Contacts of the helix formed by residues 175 - 193 (chain A) in PDB entry 5K6S
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLU 3.2 29.3 + - - +
131A TRP* 4.4 4.0 - - - -
173A SER* 3.0 9.5 + - - +
174A GLU* 1.3 79.0 - - - +
176A PRO* 1.3 68.7 - - - +
177A ARG* 3.0 48.5 + - - +
178A GLU* 3.1 14.6 + - + +
179A ARG* 3.1 25.7 + - - +
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Residues in contact with PRO 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLU 3.3 10.5 - - - +
175A ASP* 1.3 91.4 - - - +
177A ARG* 1.3 64.1 + - + +
179A ARG* 3.8 26.8 - - - +
180A ASP* 3.2 23.0 + - - +
223A GLU* 5.0 2.0 - - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU 4.2 6.5 + - - -
131A TRP* 3.4 56.6 - - + +
175A ASP* 3.0 30.7 + - - +
176A PRO* 1.3 79.4 - - + +
178A GLU* 1.3 61.6 + - - +
180A ASP* 3.4 7.0 + - - +
181A PHE* 3.3 27.8 + - + -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A MET* 4.0 0.2 - - - +
105A ARG* 2.5 36.4 + - - -
107A LEU* 5.4 0.3 - - - +
128A GLU 4.9 5.4 + - - -
131A TRP* 3.6 22.0 - - + -
134A LEU* 5.1 0.4 - - - +
138A TYR* 2.9 35.2 + - + +
170A LEU* 4.5 5.9 - - - +
173A SER* 2.9 26.1 + - - +
175A ASP* 3.1 17.5 + - + +
177A ARG* 1.3 75.8 - - - +
179A ARG* 1.3 60.6 + - - +
180A ASP 3.1 1.8 - - - -
181A PHE* 3.2 4.2 + - - +
182A LEU* 2.9 34.5 + - + +
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.5 23.0 - - + +
173A SER* 3.2 34.1 + - - +
174A GLU* 3.6 21.8 + - - +
175A ASP 3.1 12.3 + - - +
176A PRO* 3.8 25.0 - - - +
177A ARG 3.4 0.2 - - - -
178A GLU* 1.3 76.2 - - - +
180A ASP* 1.3 56.8 + - - +
182A LEU* 3.7 9.5 - - - +
183A LYS* 2.9 29.6 + - - +
219A ASN* 3.1 29.5 + - - +
220A GLY* 4.0 1.3 - - - -
223A GLU* 3.1 39.5 + - + +
262A VAL* 6.3 0.8 - - - +
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO 3.2 17.4 + - - +
177A ARG* 3.5 8.9 - - - +
178A GLU 3.1 0.4 - - - -
179A ARG* 1.3 75.1 - - - +
181A PHE* 1.3 70.5 + - - +
183A LYS* 3.0 34.3 + - - +
184A THR* 3.1 30.6 + - - -
223A GLU* 4.7 2.9 - - - +
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TRP* 3.6 18.8 - + - -
135A GLN* 3.6 42.2 - - + -
138A TYR* 3.6 36.1 - + + -
139A GLU* 4.3 18.6 - - + -
142A LEU* 3.8 22.6 - - + +
177A ARG* 3.3 19.8 + - + -
178A GLU 3.2 7.7 + - - +
180A ASP* 1.3 84.9 - - - +
182A LEU* 1.3 58.1 + - - +
184A THR* 3.3 4.8 + - - -
185A THR* 2.8 34.1 + - - -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.3 23.1 - - + +
167A LEU* 3.6 33.9 - - + +
170A LEU* 3.2 46.4 - - + +
171A PHE* 3.3 25.4 - - + +
178A GLU* 2.9 33.9 + - + +
179A ARG* 3.7 9.2 - - - +
181A PHE* 1.3 74.5 - - - +
183A LYS* 1.3 57.8 + - - +
185A THR* 3.7 5.0 - - - -
186A LEU* 2.9 26.5 + - - +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.6 10.2 - - - -
179A ARG 2.9 17.7 + - - +
180A ASP* 3.0 36.6 + - - +
181A PHE 3.2 0.2 - - - -
182A LEU* 1.3 77.0 - - - +
184A THR* 1.3 66.1 + - - +
187A HIS* 3.1 23.6 + - - +
223A GLU* 3.8 21.9 - - + +
226A GLU* 3.3 45.5 + - + +
227A ILE* 3.4 22.3 - - + +
667B LYS 5.9 0.6 + - - -
669B LEU* 4.0 12.6 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.8 27.8 - - + -
146A GLU* 4.6 4.5 - - - +
180A ASP* 3.1 17.5 + - - -
181A PHE* 3.7 7.4 - - - -
183A LYS* 1.3 82.4 - - - +
185A THR* 1.3 65.4 + - - +
187A HIS* 3.2 7.7 + - - +
188A ARG* 3.0 41.1 + - - +
669B LEU* 4.7 11.7 - - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 5.0 2.2 - - + -
138A TYR* 4.5 10.8 + - - -
141A PHE* 3.8 33.5 - - + -
142A LEU* 3.7 22.1 - - - +
145A LEU* 4.2 3.4 - - + -
167A LEU* 4.0 23.8 - - + -
181A PHE 2.8 24.9 + - - -
182A LEU* 3.7 7.4 - - - -
184A THR* 1.3 76.6 - - - +
186A LEU* 1.3 62.1 + - - +
188A ARG* 3.1 5.1 + - - +
189A ILE* 3.1 24.6 + - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 4.3 13.9 - - + -
167A LEU* 4.2 19.2 - - + +
168A LEU* 3.6 29.8 - - + -
171A PHE* 3.8 15.5 - - + -
182A LEU 2.9 17.9 + - - +
185A THR* 1.3 77.3 - - - +
187A HIS* 1.3 57.9 + - - +
189A ILE* 4.5 6.5 - - + -
190A TYR* 3.1 28.6 + - + +
200A ILE* 4.0 27.8 - - + -
204A ILE* 4.5 11.2 - - + -
224A LEU* 4.3 5.4 - - + -
227A ILE* 3.9 20.5 - - + +
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Residues in contact with HIS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS 3.1 18.9 + - - +
184A THR* 3.4 6.7 + - - +
185A THR 3.1 0.2 - - - -
186A LEU* 1.3 76.5 - - - +
188A ARG* 1.3 86.5 + - - +
190A TYR* 4.7 1.6 - - - -
191A GLY* 3.3 15.4 + - - -
227A ILE* 4.3 13.2 - - + +
230A SER* 3.1 12.3 + - - -
669B LEU* 3.8 35.7 - - + +
670B SEP 3.0 43.4 + - - -
672B ILE* 3.4 31.1 - - + +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.0 16.8 - - + -
145A LEU* 3.9 21.1 - - + -
146A GLU* 3.2 37.5 + - + +
184A THR* 3.0 24.1 + - - +
185A THR 3.1 6.7 + - - +
187A HIS* 1.3 92.7 + - - +
189A ILE* 1.3 65.2 + - - +
191A GLY* 3.1 2.7 + - - -
192A LYS* 3.0 37.9 + - + +
669B LEU* 5.4 4.6 - - - +
670B SEP 3.2 39.6 + - - -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PHE* 4.7 3.4 - - + -
145A LEU* 4.1 17.5 - - + -
159A ILE* 4.3 10.1 - - + -
163A PHE* 4.1 20.4 - - + -
164A VAL* 4.3 11.2 - - + -
167A LEU* 3.7 29.4 - - + -
185A THR* 3.1 19.8 + - + +
186A LEU* 4.0 6.7 - - + +
187A HIS 3.5 0.2 - - - -
188A ARG* 1.3 75.5 - - - +
190A TYR* 1.3 57.8 + - - +
193A PHE* 2.9 54.6 + - + +
196A LEU* 3.9 21.1 - - + -
200A ILE* 4.4 5.8 - - + -
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 3.1 18.6 + - + +
187A HIS* 4.1 4.9 - - - +
189A ILE* 1.3 77.9 - - - +
191A GLY* 1.3 59.1 + - - +
193A PHE 3.8 2.6 - - - +
197A ARG* 2.8 79.4 + - + +
200A ILE* 3.9 30.5 - - + +
201A ARG* 2.8 30.7 + - + -
227A ILE* 5.5 3.4 - - + -
231A ILE* 3.4 46.5 - - + +
672B ILE* 3.5 37.2 - - + -
674B GLU* 6.0 1.7 - - - +
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A HIS 3.3 9.9 + - - -
188A ARG* 3.1 7.4 + - - -
190A TYR* 1.3 80.7 - - - +
192A LYS* 1.3 62.2 + - - +
194A LEU* 4.5 4.2 - - - +
197A ARG* 2.9 25.2 + - - -
672B ILE* 4.2 13.2 - - - -
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU* 2.7 33.8 + - + +
146A GLU* 3.9 15.4 + - - +
147A SER 4.0 7.9 + - - -
148A PRO* 5.9 0.2 - - - +
150A PHE* 4.2 15.3 + - + +
152A PRO* 3.3 33.9 - - + +
188A ARG* 3.0 25.5 + - + +
191A GLY* 1.3 79.5 - - - +
193A PHE* 1.3 70.0 + - + +
194A LEU* 3.8 8.7 + - - +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU* 4.6 4.9 - - + -
150A PHE* 3.8 29.4 - + - -
152A PRO* 3.7 10.5 - - + -
155A ALA* 3.8 4.3 - - + -
156A LYS* 3.6 39.0 - - + -
159A ILE* 3.7 32.3 - - + -
189A ILE* 2.9 40.3 + - + +
190A TYR 3.8 4.6 - - - +
191A GLY 3.6 0.8 - - - -
192A LYS* 1.3 84.9 - - + +
194A LEU* 1.3 65.0 + - - +
195A GLY 3.1 2.5 - - - +
196A LEU* 3.0 38.3 + - + +
197A ARG* 3.4 12.8 + - - +
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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