Contacts of the helix formed by residues 185 - 203 (chain A) in PDB entry 4G84
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 MET 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASP 3.5 2.2 + - - -
184A PRO* 1.3 72.1 - - - +
186A ILE* 1.3 58.7 + - - +
187A PRO* 3.5 2.0 - - - +
188A ASP* 3.3 32.9 + - + +
189A ALA* 2.9 30.7 + - - +
301A ASP* 3.5 59.0 - - + +
304A LEU* 4.1 7.0 - - + -
305A LEU* 3.7 23.5 - - + +
308A TYR* 3.9 11.7 - - + -
334A VAL* 3.4 33.2 - - + -
362A ARG* 5.6 3.5 - - - +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP* 4.0 15.5 - - + +
184A PRO 3.1 10.1 - - - +
185A MET* 1.3 76.4 - - - +
187A PRO* 1.3 69.9 - - + +
189A ALA* 3.2 5.7 + - + +
190A GLU* 3.1 20.1 + - + +
308A TYR* 3.7 19.5 - - + +
312A PHE* 4.9 1.7 - - + -
421B LEU* 3.6 27.6 - - + -
425B LEU* 4.2 23.3 - - + -
440B LEU* 4.8 5.2 - - + -
442B TYR* 3.6 46.7 - - + +
443B LYS 3.9 6.1 - - - +
444B LYS* 5.0 0.4 - - + -
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 3.9 30.5 - - + +
182A PHE* 4.2 17.7 - - + -
183A ASP 3.8 11.2 - - - +
185A MET 3.8 0.4 - - - -
186A ILE* 1.3 95.7 - - + +
188A ASP* 1.3 62.8 + - - +
190A GLU* 3.1 4.1 + - - +
191A CYS* 3.1 26.2 + - - -
362A ARG* 3.7 18.8 - - - +
380A VAL* 4.0 7.9 - - + -
442B TYR* 4.0 24.7 - - + -
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A MET* 3.3 46.9 + - + +
186A ILE 3.2 0.2 - - - -
187A PRO* 1.3 75.2 - - - +
189A ALA* 1.3 62.0 + - - +
191A CYS* 3.3 12.5 + - - +
192A LEU* 3.4 17.0 + - - +
305A LEU* 4.2 4.5 - - + -
334A VAL* 3.7 23.8 - - + +
336A TYR* 4.6 2.6 - - - -
362A ARG* 2.8 45.7 + - - -
380A VAL* 3.8 14.6 - - + +
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Residues in contact with ALA 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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185A MET 2.9 17.7 + - - +
186A ILE* 3.5 5.8 - - - +
187A PRO 3.1 0.2 - - - -
188A ASP* 1.3 76.0 - - - +
190A GLU* 1.3 64.3 + - - +
192A LEU* 3.2 5.6 + - - +
193A LYS* 3.0 21.0 + - - +
305A LEU* 3.7 19.0 - - + +
308A TYR* 3.8 24.2 - - + -
309A LEU* 4.2 7.4 - - + +
312A PHE* 3.7 15.8 - - + -
425B LEU* 6.3 0.2 - - + -
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 2.8 47.4 + - + +
148A LYS* 4.6 2.4 + - - -
178A ILE* 4.0 6.6 - - + +
186A ILE 3.1 11.4 + - - +
187A PRO 3.1 8.7 + - - +
189A ALA* 1.3 76.4 - - - +
191A CYS* 1.3 57.5 + - - +
193A LYS* 3.1 2.1 + - - +
194A ILE* 2.9 34.5 + - + +
312A PHE* 3.8 14.1 - - + -
432B TRP* 3.4 20.7 - - + -
438B ALA 5.2 0.2 - - - +
439B GLU* 5.9 0.9 - - - -
440B LEU* 5.0 2.2 - - + +
442B TYR* 2.5 39.2 + - + -
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Residues in contact with CYS 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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176A PHE* 4.2 15.3 - - - -
178A ILE* 4.5 2.5 - - - -
187A PRO 3.1 17.1 + - - -
188A ASP 3.5 7.2 - - - +
189A ALA 3.2 0.4 - - - -
190A GLU* 1.3 77.0 - - - +
192A LEU* 1.3 57.4 + - - +
194A ILE* 3.3 3.0 + - - -
195A MET* 3.0 26.1 + - - +
336A TYR* 3.2 27.4 - - - +
380A VAL* 4.1 11.9 - - - -
381A GLY* 3.9 24.2 - - - -
382A LEU* 3.4 25.2 - - + +
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Residues in contact with LEU 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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188A ASP 3.4 7.5 + - - +
189A ALA 3.2 8.1 + - - +
191A CYS* 1.3 75.0 - - - +
193A LYS* 1.3 66.0 + - - +
195A MET* 3.3 7.1 + - - +
196A CYS* 3.0 28.2 + - - -
209A VAL* 3.6 26.0 - - + -
211A VAL* 4.2 10.3 - - + -
305A LEU* 3.8 24.5 - - + -
309A LEU* 3.8 37.0 - - + -
314A ILE* 3.9 4.0 - - + -
318A ILE* 4.4 4.9 - - + -
336A TYR* 3.5 38.4 - - + -
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Residues in contact with LYS 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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87A HIS* 4.2 2.0 - - + -
189A ALA 3.0 13.0 + - - +
190A GLU* 3.1 10.1 + - - +
192A LEU* 1.3 77.3 - - - +
194A ILE* 1.3 58.2 + - - +
196A CYS* 3.3 1.0 + - - +
197A GLU* 2.9 59.9 + - - +
312A PHE* 3.4 42.2 + - + +
314A ILE* 3.7 22.1 - - + +
429B SER* 3.6 12.6 + - - -
432B TRP* 3.9 19.5 - - + -
433B ASP* 2.9 27.3 + - - -
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Residues in contact with ILE 194 (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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83A CYS* 4.0 7.4 - - - -
84A PHE* 3.7 31.0 - - + -
87A HIS* 3.4 39.0 - - + +
176A PHE* 3.5 42.2 - - + -
190A GLU* 2.9 23.8 + - + +
191A CYS* 3.6 4.3 - - - +
193A LYS* 1.3 75.6 - - - +
195A MET* 1.3 65.9 + - - +
197A GLU* 3.4 1.1 + - - +
198A ILE* 3.1 35.7 + - + +
382A LEU* 4.0 11.0 - - + -
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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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191A CYS 3.0 14.2 + - - +
192A LEU* 3.4 11.4 - - - +
194A ILE* 1.3 80.1 - - - +
196A CYS* 1.3 59.3 + - - +
198A ILE* 3.6 3.8 - - - +
199A LEU* 2.9 38.5 + - + +
209A VAL* 4.1 18.8 - - + -
336A TYR* 3.3 35.0 - - + -
338A ALA* 4.0 15.9 - - - +
358A ALA* 3.7 21.5 - - + +
359A ALA* 3.6 34.3 - - - +
382A LEU* 4.1 15.3 - - + -
384A ILE* 4.6 5.6 - - + -
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Residues in contact with CYS 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 LEU 3.0 18.1 + - - +
193A LYS* 3.8 4.3 - - + +
195A MET* 1.3 77.2 - - - +
197A GLU* 1.3 66.7 + - - +
200A SER* 2.9 30.6 + - - +
207A PHE* 3.8 26.8 - - + -
209A VAL* 4.1 16.8 - - - -
314A ILE* 4.0 30.3 - - + -
317A LYS* 4.3 15.0 - - + -
318A ILE* 4.6 3.6 - - - -
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Residues in contact with GLU 197 (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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83A CYS* 3.4 7.7 - - - -
86A ARG* 2.9 31.4 + - - +
87A HIS* 3.0 37.4 + - - -
193A LYS* 2.9 51.2 + - - +
194A ILE 3.4 4.5 + - - +
196A CYS* 1.3 75.9 - - - +
198A ILE* 1.3 63.4 + - - +
200A SER* 3.7 4.3 - - - -
201A SER* 2.9 30.8 + - - +
432B TRP* 3.5 13.7 - - - +
433B ASP* 4.8 3.8 - - - +
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Residues in contact with ILE 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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79A VAL* 4.3 3.3 - - + +
80A ILE* 3.8 31.0 - - + -
83A CYS* 3.5 22.7 - - + -
84A PHE* 3.6 32.3 - - + -
194A ILE* 3.1 21.8 + - + +
195A MET 3.6 2.9 - - - +
197A GLU* 1.3 76.1 - - - +
199A LEU* 1.3 65.7 + - + +
201A SER* 3.0 7.1 + - - -
202A LEU* 3.0 43.4 + - + +
384A ILE* 4.2 22.0 - - + -
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Residues in contact with LEU 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* 2.9 26.0 + - + +
198A ILE* 1.3 80.5 - - + +
200A SER* 1.3 63.5 + - - +
202A LEU* 3.7 4.9 + - + -
203A GLN* 3.6 12.0 + - - -
204A ILE* 3.7 30.5 + - + +
205A GLY 4.8 1.4 - - - +
207A PHE* 3.6 40.0 - - + -
209A VAL* 5.2 0.4 - - + -
338A ALA* 3.5 32.1 - - + -
357A VAL* 3.6 29.2 - - + +
358A ALA* 4.7 5.6 - - + -
384A ILE* 5.2 4.5 - - + -
389A ILE* 4.4 11.2 - - + -
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Residues in contact with SER 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A CYS* 2.9 21.9 + - - +
197A GLU* 3.7 4.9 - - - -
199A LEU* 1.3 76.9 - - - +
201A SER* 1.3 63.2 + - - +
203A GLN* 3.1 23.6 + - - +
205A GLY 6.0 0.2 - - - -
207A PHE* 3.6 17.8 - - - -
317A LYS* 5.5 2.3 - - - +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.7 26.7 - - - +
86A ARG* 5.0 8.2 + - - -
197A GLU* 2.9 23.7 + - - +
198A ILE* 3.0 4.9 + - - -
200A SER* 1.3 76.6 - - - +
202A LEU* 1.3 62.2 + - - +
203A GLN* 3.4 15.2 + - - +
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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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76A VAL* 4.1 28.7 - - + +
79A VAL* 3.6 32.3 - - + -
80A ILE* 4.7 4.9 - - + -
198A ILE* 3.0 35.8 + - + +
199A LEU* 4.0 11.9 - - + +
200A SER 3.2 0.2 - - - -
201A SER* 1.3 78.2 - - - +
203A GLN* 1.3 69.1 + - - +
204A ILE* 4.0 16.8 - - + +
389A ILE* 3.9 33.9 - - + -
393A VAL* 4.7 5.0 - - + +
396A ARG* 4.0 14.4 + - - -
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Residues in contact with GLN 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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199A LEU 3.6 2.7 + - - -
200A SER 3.1 19.8 + - - +
201A SER* 3.8 12.1 + - - +
202A LEU* 1.3 82.7 - - - +
204A ILE* 1.3 57.6 + - - +
205A GLY 3.3 8.8 + - - +
396A ARG* 3.4 35.4 + - - +
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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