Contacts of the helix formed by residues 164 - 181 (chain B) in PDB entry 5WXN
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 HIS 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLU* 4.7 11.5 - - + +
160B MET* 3.9 25.4 - - + +
161B GLN* 3.0 34.8 + - + +
163B THR* 1.3 79.5 + - - +
165B PRO* 1.3 79.7 - - + +
166B ILE* 3.0 52.8 + - + +
167B ARG* 2.9 20.5 + - + +
168B LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 165 (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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163B THR 3.2 0.9 - - - +
164B HIS* 1.3 94.8 - - + +
166B ILE* 1.3 59.7 + - + +
168B LEU* 4.4 2.5 - - + -
169B GLY* 2.8 24.1 + - - -
210B SER* 4.1 23.6 - - - +
213B ASP* 4.2 17.5 - - + +
214B SER* 3.2 23.6 - - - +
217B ILE* 3.2 25.7 - - + +
339D PRO* 3.9 12.4 - - + +
341D LEU* 6.5 2.0 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 4.1 19.1 - - - +
113B GLU* 4.0 11.2 - - + +
116B VAL* 3.7 24.7 - - + +
117B PHE* 3.7 39.3 - - + +
120B LYS* 4.7 4.5 - - + +
160B MET* 4.4 3.8 - - + -
164B HIS* 3.0 27.1 + - + +
165B PRO* 1.3 78.6 - - + +
167B ARG* 1.3 60.5 + - - +
169B GLY* 3.5 0.5 + - - -
170B LEU* 3.1 24.9 + - - +
339D PRO* 3.7 24.5 - - + -
341D LEU* 6.3 2.0 - - + -
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Residues in contact with ARG 167 (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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156B SER* 3.4 36.1 + - - -
157B LYS* 3.8 19.4 + - - +
160B MET* 2.7 47.2 + - + -
161B GLN* 3.7 15.9 - - - +
162B PRO* 3.8 31.6 - - + +
164B HIS* 2.9 10.4 + - + +
166B ILE* 1.3 80.4 - - - +
168B LEU* 1.3 60.2 + - - +
170B LEU* 3.4 5.9 + - - +
171B ALA* 3.2 21.5 + - + +
195B ALA* 6.1 3.0 - - - +
198B GLU* 5.0 8.1 - - - +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO 3.4 19.5 - - - +
163B THR* 3.1 35.4 - - - +
164B HIS 3.0 10.6 + - - +
165B PRO* 4.2 1.8 - - + +
167B ARG* 1.3 74.2 - - - +
169B GLY* 1.3 65.6 + - - +
171B ALA* 3.6 6.7 + - - +
172B LEU* 3.1 17.2 + - - +
195B ALA* 3.8 6.7 - - + +
199B ALA* 3.7 8.7 - - + -
214B SER* 4.0 25.1 - - - +
217B ILE* 3.2 22.5 - - + +
218B MET* 3.6 26.2 - - + -
221B LEU* 3.8 19.0 - - + +
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Residues in contact with GLY 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 4.0 7.0 - - - -
165B PRO 2.8 19.1 + - - -
166B ILE 3.5 2.2 + - - -
167B ARG 3.3 0.2 - - - -
168B LEU* 1.3 76.8 - - - +
170B LEU* 1.3 61.0 + - - +
172B LEU* 3.3 0.9 + - - +
173B ASN* 3.0 30.5 + - - +
217B ILE* 4.0 2.9 - - - +
337D VAL* 3.8 21.5 - - - -
339D PRO* 4.3 6.3 - - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 4.1 4.3 - - + -
120B LYS* 3.8 20.3 - - + +
149B TYR* 3.5 37.0 - - + +
152B ALA* 3.3 20.6 - - + +
153B PHE* 3.3 44.6 - - + +
156B SER* 3.6 9.0 - - - +
166B ILE 3.1 18.0 + - - +
167B ARG* 3.8 6.5 - - - +
168B LEU 3.3 0.2 - - - -
169B GLY* 1.3 72.7 - - - +
171B ALA* 1.3 59.9 + - - +
173B ASN* 4.9 0.4 - - - -
174B PHE* 2.8 40.0 + - + +
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Residues in contact with ALA 171 (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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153B PHE* 5.3 6.2 - - + -
167B ARG 3.2 15.8 + - - +
168B LEU* 3.9 6.5 - - - +
169B GLY 3.3 0.2 - - - -
170B LEU* 1.3 76.6 - - - +
172B LEU* 1.3 56.2 + - - +
174B PHE* 4.0 1.5 - - - +
175B SER* 2.8 35.3 + - - -
191B LEU* 4.4 17.6 - - + +
192B ALA* 5.5 0.2 - - - -
195B ALA* 3.4 33.7 - - + -
221B LEU* 4.3 4.5 - - + -
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Residues in contact with LEU 172 (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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168B LEU 3.1 18.7 + - - +
169B GLY 3.7 3.4 - - - +
170B LEU 3.3 0.4 - - - -
171B ALA* 1.3 76.7 - - - +
173B ASN* 1.3 60.2 + - - +
175B SER* 3.7 3.0 - - - +
176B VAL* 3.2 28.8 + - - +
217B ILE* 4.2 6.1 - - + -
220B LEU* 3.4 49.1 - - + +
221B LEU* 3.6 21.7 - - + +
224B ASN* 3.2 25.3 + - - +
335D MET 3.7 4.9 - - - +
336D TPO 3.8 13.9 - - - -
337D VAL* 3.6 27.8 - - + -
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Residues in contact with ASN 173 (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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120B LYS* 2.7 30.7 - - + +
124B ASP* 2.9 30.0 + - - +
127B ARG* 4.2 3.3 + - - +
149B TYR* 4.2 10.6 + - + +
169B GLY 3.0 13.1 + - - +
170B LEU* 4.2 2.2 - - - +
172B LEU* 1.3 73.5 - - - +
174B PHE* 1.3 62.1 + - - +
176B VAL* 3.2 7.9 + - - +
177B PHE* 2.9 26.0 + - - +
336D TPO 3.5 17.2 + - - -
337D VAL* 2.9 36.4 + - - +
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLN* 4.2 10.5 - - + -
149B TYR* 3.4 53.5 - + + -
150B GLN* 3.8 31.0 - - - -
153B PHE* 4.0 26.5 - + + -
170B LEU* 2.8 29.0 + - + +
171B ALA* 4.0 2.2 - - - +
173B ASN* 1.3 68.9 - - - +
175B SER* 1.3 61.4 + - - +
177B PHE* 2.8 37.9 + + + +
178B TYR* 2.9 34.4 + + - +
191B LEU* 4.2 14.1 - - + -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA 2.8 20.0 + - - -
172B LEU* 3.7 5.1 + - - -
174B PHE* 1.3 75.7 - - - +
176B VAL* 1.3 60.9 + - - +
178B TYR* 3.4 0.4 + - - -
179B TYR 3.2 4.9 + - - -
188B ALA* 2.9 42.6 + - - +
191B LEU* 4.1 11.0 - - - +
192B ALA* 3.3 21.3 - - - +
221B LEU* 5.3 0.2 - - - -
224B ASN* 5.2 0.9 + - - +
228B TRP* 2.9 29.2 - - - -
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Residues in contact with VAL 176 (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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127B ARG* 4.1 14.8 - - - +
172B LEU 3.2 9.3 + - - +
173B ASN 3.5 7.6 - - - +
174B PHE 3.1 1.0 - - - -
175B SER* 1.3 72.4 - - - +
177B PHE* 1.3 60.3 + - - +
180B GLU* 2.8 35.7 + - + +
181B ILE* 5.1 0.2 - - - +
224B ASN* 3.3 17.3 - - - +
228B TRP* 3.7 15.0 - - + -
334D SER* 3.7 21.8 - - - +
335D MET 3.2 26.2 - - - +
336D TPO 3.6 19.1 - - + +
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Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 3.6 27.1 - - + +
142B VAL* 3.5 35.7 - - + -
145B SER* 3.2 26.2 - - - -
146B GLN* 3.7 17.7 - - + -
149B TYR* 3.8 14.1 - + + -
173B ASN 2.9 12.7 + - - +
174B PHE* 2.8 27.6 + + + +
176B VAL* 1.3 75.7 - - - +
178B TYR* 1.3 63.1 + + - +
181B ILE* 2.9 47.6 + - + +
182B LEU* 3.2 31.8 + - + -
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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
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146B GLN* 3.4 21.1 + - - -
150B GLN* 3.8 13.9 + - - -
174B PHE* 2.9 27.5 + + - -
175B SER 3.7 1.8 - - - +
176B VAL 3.3 0.2 - - - -
177B PHE* 1.3 77.7 - + - +
179B TYR* 1.3 60.7 + - - +
182B LEU* 3.4 35.1 + - + +
183B ASN 3.2 7.1 + - - -
184B SER* 3.0 30.6 + - - +
187B LYS* 4.0 27.6 - - + -
188B ALA* 3.5 21.3 - - + +
191B LEU* 3.7 32.5 - - + -
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Residues in contact with TYR 179 (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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175B SER 3.2 8.9 + - - +
176B VAL 3.2 1.5 + - - +
178B TYR* 1.3 81.3 - - - +
180B GLU* 1.3 67.0 + - + +
183B ASN* 3.5 20.8 + - - +
184B SER 4.6 3.4 - - - +
185B PRO* 3.9 35.3 - - + +
188B ALA* 3.9 3.8 - - + -
227B LEU* 5.3 0.3 + - - +
228B TRP* 3.3 85.6 + + + -
334D SER* 4.0 8.5 - - - +
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 6.2 0.9 - - - +
131B GLU* 5.8 4.7 - - + +
176B VAL* 2.8 22.1 + - + +
179B TYR* 1.3 78.9 - - + +
181B ILE* 1.3 71.1 + - + +
183B ASN* 4.8 5.2 - - - +
334D SER* 4.4 15.9 - - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 3.9 26.5 - - + -
130B ALA* 4.1 9.0 - - + +
131B GLU* 4.0 39.7 - - + +
142B VAL* 4.0 26.8 - - + +
177B PHE* 2.9 34.9 + - + +
180B GLU* 1.3 89.5 - - + +
182B LEU* 1.3 66.1 + - - +
183B ASN* 3.6 2.8 - - - -
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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