Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 5SWW
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 GLY 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASN* 3.9 1.9 - - - +
176B TRP* 3.3 1.2 + - - -
177B ASP* 1.3 72.9 - - - +
179B LEU* 1.3 59.8 + - - +
180B ASP 3.5 1.8 - - - -
181B GLU* 3.8 14.8 - - - -
182B HIS* 2.5 50.6 + - - +
111D ARG* 5.8 2.9 - - - -
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Residues in contact with LEU 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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24B ASN* 3.0 5.3 + - - -
154B THR 4.5 0.2 - - - -
155B TYR* 3.8 38.6 - - + +
158B PHE* 3.8 17.5 - - + -
173B PHE* 3.8 18.2 - - + -
175B PRO* 3.7 23.6 - - + -
176B TRP* 3.4 53.5 + - + +
177B ASP 3.4 0.8 + - - -
178B GLY* 1.3 75.9 - - - +
180B ASP* 1.3 71.4 + - - +
183B SER* 2.9 33.3 + - - -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR* 4.1 20.3 - - - +
175B PRO* 5.4 4.3 - - - +
179B LEU* 1.3 88.1 + - - +
181B GLU* 1.3 57.6 + - - +
183B SER* 3.8 4.8 - - - -
184B GLN* 2.9 46.7 + - + +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLY* 3.5 13.3 + - - +
179B LEU 3.2 0.6 - - - -
180B ASP* 1.3 79.7 - - - +
182B HIS* 1.3 78.2 + - + +
184B GLN* 3.1 10.4 + - - +
185B ALA* 2.9 29.3 + - + +
102D PHE* 4.3 8.7 - - + -
108D GLY* 3.8 23.0 - - - -
111D ARG* 2.6 43.0 + - - +
142D MET* 3.7 17.4 - - + +
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Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 3.4 27.4 - - - +
25B GLY* 3.9 26.8 + - - -
177B ASP 4.5 4.2 + - - -
178B GLY* 2.5 48.6 + - - +
181B GLU* 1.3 88.5 + - + +
183B SER* 1.3 57.7 + - - +
185B ALA* 3.8 7.5 - - + +
186B LEU* 2.9 37.9 + - + +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 3.4 8.6 - - - +
152B ILE* 3.9 6.5 - - - +
153B MET 2.6 28.0 + - - -
154B THR* 3.3 22.4 - - - +
155B TYR 5.3 0.2 - - - -
179B LEU* 2.9 25.7 + - - -
180B ASP* 3.8 6.1 - - - -
182B HIS* 1.3 77.2 - - - +
184B GLN* 1.3 57.5 + - - +
186B LEU* 4.8 0.9 - - - -
187B SER* 2.8 34.3 + - - -
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 2.9 30.9 + - - +
181B GLU* 3.6 4.7 - - - +
183B SER* 1.3 74.7 - - - +
185B ALA* 1.3 59.9 + - - +
187B SER* 3.2 8.2 + - - -
188B GLY 2.9 23.7 + - - -
102D PHE* 3.7 23.3 - - + -
135D LEU* 3.2 15.6 - - + +
138D GLU* 5.1 7.4 - - - +
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Residues in contact with ALA 185 (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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181B GLU* 2.9 17.7 + - + +
182B HIS* 3.8 8.5 - - + +
184B GLN* 1.3 76.3 - - - +
186B LEU* 1.3 59.3 + - + +
188B GLY 3.0 2.6 + - - -
189B ARG* 2.9 23.9 + - - +
102D PHE* 3.6 23.5 - - + +
103D SER* 3.4 34.1 - - - +
105D GLY* 5.1 3.6 - - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 4.2 17.9 - - + +
127B ALA 3.2 27.4 - - - +
128B ARG* 3.8 14.4 - - + -
129B ILE* 3.8 15.2 - - + +
152B ILE* 3.6 22.0 - - + +
182B HIS* 2.9 22.7 + - + +
183B SER* 5.2 0.2 - - - -
185B ALA* 1.3 75.6 - - + +
187B SER* 1.3 57.9 + - - +
189B ARG* 3.2 36.6 + - - +
190B LEU* 2.9 30.3 + - - +
103D SER 5.2 0.4 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 3.6 25.2 + - - +
154B THR* 4.6 6.4 - - - +
183B SER* 2.8 27.5 + - - -
184B GLN* 3.2 8.8 + - - -
186B LEU* 1.3 76.0 - - - +
188B GLY* 1.3 57.3 + - - +
190B LEU* 3.6 1.4 + - - +
191B ARG* 2.9 29.8 + - - +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN 2.9 13.6 + - - -
185B ALA 3.0 4.6 + - - -
187B SER* 1.3 75.2 - - - +
189B ARG* 1.3 58.5 + - - +
191B ARG* 3.3 7.1 + - - +
192B ALA* 2.9 29.3 + - - +
103D SER* 3.6 17.0 - - - -
134D PRO* 3.8 9.8 - - - +
135D LEU* 3.9 12.1 - - - +
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 3.7 25.1 + - + +
131B ASP* 3.4 39.3 + - - +
136B TYR* 3.9 15.6 + - - -
185B ALA 2.9 8.6 + - - +
186B LEU* 3.2 33.3 + - - +
188B GLY* 1.3 75.6 - - - +
190B LEU* 1.3 57.3 + - - +
192B ALA* 3.0 8.6 + - - +
193B ILE* 2.9 36.2 + - + +
60D LYS* 5.6 3.2 - - - +
103D SER* 3.2 36.5 - - - +
104D TRP* 3.9 32.5 - - + +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 4.1 2.8 - - + +
140B LEU* 3.6 31.2 - - + -
150B VAL* 3.6 34.8 - - + +
151B SER* 3.8 11.2 - - - -
152B ILE* 3.6 28.9 - - + +
186B LEU 2.9 16.8 + - - +
187B SER* 4.0 2.5 - - - +
189B ARG* 1.3 77.1 - - - +
191B ARG* 1.3 62.4 + - - +
193B ILE* 4.2 6.1 - - + -
194B LEU* 3.0 47.9 + - + +
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Residues in contact with ARG 191 (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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187B SER 2.9 20.1 + - - +
188B GLY* 3.5 7.2 - - - +
190B LEU* 1.3 75.5 - - - +
192B ALA* 1.3 59.9 + - - +
193B ILE 3.7 0.2 + - - -
194B LEU* 3.9 8.9 + - - +
195B GLN* 3.3 38.0 - - - +
132D TYR 5.6 0.4 + - - -
134D PRO* 3.6 32.3 - - + +
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Residues in contact with ALA 192 (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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188B GLY 2.9 13.2 + - - +
189B ARG* 3.0 10.7 + - - +
191B ARG* 1.3 76.5 - - - +
193B ILE* 1.3 64.8 + - + +
195B GLN* 3.6 28.2 - - - +
104D TRP* 5.1 9.2 - - + -
132D TYR* 4.3 25.0 + - + +
134D PRO* 4.3 16.4 - - + -
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Residues in contact with ILE 193 (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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129B ILE* 4.7 6.1 - - + -
136B TYR* 3.6 32.3 - - + +
137B LYS* 3.9 44.6 - - + +
140B LEU* 3.9 19.3 - - + -
141B GLN* 3.1 35.0 + - + +
144B ARG* 4.7 0.2 + - - -
189B ARG* 2.9 27.0 + - + +
190B LEU* 3.1 9.1 + - + +
192B ALA* 1.3 81.8 - - + +
194B LEU* 1.3 63.8 + - + +
195B GLN 3.1 6.6 + - - -
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Residues in contact with LEU 194 (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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140B LEU* 3.9 23.1 - - + +
141B GLN* 3.9 23.1 - - + +
144B ARG* 3.3 38.3 + - + +
150B VAL* 4.0 25.1 - - + +
190B LEU* 3.0 39.2 + - + +
191B ARG* 4.1 5.5 - - - +
192B ALA 3.5 0.2 - - - -
193B ILE* 1.3 78.9 - - + +
195B GLN* 1.3 60.9 + - - +
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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