Contacts of the helix formed by residues 184 - 201 (chain A) in PDB entry 3GUU
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 4.1 10.3 - - - -
183A TYR* 1.3 80.3 - - - +
185A GLY* 1.3 61.0 + - - -
187A ALA* 2.9 17.0 + - - +
188A HIS 3.1 9.2 + - - -
212A GLY 2.9 12.9 + - - -
213A GLY 3.5 12.8 - - - -
215A PRO* 3.2 15.5 - - - +
366A HIS* 2.8 29.3 + - - -
431A PHE* 3.6 5.8 - - - -
442A 1PE 2.4 28.0 + - - -
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL 4.4 1.3 - - - -
93A TYR* 3.8 5.6 - - - +
95A ASP* 3.3 20.4 - - - -
142A HIS* 4.7 3.5 + - - -
149A PHE* 4.6 8.3 - - - -
150A ILE* 5.1 0.9 - - - +
155A GLU* 4.7 2.6 - - - +
184A SER* 1.3 78.1 - - - +
186A GLY* 1.3 59.6 + - - +
188A HIS* 3.4 10.9 + - - +
189A ALA* 3.3 20.8 + - - +
442A 1PE 3.0 17.2 + - - -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 3.1 28.2 - - - +
92A VAL 3.6 11.9 - - - -
93A TYR* 3.7 5.7 - - - +
183A TYR 2.9 15.7 + - - -
185A GLY* 1.3 76.5 - - - +
187A ALA* 1.3 53.6 + - - +
189A ALA* 3.5 2.2 + - - -
190A THR* 2.7 36.3 + - - -
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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
----------------------------------------------------------
182A GLY 3.7 3.1 - - - +
183A TYR 3.4 4.2 + - - +
184A SER 2.9 10.9 + - - +
186A GLY* 1.3 75.5 - - - +
188A HIS* 1.3 58.7 + - - +
190A THR* 3.7 1.0 - - - -
191A VAL* 2.9 30.5 + - - +
211A HIS* 3.6 26.0 + - + -
212A GLY 3.0 28.3 - - - +
214A THR* 3.5 18.0 - - - +
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.3 55.6 + - + +
152A GLY* 3.6 6.5 + - - -
155A GLU* 2.4 33.9 + - - -
184A SER 3.1 5.9 + - - -
185A GLY 3.6 8.1 - - - +
187A ALA* 1.3 75.7 - - - +
189A ALA* 1.3 62.3 + - - +
191A VAL* 3.3 2.3 - - - +
192A TRP* 3.0 61.7 + + - -
215A PRO* 3.3 43.1 - - + +
216A VAL* 5.4 2.5 - - - -
218A ALA* 5.9 5.5 + - - +
308A GLU* 5.2 3.8 + - - -
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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
----------------------------------------------------------
91A GLN* 4.0 4.7 - - + -
142A HIS* 3.8 25.8 - - + +
155A GLU* 3.3 20.6 + - - +
156A GLY* 4.7 0.5 - - - -
159A ILE* 3.3 31.0 - - + +
185A GLY 3.3 8.4 + - - +
186A GLY 3.6 7.9 - - - +
187A ALA 3.3 0.2 - - - -
188A HIS* 1.3 81.1 - - - +
190A THR* 1.3 62.1 + - - +
192A TRP* 3.4 2.4 + - - +
193A ALA 3.0 17.5 + - - -
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Residues in contact with THR 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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91A GLN* 3.1 23.4 + - - +
180A LEU* 3.9 33.4 - - + +
181A GLU 4.3 0.7 - - - +
182A GLY 3.6 8.0 + - - -
186A GLY 2.7 22.6 + - - -
187A ALA* 3.7 8.3 - - - -
188A HIS 3.3 0.2 - - - -
189A ALA* 1.3 76.8 - - - +
191A VAL* 1.3 56.4 + - - +
193A ALA* 3.1 5.5 + - - +
194A THR* 3.0 32.0 + - + +
209A ALA* 4.7 0.9 - - + -
210A SER 4.4 0.7 - - - +
211A HIS* 3.7 25.4 - - + -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA 2.9 18.7 + - - +
188A HIS* 3.3 14.1 - - - +
190A THR* 1.3 72.5 - - - +
192A TRP* 1.3 69.5 + - + +
194A THR* 2.9 18.3 + - - +
195A SER* 2.8 24.6 + - - +
211A HIS* 3.7 27.1 - - + +
214A THR* 3.8 13.5 - - + -
215A PRO 4.5 3.8 - - - +
310A VAL* 4.3 18.4 - - + -
326A ARG* 4.9 0.2 - - - +
345A TYR* 3.6 34.1 - - + +
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Residues in contact with TRP 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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152A GLY* 3.3 35.4 - - - +
153A TYR* 3.6 33.9 - + - -
155A GLU* 5.0 0.2 - - - +
156A GLY* 3.9 4.6 - - - +
188A HIS* 3.0 59.4 + + - +
189A ALA* 3.7 5.4 - - - +
191A VAL* 1.3 85.0 - - + +
193A ALA* 1.3 60.3 + - - +
195A SER* 3.3 4.7 + - - -
196A LEU* 3.1 42.8 + - + +
215A PRO 5.4 0.2 + - - -
216A VAL 4.9 5.7 + - - -
307A GLN 3.4 19.7 - - - -
308A GLU* 3.9 6.8 + - - -
309A THR 3.6 22.0 - - - +
310A VAL* 3.8 19.7 - - + +
317A TYR* 3.5 15.7 - - - -
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Residues in contact with ALA 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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156A GLY* 3.8 14.3 - - - +
159A ILE* 3.6 36.8 - - + -
160A LEU* 3.6 16.5 - - + +
180A LEU* 3.9 11.9 - - + -
189A ALA 3.0 15.7 + - - +
190A THR 3.1 4.7 + - - +
192A TRP* 1.3 73.9 - - - +
194A THR* 1.3 65.1 + - - +
195A SER 3.3 0.2 + - - -
196A LEU 3.4 1.0 + - - -
197A ALA* 3.1 19.2 + - - +
206A ILE* 5.7 0.4 - - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.7 9.6 - - + -
190A THR* 3.0 21.7 + - + +
191A VAL* 2.9 28.3 + - - +
193A ALA* 1.3 77.5 - - - +
195A SER* 1.3 59.7 + - - +
197A ALA* 3.6 17.0 + - - +
198A GLU* 4.8 2.1 + - - +
206A ILE* 5.2 2.0 - - + -
209A ALA* 3.6 30.7 - - + -
211A HIS* 5.0 3.8 + - + +
320A SER* 4.6 1.0 + - - -
322A PRO* 3.4 24.7 - - - +
324A PHE* 3.8 21.2 - - + -
326A ARG* 4.4 7.0 + - - +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 2.8 26.0 + - - +
192A TRP* 3.7 9.9 - - - -
193A ALA 3.2 0.4 - - - -
194A THR* 1.3 77.7 + - - +
196A LEU* 1.3 69.9 + - - +
197A ALA 3.6 0.2 + - - -
198A GLU* 4.6 2.4 + - - +
199A SER* 4.8 2.6 + - - -
310A VAL* 3.7 23.7 - - - +
317A TYR* 5.9 0.7 - - - -
319A VAL* 4.8 7.0 - - - +
320A SER* 3.0 37.6 + - - -
322A PRO* 4.6 3.9 - - - +
345A TYR* 4.4 5.9 + - - -
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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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152A GLY 4.2 1.6 - - - +
153A TYR* 3.8 57.2 - - + +
156A GLY* 4.1 7.9 - - - -
157A MET* 4.2 16.8 - - + +
160A LEU* 3.7 16.2 - - + -
192A TRP* 3.1 28.0 + - + +
195A SER* 1.3 84.1 - - - +
197A ALA* 1.3 55.1 + - - +
198A GLU 3.4 1.6 - - - -
199A SER* 3.4 12.7 + - - +
200A TYR* 2.8 40.4 + - + +
317A TYR* 6.2 2.7 - - + -
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Residues in contact with ALA 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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160A LEU* 3.9 12.6 - - + -
193A ALA 3.1 13.3 + - - +
194A THR* 3.7 10.1 - - - +
195A SER 3.4 1.8 - - - -
196A LEU* 1.3 75.4 - - - +
198A GLU* 1.3 58.5 + - + +
201A ALA 2.8 40.5 + - - +
202A PRO* 3.0 2.3 - - - -
204A LEU 5.9 0.7 - - - +
206A ILE* 3.6 31.4 - - + -
324A PHE* 5.3 4.0 - - + -
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Residues in contact with GLU 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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194A THR 5.3 2.0 - - - +
195A SER 4.9 1.8 - - - +
196A LEU 3.4 0.2 - - - -
197A ALA* 1.3 77.4 - - + +
199A SER* 1.3 61.7 + - - +
202A PRO* 3.1 30.7 - - - +
320A SER* 2.5 36.3 + - - +
321A VAL 3.5 20.5 + - - +
322A PRO* 4.1 6.9 - - + +
323A LYS* 4.7 6.8 + - - +
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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
----------------------------------------------------------
195A SER 4.8 1.9 + - - -
196A LEU* 3.4 21.4 + - - +
198A GLU* 1.3 80.9 - - - +
200A TYR* 1.3 63.1 + - - +
202A PRO* 4.3 4.4 - - - +
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Residues in contact with TYR 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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33A LYS* 3.4 36.3 + - + +
62A THR* 2.8 23.8 + - + -
157A MET* 3.4 53.4 - - + -
160A LEU* 3.9 20.0 - - + -
161A ASP* 2.5 42.7 + - - -
164A ARG* 3.0 23.9 + - - -
196A LEU* 2.8 25.5 + - + +
199A SER* 1.3 77.0 + - - +
201A ALA* 1.3 55.0 + - - +
202A PRO* 3.6 3.4 - - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.9 20.2 - - + -
164A ARG* 3.3 23.6 - - - +
196A LEU 3.8 0.2 + - - -
197A ALA* 2.8 20.3 + - - +
200A TYR* 1.3 76.4 - - - +
202A PRO* 1.3 63.7 - - - +
203A GLU* 3.3 3.8 - - - -
204A LEU* 3.2 40.5 + - + +
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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