Contacts of the helix formed by residues 167 - 186 (chain t) in PDB entry 5GJQ
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 SER 167 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20t PHE* 4.0 1.6 - - - -
165t PRO 3.5 4.0 + - - -
166t LEU* 1.3 76.9 - - - +
168t LEU* 1.3 64.5 + - - +
169t ASP* 3.5 6.5 + - - +
170t ARG* 3.2 24.4 + - - +
171t ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 168 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20t PHE* 3.6 43.1 - - + -
22t ILE* 4.1 3.8 - - + -
167t SER* 1.3 72.0 - - - +
169t ASP* 1.3 64.4 + - - +
171t ALA* 3.4 0.7 + - - +
172t MET* 2.9 44.1 + - + +
197t ILE* 3.9 28.7 - - + -
199t THR* 5.1 9.9 - - + -
204t ARG* 6.0 3.1 - - - +
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Residues in contact with ASP 169 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167t SER* 3.2 6.3 + - - +
168t LEU* 1.3 79.2 - - - +
170t ARG* 1.3 63.5 + - - +
172t MET* 3.1 10.0 + - - +
173t ARG* 2.3 53.8 + - - +
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Residues in contact with ARG 170 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152t GLN* 3.1 51.1 + - - +
153t VAL* 5.1 0.4 - - - +
155t PHE* 4.2 23.6 - - - -
158t MET* 5.9 1.2 - - - +
164t VAL* 5.3 2.2 + - - +
166t LEU* 3.4 27.5 - - + +
167t SER* 3.2 18.6 + - - +
169t ASP* 1.3 75.4 - - - +
171t ALA* 1.3 65.2 + - - +
173t ARG* 3.3 26.1 - - + +
174t LEU* 2.9 31.8 + - + +
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Residues in contact with ALA 171 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15t ILE* 4.9 3.1 - - + -
20t PHE* 4.0 9.6 - - + -
22t ILE* 3.7 21.1 - - + -
166t LEU* 3.6 27.7 - - + +
167t SER 3.0 19.2 + - - +
168t LEU 3.5 4.7 - - - +
170t ARG* 1.3 75.1 - - - +
172t MET* 1.3 63.5 + - - +
174t LEU* 3.2 6.2 - - - +
175t VAL* 3.0 27.5 + - - +
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Residues in contact with MET 172 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22t ILE* 3.6 20.2 - - - -
168t LEU* 2.9 31.7 + - + +
169t ASP* 3.1 8.7 + - - +
171t ALA* 1.3 75.3 - - - +
173t ARG* 1.3 62.8 + - - +
175t VAL* 3.2 4.7 + - - +
176t LYS* 3.0 35.3 + - - +
195t ILE* 3.8 35.9 - - + -
197t ILE* 3.7 25.8 - - + -
206t GLU* 3.3 30.3 - - + +
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Residues in contact with ARG 173 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199b LEU* 3.7 51.1 + - + +
200b GLY* 4.3 9.2 - - - -
169t ASP* 2.3 42.7 + - - +
170t ARG* 3.3 40.4 - - + +
172t MET* 1.3 73.8 - - - +
174t LEU* 1.3 68.2 + - - +
176t LYS* 3.5 3.5 + - - +
177t ASP* 3.0 31.3 + - - +
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Residues in contact with LEU 174 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200b GLY* 6.0 0.2 - - - -
202b TYR* 3.9 25.4 - - + -
15t ILE* 4.9 4.5 - - + -
148t LEU* 5.4 0.9 - - + -
149t LEU* 4.6 9.9 - - + -
152t GLN* 4.0 19.1 - - + +
153t VAL* 3.6 28.5 - - + -
166t LEU* 4.2 24.9 - - + -
170t ARG* 2.9 18.8 + - + +
171t ALA* 3.2 9.2 - - - +
173t ARG* 1.3 77.1 - - - +
175t VAL* 1.3 69.0 + - + +
177t ASP* 3.1 6.0 + - - +
178t VAL* 2.9 41.0 + - + +
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Residues in contact with VAL 175 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13t LEU* 3.9 11.7 - - + -
15t ILE* 3.4 32.5 - - + -
22t ILE* 4.1 14.1 - - + -
24t ALA* 3.9 27.4 - - + -
149t LEU* 5.9 0.7 - - + -
171t ALA 3.0 12.6 + - - +
172t MET* 3.2 5.8 + - - +
174t LEU* 1.3 79.7 - - + +
176t LYS* 1.3 65.7 + - - +
178t VAL* 3.2 9.1 - - + +
179t PHE* 3.1 31.7 + - + -
193t LEU* 5.1 1.1 - - + -
195t ILE* 3.9 19.5 - - + -
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Residues in contact with LYS 176 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199b LEU* 4.4 27.6 - - + +
172t MET* 3.0 24.7 + - - +
173t ARG* 3.9 4.9 - - - +
175t VAL* 1.3 76.7 - - - +
177t ASP* 1.3 61.7 + - - +
179t PHE* 3.5 1.9 + - - +
180t ILE* 3.0 37.1 + - + +
193t LEU* 4.4 8.8 - - + +
195t ILE* 3.9 19.1 - - + -
206t GLU* 2.4 34.1 + - - -
208t VAL* 3.8 31.1 - - + +
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Residues in contact with ASP 177 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195b LYS* 5.0 0.3 + - - -
197b THR 4.1 2.9 - - - +
198b ARG* 3.5 19.5 - - + +
199b LEU* 3.1 20.6 + - - +
200b GLY* 2.4 40.3 + - - -
202b TYR* 3.0 23.1 - - + +
173t ARG 3.0 21.3 + - - +
174t LEU* 3.6 2.2 - - - +
176t LYS* 1.3 78.7 - - - +
178t VAL* 1.3 62.1 + - - +
180t ILE* 3.1 11.8 + - - +
181t SER* 3.0 26.3 + - - +
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Residues in contact with VAL 178 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202b TYR* 4.0 4.5 - - - +
152c SER* 4.8 1.8 - - - -
13t LEU* 3.6 28.0 - - + -
145t LEU* 3.6 19.0 - - + +
148t LEU* 3.4 32.8 - - + -
149t LEU* 4.3 10.8 - - + -
174t LEU* 2.9 31.8 + - + +
175t VAL* 3.2 13.9 - - - +
177t ASP* 1.3 72.9 - - - +
179t PHE* 1.3 63.0 + - + +
181t SER* 3.5 6.7 + - - -
182t ALA* 3.0 29.8 + - - +
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Residues in contact with PHE 179 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11t THR* 4.0 22.2 - - + -
13t LEU* 3.5 39.3 - - + -
24t ALA* 3.9 22.0 - - + -
25t SER* 4.1 1.3 - - - -
26t ASP* 3.8 17.3 - - + -
145t LEU* 4.4 8.5 - - + -
175t VAL* 3.1 27.1 + - + +
176t LYS 4.0 0.2 - - - +
178t VAL* 1.3 82.8 - - + +
180t ILE* 1.3 57.1 - - - +
182t ALA* 3.9 3.7 - - + +
183t ALA* 2.9 30.8 + - - +
189t THR* 4.3 16.1 - - + +
193t LEU* 3.6 40.2 - - + -
210t LEU* 4.4 10.5 - - + +
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Residues in contact with ILE 180 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195b LYS* 3.7 33.7 - - + +
196b GLY* 3.9 21.3 - - - +
197b THR 4.2 13.9 - - - +
198b ARG* 5.8 1.1 - - - -
199b LEU* 5.2 4.5 - - + -
176t LYS* 3.0 32.4 + - + +
177t ASP* 3.1 17.0 + - - +
179t PHE* 1.3 79.5 - - - +
181t SER* 1.3 61.9 + - - +
183t ALA* 3.6 4.7 + - - +
184t GLU* 3.4 20.8 + - + +
208t VAL* 5.9 5.8 - - + -
209t SER 5.2 3.8 - - - +
210t LEU* 4.2 19.3 - - + -
211t ARG* 5.7 0.2 - - - -
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Residues in contact with SER 181 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195b LYS* 3.4 19.9 + - - +
198b ARG* 4.8 2.4 + - - -
202b TYR* 5.2 0.3 + - - -
148c GLY* 5.1 2.2 - - - -
151c GLU* 3.5 21.9 + - - +
152c SER* 3.2 26.2 + - - -
177t ASP 3.0 15.8 + - - -
178t VAL* 3.8 4.3 - - - -
180t ILE* 1.3 76.0 - - - +
182t ALA* 1.3 60.7 + - - +
184t GLU* 2.9 27.1 + - - +
185t ARG* 3.2 10.6 + - - +
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Residues in contact with ALA 182 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148c GLY* 6.5 0.7 - - - -
11t THR* 5.8 0.4 - - + -
141t ALA* 4.1 18.6 - - + -
144t MET* 5.0 8.5 - - + -
145t LEU* 3.7 21.8 - - + -
178t VAL 3.0 18.0 + - - +
179t PHE* 4.0 5.2 - - + +
181t SER* 1.3 77.4 - - - +
183t ALA* 1.3 56.9 + - - +
185t ARG* 3.1 4.0 + - - +
186t ASP* 2.7 37.1 + - - +
189t THR* 4.5 7.4 - - + -
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Residues in contact with ALA 183 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19b ARG* 5.2 4.7 + - - -
179t PHE 2.9 18.3 + - - +
180t ILE* 3.7 8.5 - - - +
182t ALA* 1.3 76.8 - - - +
184t GLU* 1.3 60.2 + - - +
186t ASP 3.8 9.1 - - - +
189t THR* 3.6 30.1 - - + +
190t GLY* 4.6 6.1 - - - -
210t LEU* 4.6 9.6 - - + -
211t ARG* 4.3 25.9 - - + +
213t ASP* 5.1 5.5 - - - +
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Residues in contact with GLU 184 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19b ARG* 5.1 3.1 + - - -
26b VAL* 3.7 16.3 - - - +
29b LYS* 3.1 53.4 + - - +
195b LYS* 3.7 38.6 - - - +
151c GLU* 4.3 1.8 - - - +
180t ILE* 3.5 15.2 - - - +
181t SER 2.9 12.2 + - - +
183t ALA* 1.3 78.7 - - - +
185t ARG* 1.3 58.2 + - + +
186t ASP 5.0 0.2 - - - -
211t ARG* 2.6 45.2 + - - +
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Residues in contact with ARG 185 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25b VAL* 3.2 8.8 - - + -
26b VAL* 2.7 55.9 + - - +
27b ALA 3.1 21.8 + - - -
29b LYS* 3.4 28.9 - - - +
135c ASP* 4.2 11.3 + - - -
136c PHE* 3.5 20.0 + - - -
147c TYR* 4.0 31.0 - - + +
148c GLY* 5.7 0.4 - - - -
151c GLU* 3.2 40.4 + - + +
144t MET* 3.7 24.6 - - + +
181t SER 3.2 6.0 + - - +
182t ALA 3.1 1.8 + - - +
184t GLU* 1.3 80.3 - - - +
186t ASP* 1.3 60.7 + - - +
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Residues in contact with ASP 186 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24b MET 3.7 11.6 - - - +
26b VAL* 5.2 1.1 - - - -
140t SER* 3.0 26.9 + - - -
141t ALA* 3.3 19.2 - - + +
144t MET* 3.9 10.3 - - + +
182t ALA 2.7 20.7 + - - +
183t ALA 3.8 6.8 - - - +
185t ARG* 1.3 73.5 - - - +
187t VAL* 1.3 77.3 + - - +
188t TYR* 2.8 24.0 + - - +
189t THR* 2.9 38.9 + - - +
213t ASP 5.6 0.5 - - - +
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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
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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