3.5 5.3 + - + +
184B ASN* 3.1 50.3 + - - +
186B LEU* 3.4 26.8 - - + +
278B PHE* 5.0 3.4 - + - -
279B PHE* 3.6 30.1 - + + -
281B PRO 5.6 1.4 + - - -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.8 28.7 - - + -
177B TYR 3.0 17.1 + - - +
178B TYR* 3.5 27.1 - - + +
180B TYR* 1.3 75.8 - - - +
182B LEU* 1.3 58.8 + - + +
185B HIS* 3.1 9.0 + - - -
186B LEU* 3.0 52.1 + - + +
188B TYR* 4.1 15.7 - - + +
278B PHE* 3.8 22.9 - - + -
279B PHE* 3.7 21.5 - - + -
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.8 16.2 - - + +
141B HIS* 3.7 44.2 - - + +
178B TYR* 3.0 51.6 + - + +
179B SER* 3.7 8.3 - - - +
180B TYR 3.3 0.2 - - - -
181B LEU* 1.3 74.9 - - + +
183B LYS* 1.3 65.6 + - - +
184B ASN 3.3 0.5 + - - -
185B HIS* 3.4 17.5 + - - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU 5.8 4.3 - - - +
179B SER* 3.0 21.5 + - - +
180B TYR* 4.0 6.5 - - + +
181B LEU 3.5 0.2 - - - -
182B LEU* 1.3 78.0 - - - +
184B ASN* 1.3 77.3 + - - +
185B HIS* 3.8 13.0 + - - -
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Residues in contact with ASN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B TYR* 3.1 51.4 + - - +
183B LYS* 1.3 98.0 + - - +
185B HIS* 1.3 74.4 + - - +
186B LEU* 3.2 26.5 + - + +
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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
------------------------------------------------------------
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