Contacts of the helix formed by residues 175 - 191 (chain A) in PDB entry 5K9S
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR* 5.0 7.6 - - - -
134A SER* 3.7 27.3 + - - -
137A GLN* 5.0 2.5 + - - -
173A SER* 3.1 22.6 + - - +
174A PRO* 1.3 94.4 - - + +
176A ALA* 1.3 64.9 + - - +
177A HIS* 3.2 26.2 - + + -
178A ILE* 3.1 26.7 + - + +
179A SER* 3.1 12.0 + - - -
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Residues in contact with ALA 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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173A SER 5.1 0.9 - - - -
174A PRO 3.4 6.4 + - - +
175A HIS* 1.3 71.7 - - - +
177A HIS* 1.3 59.8 + - - +
179A SER* 3.2 8.6 + - - -
180A GLU* 2.8 31.1 + - - +
225A TYR* 4.3 20.1 - - + -
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 5.8 1.8 + - - -
138A PHE* 3.6 43.5 - + + +
175A HIS* 3.6 32.2 - + + +
176A ALA* 1.3 80.7 + - - +
178A ILE* 1.3 70.2 + - + +
180A GLU* 3.9 12.1 - - - +
181A GLN* 3.2 22.2 + - - +
19B ARG* 5.4 0.9 + - - -
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Residues in contact with ILE 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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134A SER* 3.6 41.7 - - - +
137A GLN* 3.8 14.6 - - + +
138A PHE* 3.9 24.0 - - + +
141A ALA* 5.3 2.0 - - + +
170A LEU* 4.0 36.6 - - + -
173A SER* 4.0 9.2 - - - +
175A HIS* 3.1 25.4 + - + +
177A HIS* 1.3 82.5 - - - +
179A SER* 1.3 67.0 + - - +
181A GLN* 3.1 7.7 + - - +
182A ALA* 3.0 20.3 + - - +
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Residues in contact with SER 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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170A LEU 3.7 14.5 + - - -
171A LEU* 3.1 26.1 + - - +
173A SER 4.3 7.6 - - - -
175A HIS 3.1 11.2 + - - -
176A ALA* 3.5 7.9 - - - -
178A ILE* 1.3 77.3 - - - +
180A GLU* 1.3 62.1 + - - +
182A ALA* 3.1 5.4 + - - +
183A VAL* 3.0 22.9 + - - +
212A LEU* 3.7 6.1 - - - +
225A TYR* 2.6 26.5 + - - -
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Residues in contact with GLU 180 (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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176A ALA 2.8 16.8 + - - +
177A HIS* 3.9 12.0 - - - +
179A SER* 1.3 73.1 - - - +
181A GLN* 1.3 60.6 + - - +
183A VAL* 3.2 4.9 + - - +
184A TRP* 3.0 29.8 + - + +
222A ALA* 5.8 1.0 - - - +
224A GLY* 3.5 13.5 - - - -
225A TYR* 3.4 44.2 + - + +
228A ASN* 2.9 32.6 + - + +
19B ARG* 6.3 1.3 - - - +
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Residues in contact with GLN 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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138A PHE* 4.7 8.1 - - + +
141A ALA* 3.7 31.0 - - + -
142A TRP* 3.8 12.9 - - + +
145A THR* 2.9 42.1 + - - +
177A HIS 3.2 14.3 + - - +
178A ILE* 3.1 7.4 + - - +
180A GLU* 1.3 79.7 - - - +
182A ALA* 1.3 57.0 + - - +
184A TRP* 3.3 17.6 + - - +
185A ALA* 2.9 24.6 + - - +
19B ARG* 2.6 41.0 + - - +
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Residues in contact with ALA 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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141A ALA* 4.9 0.8 - - + +
167A PHE* 3.6 44.4 - - + +
170A LEU* 3.9 13.7 - - + -
171A LEU* 4.1 8.7 - - + +
178A ILE 3.0 11.6 + - - +
179A SER 3.1 7.8 + - - +
181A GLN* 1.3 75.4 - - - +
183A VAL* 1.3 65.0 + - - +
185A ALA* 3.4 1.4 + - - +
186A LEU* 3.0 28.9 + - - +
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Residues in contact with VAL 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 LEU* 3.4 21.3 - - + -
179A SER 3.0 16.3 + - - +
180A GLU* 3.4 10.3 - - - +
182A ALA* 1.3 76.8 - - - +
184A TRP* 1.3 61.8 + - - +
186A LEU* 3.4 4.2 + - - +
187A GLY 3.0 10.0 + - - -
209A LEU* 3.9 11.4 - - + -
212A LEU* 4.0 7.4 - - + -
225A TYR* 4.5 1.6 - - + -
228A ASN* 3.7 19.5 - - + +
229A LEU* 3.8 31.9 - - + +
232A THR* 2.7 37.4 + - - +
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Residues in contact with TRP 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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145A THR* 3.6 17.8 - - + +
180A GLU* 3.0 17.1 + - + +
181A GLN* 3.5 24.9 - - - +
182A ALA 3.2 0.2 - - - -
183A VAL* 1.3 76.6 - - - +
185A ALA* 1.3 63.0 + - - +
187A GLY* 2.9 12.3 + - - -
188A ASN* 3.0 14.7 + - - -
228A ASN* 3.8 32.7 - - - +
231A TRP* 3.8 12.5 - + - -
232A THR* 4.3 3.8 - - - -
17B MET* 2.8 44.0 + - + +
18B ARG 3.4 22.4 - - - -
19B ARG* 3.5 35.9 - - + -
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Residues in contact with ALA 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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144A LEU 5.2 0.2 - - - -
145A THR* 3.2 31.7 + - - +
148A ALA* 4.7 1.8 - - + +
167A PHE* 3.5 37.5 - - + -
181A GLN 2.9 13.0 + - - +
182A ALA 3.8 2.7 - - - +
183A VAL 3.4 0.2 - - - -
184A TRP* 1.3 75.0 - - - +
186A LEU* 1.3 62.4 - - - +
188A ASN* 3.1 6.0 + - - +
189A ILE* 3.1 27.1 + - + +
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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 ILE* 4.2 26.0 - - + +
167A PHE* 3.9 27.1 - - + -
168A ILE* 4.2 13.0 - - + -
171A LEU* 4.0 32.5 - - + -
182A ALA 3.0 21.0 + - - +
183A VAL* 3.8 4.9 - - - +
185A ALA* 1.3 76.5 - - - +
187A GLY* 1.3 58.0 + - - +
189A ILE* 3.3 7.1 + - + +
190A ALA* 2.9 32.6 + - - +
200A VAL* 4.4 20.4 - - + +
205A ALA* 4.8 6.7 - - + -
209A LEU* 4.9 4.5 - - + -
232A THR* 4.3 9.0 - - + -
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Residues in contact with GLY 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 VAL 3.0 7.9 + - - -
184A TRP 2.9 8.1 + - - -
186A LEU* 1.3 76.8 - - - +
188A ASN* 1.3 56.3 + - - +
190A ALA* 3.9 2.4 - - - -
191A GLY 2.9 23.0 + - - -
231A TRP* 3.6 13.2 - - - -
232A THR* 3.4 28.6 + - - +
235A ASN* 2.9 13.6 + - - -
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Residues in contact with ASN 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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145A THR* 3.1 33.1 + - - +
148A ALA* 3.9 19.8 - - + +
149A SER* 3.4 7.7 - - - -
155A THR* 4.3 0.5 - - - +
184A TRP* 3.0 11.1 + - - -
185A ALA 3.1 7.2 + - - +
187A GLY* 1.3 77.0 - - - +
189A ILE* 1.3 63.6 + - - +
191A GLY 3.4 6.4 + - - -
192A ASP 3.5 6.8 + - - -
231A TRP* 3.1 12.6 - - - -
16B LYS* 3.3 21.5 - - + +
17B MET 2.8 47.3 + - - +
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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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148A ALA* 4.1 16.2 - - + -
155A THR* 4.0 10.3 - - + -
158A VAL* 4.2 19.5 - - + -
159A VAL* 4.0 15.5 - - + -
163A ALA* 4.9 0.7 - - + -
164A ILE* 4.0 30.5 - - + -
167A PHE* 4.4 17.9 - - + -
185A ALA 3.1 15.3 + - - +
186A LEU* 3.3 10.0 + - + +
188A ASN* 1.3 75.7 - - - +
190A ALA* 1.3 62.3 + - - +
192A ASP* 3.2 13.3 + - - +
196A PHE* 3.3 21.3 - - + +
200A VAL* 3.8 20.4 - - + -
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Residues in contact with ALA 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 2.9 17.0 + - - +
187A GLY* 4.1 2.7 - - - +
189A ILE* 1.3 78.1 - - - +
191A GLY* 1.3 58.5 + - - +
192A ASP 3.1 4.9 + - - -
193A GLY 3.4 18.2 + - - +
196A PHE 4.5 1.1 - - - -
197A ARG* 3.9 21.9 - - - +
200A VAL* 4.4 4.7 - - + +
232A THR 5.3 0.4 - - - +
235A ASN* 4.3 17.5 - - + +
236A LEU* 3.7 29.8 - - + -
239A ASN* 4.6 2.8 - - - +
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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 GLY 2.9 12.3 + - - -
188A ASN 3.8 3.8 - - - -
189A ILE 3.2 1.0 - - - -
190A ALA* 1.3 75.9 - - - +
192A ASP* 1.3 60.8 + - - +
193A GLY 3.3 0.6 + - - -
235A ASN* 3.3 26.7 - - - -
238A ARG* 5.6 2.8 - - - -
239A ASN* 4.6 7.6 - - - +
15B LYS* 3.4 32.2 - - - +
16B LYS* 4.3 1.8 - - - -
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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