Contacts of the helix formed by residues 186 - 204 (chain A) in PDB entry 4GL5
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 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.1 27.3 + - + +
184A TYR 4.0 0.2 + - - -
185A VAL* 1.3 69.4 - - - +
187A VAL* 1.3 67.5 + - - +
188A LEU* 3.3 9.1 + - - +
189A THR* 2.5 44.5 + - - +
190A LEU* 3.1 9.2 + - - +
489A GLU* 4.4 16.7 - - + +
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Residues in contact with VAL 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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185A VAL* 3.1 17.4 + - + +
186A ASP* 1.3 73.6 - - - +
188A LEU* 1.3 66.8 + - - +
190A LEU* 3.1 9.4 + - + +
191A LEU* 2.9 42.6 + - + +
316A PHE* 3.7 24.7 - - + -
319A LEU* 3.8 16.8 - - + -
488A LEU 5.0 3.4 + - - +
490A MET* 3.3 43.7 - - + -
492A PHE* 4.0 8.1 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP* 3.1 6.0 + - - +
187A VAL* 1.3 78.1 - - - +
189A THR* 1.3 65.0 + - - +
191A LEU* 3.2 4.4 + - - +
192A ARG* 2.9 55.3 + - - +
312A SER* 4.3 3.1 - - - +
313A VAL* 4.4 13.5 - - + -
316A PHE* 3.5 57.4 - - + -
481A PRO* 4.8 7.0 - - + -
483A GLU* 3.5 25.6 - - - +
488A LEU* 4.5 16.8 - - + +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 4.5 5.2 - - - -
186A ASP* 2.5 37.8 + - - +
188A LEU* 1.3 72.9 - - - +
190A LEU* 1.3 70.8 + - - +
192A ARG* 3.3 10.5 + - - +
193A ARG* 3.0 56.0 + - - +
214A VAL* 4.8 12.6 - - + -
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Residues in contact with LEU 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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168A LEU* 5.0 5.8 - - + -
171A HIS* 3.9 37.5 - - + +
172A LEU* 4.4 12.8 - - + -
174A ARG 6.0 0.4 - - - +
175A LEU* 4.4 13.5 - - + -
178A VAL* 4.0 23.1 - - + +
185A VAL* 6.0 0.4 - - + -
186A ASP 3.1 9.9 + - - +
187A VAL* 3.1 12.7 + - + +
189A THR* 1.3 78.3 - - - +
191A LEU* 1.3 76.7 + - + +
193A ARG* 3.2 12.6 + - + +
194A VAL* 3.2 19.7 + - + +
454A LEU* 5.8 3.4 - - + -
492A PHE* 4.2 26.7 - - + -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 5.5 3.1 - - + -
187A VAL* 2.9 32.7 + - + +
188A LEU* 3.5 6.7 - - - +
190A LEU* 1.3 89.9 - - + +
192A ARG* 1.3 64.3 + - - +
194A VAL* 3.1 13.9 + - + +
195A MET* 2.8 25.2 + - + +
312A SER* 3.2 37.7 - - - +
315A LEU* 3.7 12.3 - - + -
316A PHE* 3.6 18.2 - - + +
319A LEU* 4.7 7.9 - - + -
450A ILE* 4.3 22.4 - - + -
454A LEU* 5.4 4.5 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 2.9 43.1 + - - +
189A THR* 3.6 9.0 + - - +
191A LEU* 1.3 74.5 - - - +
193A ARG* 1.3 57.4 + - - +
195A MET* 3.3 4.5 + - - +
196A LEU* 2.8 31.7 + - - +
214A VAL* 3.7 31.4 - - + -
218A GLN* 3.1 26.2 - - - +
308A PRO* 4.0 16.1 + - + +
309A ASP* 4.9 2.6 + - - +
312A SER* 3.4 22.2 + - - +
313A VAL* 3.6 26.1 - - - +
480A HIS* 5.9 3.2 - - - +
481A PRO* 6.2 0.4 - - - +
483A GLU* 2.9 30.8 + - - -
601A G29 5.4 3.4 - - - +
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Residues in contact with ARG 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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171A HIS* 4.3 11.7 - - + +
177A GLU* 3.8 30.1 + - - +
178A VAL* 4.2 8.3 - - - +
189A THR* 3.0 40.4 + - + +
190A LEU* 3.6 9.4 - - - +
192A ARG* 1.3 76.6 - - - +
194A VAL* 1.3 53.1 + - - +
196A LEU* 3.7 2.1 - - - +
197A ASP* 2.8 35.5 + - - +
210A GLU* 3.6 23.7 - - + +
211A SER* 3.6 46.7 + - - +
214A VAL* 3.8 20.0 - - + +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 3.6 15.6 + - - +
168A LEU* 4.2 25.6 - - + -
171A HIS* 3.4 38.4 - - + +
190A LEU* 3.4 14.6 - - + +
191A LEU* 3.1 24.7 + - + +
193A ARG* 1.3 76.8 - - - +
195A MET* 1.3 64.2 + - + +
197A ASP* 4.1 6.1 - - - -
198A THR* 2.8 38.2 + - - +
450A ILE* 5.4 7.4 - - + -
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Residues in contact with MET 195 (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 CYS* 4.5 8.3 - - - -
191A LEU* 2.8 19.6 + - - +
192A ARG* 3.4 5.2 - - - +
194A VAL* 1.3 86.2 - - - +
196A LEU* 1.3 57.9 + - - +
198A THR* 3.5 24.2 + - + +
199A SER* 3.0 31.5 + - - -
307A ALA* 3.6 24.6 - - + +
308A PRO* 3.7 14.1 - - + -
311A MET* 3.6 16.4 - - + -
312A SER* 4.2 5.4 - - - +
315A LEU* 4.5 14.1 - - - -
446A MET* 3.6 32.1 - - + -
450A ILE* 5.2 6.7 - - + -
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Residues in contact with LEU 196 (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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192A ARG 2.8 20.8 + - - +
193A ARG 3.9 2.2 - - - +
195A MET* 1.3 71.3 - - - +
197A ASP* 1.3 61.4 + - - +
199A SER* 3.4 1.7 + - - -
200A ASN* 3.0 27.9 + - - +
208A LEU* 3.9 21.3 - - + -
210A GLU* 3.9 16.6 - - + -
213A ILE* 3.8 32.5 - - + -
214A VAL* 4.0 13.9 - - + -
217A ILE* 3.7 20.4 - - + -
304A LEU* 4.3 25.8 - - + +
308A PRO* 3.7 14.3 - - + +
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 2.7 25.5 + - - +
170A THR* 4.3 3.8 - - - +
171A HIS* 3.4 23.2 + - + -
193A ARG 2.8 19.0 + - - +
194A VAL 3.7 1.6 - - - +
196A LEU* 1.3 78.0 - - - +
198A THR* 1.3 54.3 + - - +
200A ASN* 3.5 9.2 + - - +
201A THR* 2.7 43.5 + - - +
208A LEU* 6.5 0.2 - - - -
210A GLU* 4.1 17.6 - - - +
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Residues in contact with THR 198 (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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160A MET* 3.4 34.8 - - + -
163A VAL* 3.9 3.8 + - + +
164A CYS* 3.7 18.5 + - - -
167A SER* 3.6 16.6 + - - -
194A VAL* 2.8 20.9 + - - +
195A MET* 3.6 24.9 - - + +
196A LEU 3.3 0.2 - - - -
197A ASP* 1.3 73.8 - - - +
199A SER* 1.3 67.8 + - - +
201A THR* 3.2 8.6 + - - -
202A LEU* 3.1 23.0 + - - +
446A MET* 4.2 1.6 - - - -
450A ILE* 5.9 0.2 - - - +
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Residues in contact with SER 199 (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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195A MET 3.0 20.3 + - - -
196A LEU 3.8 4.3 - - - -
198A THR* 1.3 77.5 - - - +
200A ASN* 1.3 57.3 + - - +
203A PHE* 2.9 56.4 + - - +
204A LEU 3.9 0.3 + - - -
303A MET 4.1 5.3 + - - -
304A LEU* 4.0 29.2 + - - +
307A ALA* 3.4 21.3 - - - +
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Residues in contact with ASN 200 (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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196A LEU* 3.0 19.2 + - + +
197A ASP* 3.6 12.2 + - - +
199A SER* 1.3 75.4 - - - +
201A THR* 1.3 61.6 + - + +
204A LEU* 2.9 17.1 + - - +
205A ARG* 2.5 30.1 + - - -
206A ILE 3.0 43.9 + - - +
207A PRO* 4.7 0.8 - - - +
208A LEU* 3.1 33.0 - - + +
304A LEU* 4.0 9.7 - - + +
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Residues in contact with THR 201 (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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159A ARG* 3.6 19.3 + - - -
163A VAL* 3.4 20.7 - - + +
167A SER* 5.0 2.7 + - - -
197A ASP* 2.7 30.5 + - - +
198A THR* 3.2 9.4 + - - -
200A ASN* 1.3 80.2 - - + +
202A LEU* 1.3 56.5 + - - +
205A ARG* 3.3 27.7 + - + +
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Residues in contact with LEU 202 (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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151A ALA 4.5 1.3 - - - +
156A GLY* 3.4 28.0 - - - +
159A ARG* 3.9 18.3 + - + +
160A MET* 3.5 39.5 - - + +
163A VAL* 3.7 31.6 - - + -
198A THR 3.1 13.6 + - - +
199A SER 4.1 1.1 - - - +
200A ASN 3.1 1.0 - - - -
201A THR* 1.3 80.2 - - - +
203A PHE* 1.3 90.9 + - + +
204A LEU 3.7 0.2 - - - -
205A ARG* 4.5 2.4 + - - +
277A ASP* 3.8 15.6 - - - +
278A PHE 4.9 0.2 + - - -
442A ILE* 4.3 2.0 - - + -
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Residues in contact with PHE 203 (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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151A ALA* 3.6 20.2 - - + -
152A LEU* 3.5 26.0 - - + -
160A MET* 4.1 12.8 - - + -
199A SER* 2.9 44.2 + - - +
202A LEU* 1.3 102.1 - - + +
204A LEU* 1.3 60.9 + - + +
277A ASP* 3.8 5.1 - - - +
278A PHE* 3.8 25.5 + - + +
279A ALA* 3.0 31.0 + - - +
303A MET* 3.6 38.6 - - + -
304A LEU* 5.6 2.7 - - + -
442A ILE* 4.3 1.1 - - + -
600A HEM 4.6 6.1 - - + -
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Residues in contact with LEU 204 (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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200A ASN* 2.9 21.7 + - - +
202A LEU 3.7 0.2 - - - -
203A PHE* 1.3 80.2 - - + +
205A ARG* 1.3 75.2 + - - +
206A ILE* 4.0 16.6 - - + +
208A LEU* 4.8 0.4 - - + -
255A ILE* 6.3 0.2 - - + -
258A LEU* 3.9 32.3 - - + +
259A ILE* 5.0 4.5 - - + -
262A LYS* 3.1 36.5 + - + +
277A ASP* 4.9 0.2 - - - -
279A ALA* 3.9 19.1 - - + -
300A ILE* 4.7 13.7 - - + -
304A LEU* 3.9 30.3 - - + -
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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
------------------------------------------------------------
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