Contacts of the helix formed by residues 170 - 188 (chain A) in PDB entry 4GEK
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PHE* 3.3 4.9 - - + +
169A GLU* 1.3 75.5 - - - +
171A ALA* 1.3 57.5 + - - +
172A LYS* 2.8 16.6 + - - +
173A VAL* 3.0 27.2 + - + +
174A GLY* 2.8 26.3 + - - -
224G GLU 4.1 2.3 - - - +
225G HIS* 2.7 40.4 + - - +
226G SER 4.8 2.4 + - - +
227G GLU* 5.8 3.1 - - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE 4.8 3.1 - - - -
169A GLU 3.2 8.5 + - - +
170A ASP* 1.3 72.2 + - - +
172A LYS* 1.3 55.9 + - - +
174A GLY* 3.8 2.7 - - - +
175A GLU* 3.0 28.8 + - - +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 2.8 14.1 + - - +
171A ALA* 1.3 71.7 - - - +
173A VAL* 1.3 62.5 + - - +
175A GLU* 3.5 26.1 + - - +
176A LEU* 3.1 26.5 + - - +
53G PHE* 6.4 2.0 - - - -
225G HIS* 3.7 32.1 - - + +
241G LEU* 4.0 16.6 - - + +
244G GLU* 2.9 29.7 + - - -
301G SO4 3.5 31.4 + - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 4.1 8.3 - - + -
170A ASP* 3.0 34.1 + - + +
172A LYS* 1.3 76.0 - - - +
174A GLY* 1.3 66.2 + - - +
176A LEU* 3.1 8.7 + - + +
177A LEU* 2.9 37.5 + - + +
225G HIS* 4.1 15.5 - - + -
226G SER 4.2 8.1 - - - +
227G GLU* 3.5 42.8 - - + +
239G VAL* 5.8 4.5 - - + +
241G LEU* 4.9 6.7 - - + -
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Residues in contact with GLY 174 (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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168A PHE* 4.1 24.8 - - - +
170A ASP 2.8 14.6 + - - -
171A ALA* 3.4 4.9 + - - -
173A VAL* 1.3 78.1 - - - +
175A GLU* 1.3 54.9 + - - +
177A LEU* 3.3 2.0 + - - +
178A PHE* 2.8 45.4 + - - -
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Residues in contact with GLU 175 (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 ALA 3.0 18.3 + - - +
172A LYS* 3.7 33.6 + - - +
174A GLY* 1.3 71.5 - - - +
176A LEU* 1.3 67.6 + - - +
178A PHE* 3.3 12.1 + - + +
179A ASN* 2.9 44.2 + - - +
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Residues in contact with LEU 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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172A LYS 3.1 14.0 + - - +
173A VAL* 3.5 10.3 - - + +
175A GLU* 1.3 77.0 - - - +
177A LEU* 1.3 68.7 + - + +
179A ASN* 3.2 11.8 + - + +
180A MET* 2.9 40.0 + - + +
49G LEU* 3.8 13.2 - - + -
52G ARG* 5.5 1.1 - - - -
53G PHE* 3.6 29.8 - - + -
229G TRP* 5.2 2.0 - - + -
239G VAL* 3.9 39.3 - - + -
241G LEU* 4.2 21.3 - - + -
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Residues in contact with LEU 177 (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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168A PHE* 3.5 40.4 - - + -
173A VAL* 2.9 30.6 + - + +
174A GLY* 4.0 3.1 - - - +
176A LEU* 1.3 86.9 - - + +
178A PHE* 1.3 60.5 + - - +
180A MET* 3.7 3.0 - - + +
181A HIS* 2.9 29.5 + - - +
231A GLN* 4.4 3.8 - - - +
233A PHE* 3.8 33.9 - - + +
234A ASN* 3.8 22.1 - - + +
227G GLU* 4.8 3.1 - - + -
228G LEU 4.9 1.6 - - - +
229G TRP* 4.1 20.2 - - + -
239G VAL* 5.2 1.1 - - + -
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 4.7 14.8 - - - -
166A PHE 6.0 1.8 - - - -
167A SER* 6.4 2.0 - - - -
174A GLY* 2.8 32.9 + - - +
175A GLU* 3.3 8.9 + - - +
177A LEU* 1.3 77.8 - - - +
179A ASN* 1.3 58.8 + - - +
181A HIS* 3.2 7.9 + - - +
182A HIS* 2.8 29.7 + - - +
234A ASN* 4.0 18.1 - - - +
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Residues in contact with ASN 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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175A GLU* 2.9 35.8 + - - +
176A LEU* 3.4 12.8 - - + +
178A PHE* 1.3 76.8 - - - +
180A MET* 1.3 62.4 + - + +
182A HIS* 3.3 8.2 + - - +
183A ASP* 2.9 36.2 + - - +
52G ARG* 3.7 40.7 + - - +
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Residues in contact with MET 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 LEU* 2.9 38.2 + - + +
177A LEU* 3.7 4.9 - - + +
179A ASN* 1.3 75.9 - - - +
181A HIS* 1.3 59.4 + - - +
183A ASP* 3.2 10.6 + - - +
184A PHE* 2.8 30.0 + - - +
233A PHE* 3.4 45.0 - - + -
48G MET* 3.5 38.0 - - + +
49G LEU* 4.2 12.3 - - + -
52G ARG* 3.7 29.8 - - - -
229G TRP* 4.3 10.1 - - + -
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 2.7 28.0 + - - -
37A PRO* 3.9 11.2 - - + -
165A LYS* 4.2 4.7 + - - -
177A LEU 2.9 18.1 + - - +
178A PHE* 3.5 7.3 - - - +
180A MET* 1.3 77.2 - - - +
182A HIS* 1.4 62.1 + - - +
184A PHE* 3.2 6.1 + + - +
185A LYS* 2.9 52.7 + - + +
203A GLU* 3.5 26.0 - - - -
233A PHE* 4.6 4.6 - - - -
234A ASN* 3.5 22.2 + - - +
235A PHE* 3.5 20.8 - + - -
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE 2.8 20.8 + - - +
179A ASN* 3.4 9.6 - - - +
181A HIS* 1.4 72.7 - - - +
183A ASP* 1.3 78.8 + - - +
185A LYS* 3.3 17.7 + - - +
186A ARG* 3.0 47.8 + - + +
52G ARG* 3.9 9.6 + - - -
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN 2.9 16.8 + - - +
180A MET* 3.2 12.6 + - - +
182A HIS* 1.3 75.5 + - - +
184A PHE* 1.3 61.6 + - - +
186A ARG* 3.0 38.9 + - - +
187A ALA* 2.9 30.3 + - - +
48G MET* 3.8 19.3 - - + +
51G GLU* 6.0 1.0 - - - +
52G ARG* 2.7 44.4 + - - +
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Residues in contact with PHE 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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33A GLN 3.9 11.4 - - - -
34A ARG 3.6 28.3 - - - -
35A SER 4.7 0.2 - - - -
36A VAL 4.3 0.7 - - - -
37A PRO* 3.6 50.3 - - + -
38A GLY 4.9 2.0 - - - -
180A MET 2.8 13.0 + - - +
181A HIS* 3.4 13.5 - + - +
183A ASP* 1.3 76.8 - - - +
185A LYS* 1.3 67.1 + - + +
187A ALA* 3.2 4.3 + - - -
188A ASN* 2.9 50.8 + - - +
232A CYS* 6.0 1.3 - - - -
233A PHE* 4.5 12.1 - + + -
48G MET* 3.7 15.1 - - + +
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Residues in contact with LYS 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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34A ARG 3.7 22.7 - - - +
35A SER* 4.2 3.6 - - - -
181A HIS* 2.9 60.8 + - + +
182A HIS* 3.6 12.8 - - - +
184A PHE* 1.3 76.3 - - + +
186A ARG* 1.3 61.5 + - - +
188A ASN* 3.2 6.6 + - - -
190A TYR* 3.1 63.1 + - + +
191A SER 5.6 0.2 - - - -
200A SER* 4.6 12.7 + - - +
203A GLU* 5.1 4.9 + - - +
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Residues in contact with ARG 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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182A HIS* 3.0 40.5 + - + +
183A ASP* 3.0 40.5 + - - +
184A PHE 3.2 0.2 - - - -
185A LYS* 1.3 75.1 - - - +
187A ALA* 1.3 63.4 + - - +
188A ASN 3.2 1.2 + - - -
189A GLY* 3.3 12.2 + - - -
190A TYR 5.2 0.2 - - - +
191A SER 6.2 0.2 - - - +
51G GLU* 4.1 17.6 + - - -
52G ARG* 4.9 0.8 - - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP 2.9 16.6 + - - +
184A PHE* 3.2 7.6 + - + +
186A ARG* 1.3 76.9 - - - +
188A ASN* 1.3 65.1 + - - +
189A GLY 3.4 0.8 + - - -
48G MET* 6.0 3.6 - - + -
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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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33A GLN* 5.0 5.5 - - - +
34A ARG* 3.2 41.0 + - + +
184A PHE* 2.9 56.9 + - - +
185A LYS 3.2 3.0 + - - +
187A ALA* 1.3 82.9 - - - +
189A GLY* 1.3 63.4 + - - +
190A TYR 3.3 1.3 - - - -
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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