Contacts of the helix formed by residues 180 - 196 (chain A) in PDB entry 6G2T
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 ALA 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLY 3.6 6.3 - - - +
156A ASP 3.0 14.6 - - - +
157A GLY 2.8 34.1 - - - +
159A THR* 4.6 1.3 - - - -
179A LEU* 1.3 76.3 - - - +
181A GLY* 1.3 64.6 + - - +
182A ARG* 3.3 2.0 - - + +
183A ASP* 3.1 19.7 + - - +
184A LEU* 3.0 27.7 + - - +
260A LEU* 4.4 4.1 - - - +
302A THR* 5.2 1.3 - - - -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLY 3.2 12.0 + - - -
156A ASP* 4.4 6.1 - - - -
180A ALA* 1.3 73.1 - - - +
182A ARG* 1.3 61.8 + - - +
184A LEU* 3.0 14.8 + - - +
185A THR 2.9 11.3 + - - -
212A LYS* 2.6 32.1 + - - -
302A THR* 4.1 16.5 - - - -
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 5.7 1.3 - - - -
68A TYR* 4.1 14.9 - - + -
70A ILE 5.6 0.9 - - - -
71A GLU* 2.9 42.3 + - - -
72A HIS* 5.1 5.9 + - - -
156A ASP* 3.3 41.2 + - - +
157A GLY* 6.4 0.2 - - - -
180A ALA* 3.3 0.6 - - + -
181A GLY* 1.3 75.5 - - - +
183A ASP* 1.3 70.7 + - - +
185A THR* 3.1 23.6 + - - -
186A ASP* 3.2 15.6 + - - -
205A ARG* 3.2 49.3 + - - +
209A ARG* 6.4 0.2 - - - +
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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
----------------------------------------------------------
72A HIS* 3.6 26.2 + - - -
178A ASP 2.8 27.2 - - - +
179A LEU* 5.1 0.9 - - + -
180A ALA* 3.1 24.8 + - - +
182A ARG* 1.3 84.8 + - - +
184A LEU* 1.3 63.8 + - + +
186A ASP* 3.3 14.9 + - - +
187A TYR* 3.2 18.9 + - - +
266A LEU* 4.4 19.0 - - + +
268A MET* 5.4 3.4 - - + +
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Residues in contact with LEU 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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179A LEU* 6.1 0.2 - - + -
180A ALA 3.0 17.9 + - - +
181A GLY* 3.0 8.5 + - - +
183A ASP* 1.3 74.8 - - - +
185A THR* 1.3 53.5 + - - +
187A TYR* 3.1 6.1 + - + +
188A LEU 2.8 30.8 + - - -
212A LYS* 4.3 9.6 - - + -
256A CYS* 3.2 40.2 - - - +
257A PRO* 5.1 1.6 - - + -
259A ALA* 3.8 17.0 - - + -
260A LEU* 3.8 32.1 - - + -
266A LEU* 5.1 5.6 - - + -
302A THR* 3.7 22.9 - - - +
305A TYR* 3.9 16.4 - - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY 2.9 6.0 + - - -
182A ARG* 3.1 14.6 + - - -
184A LEU* 1.3 77.4 - - - +
186A ASP* 1.3 56.9 + - - +
188A LEU* 3.2 7.9 + - - +
189A MET* 2.8 29.0 + - - +
205A ARG* 3.7 30.1 - - + +
208A VAL* 3.5 26.4 - - + +
209A ARG* 4.1 14.1 - - + +
212A LYS* 2.8 31.5 + - - +
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Residues in contact with ASP 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 ARG* 3.2 15.7 + - - +
183A ASP* 3.3 13.9 + - - +
185A THR* 1.3 76.1 - - - +
187A TYR* 1.3 62.6 + - - +
189A MET* 3.0 30.4 - - - +
190A LYS* 3.1 11.4 + - - +
205A ARG* 3.0 39.6 + - - -
283B LYS* 5.8 5.1 + - - +
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Residues in contact with TYR 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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183A ASP 3.2 4.2 + - - +
184A LEU* 3.1 11.3 + - - +
186A ASP* 1.3 80.0 - - - +
188A LEU* 1.3 55.5 + - - +
190A LYS* 3.3 33.0 + - - +
191A ILE* 2.9 49.2 + - + +
255A ARG* 4.4 13.6 - - + +
256A CYS* 3.4 38.6 - - - -
259A ALA* 4.8 5.8 - - + -
265A PHE* 3.8 48.8 - + + +
266A LEU* 3.6 33.8 - - + +
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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
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184A LEU 2.8 10.8 + - - +
185A THR* 3.4 9.6 - - - +
187A TYR* 1.3 71.0 - - - +
189A MET* 1.3 63.9 + - - +
191A ILE* 2.9 19.8 - - + +
192A LEU* 2.8 43.3 - - + +
208A VAL* 3.4 39.0 - - + +
211A ILE* 5.0 7.0 - - + -
212A LYS* 3.9 24.0 - - + +
216A CYS* 4.7 9.2 - - - -
249A ILE* 6.0 4.0 - - + -
252A GLU* 4.8 6.1 - - + +
253A ARG* 5.6 2.5 - - - -
256A CYS* 3.3 30.0 - - + -
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Residues in contact with MET 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 THR 2.8 15.5 + - - +
186A ASP* 3.0 44.9 - - - +
188A LEU* 1.3 72.3 - - - +
190A LYS* 1.3 62.5 + - + +
192A LEU* 3.3 18.8 + - - +
193A THR* 3.4 17.3 + - - +
197A TYR 5.0 0.2 - - - +
199A PHE* 3.2 41.5 + - + +
200A THR* 4.6 8.3 - - - -
201A THR 5.3 0.4 - - - +
205A ARG* 4.4 26.2 - - + -
208A VAL* 4.6 16.5 - - + +
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Residues in contact with LYS 190 (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 9.6 + - - +
187A TYR* 3.4 41.3 + - - +
189A MET* 1.3 84.7 - - + +
191A ILE* 1.3 63.0 + - - +
193A THR* 2.7 29.3 + - - -
194A GLU* 4.1 1.9 + - - +
265A PHE 5.0 4.5 + - - -
266A LEU* 5.9 1.6 - - - +
109B LEU* 4.4 24.6 - - + +
171B PRO* 4.5 22.1 + - - +
172B HIS* 5.0 12.6 - - - +
174B ILE 5.5 2.0 - - - +
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Residues in contact with ILE 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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187A TYR* 2.9 33.6 + - + +
188A LEU* 2.9 39.4 + - + +
190A LYS* 1.3 80.4 - - - +
192A LEU* 1.3 58.1 + - - +
194A GLU* 2.9 57.8 - - - +
252A GLU* 3.1 36.4 - - + +
255A ARG* 3.5 22.4 - - - +
256A CYS* 5.1 0.2 - - - -
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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
----------------------------------------------------------
188A LEU* 2.8 53.7 + - + +
189A MET* 3.3 9.6 + - - +
191A ILE* 1.3 75.5 - - - +
193A THR* 1.3 61.9 + - - +
195A ARG* 3.1 15.2 + - - +
196A GLY 3.3 0.5 + - - -
197A TYR* 3.1 35.2 + - + +
199A PHE* 3.5 36.3 - - + +
208A VAL* 3.9 9.0 - - + -
211A ILE* 5.2 7.0 - - + -
247A ILE* 5.2 10.3 - - + -
249A ILE* 5.3 7.6 - - + -
252A GLU* 3.0 25.7 + - - +
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Residues in contact with THR 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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189A MET 3.4 15.9 - - - +
190A LYS* 2.7 21.0 + - - +
192A LEU* 1.3 77.4 - - - +
194A GLU* 1.3 62.6 + - - +
196A GLY* 3.1 10.9 + - - -
197A TYR 3.2 14.8 + - - +
198A SER* 4.1 21.0 + - - +
199A PHE 5.0 4.0 - - - +
200A THR* 6.5 0.9 - - + -
109B LEU* 3.7 35.8 + - + +
111B PRO* 3.5 18.3 - - - +
176B ARG* 5.4 4.9 - - - -
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Residues in contact with GLU 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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190A LYS 5.1 1.1 - - - +
191A ILE* 2.9 36.3 + - - +
193A THR* 1.3 82.3 + - - +
195A ARG* 1.3 66.8 + - + +
252A GLU* 4.6 6.1 - - - +
255A ARG* 2.6 32.3 + - - -
109B LEU 5.3 0.7 - - - -
110B ASN 4.2 6.1 - - - +
111B PRO* 2.9 12.2 - - - +
112B LYS* 2.6 60.4 + - + +
113B ALA 4.5 0.2 + - - -
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Residues in contact with ARG 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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192A LEU* 3.1 12.0 + - - +
194A GLU* 1.3 85.6 - - + +
196A GLY* 1.3 56.7 + - - +
197A TYR* 3.6 24.6 - - + -
236A GLU* 4.5 12.7 + - - -
248A THR* 3.2 25.5 + - - +
249A ILE* 4.0 3.9 - - - +
250A GLY* 3.0 34.4 - - - +
251A ASN* 4.2 7.9 + - - -
252A GLU* 2.9 36.0 + - - +
111B PRO* 4.2 2.8 - - - +
112B LYS* 5.6 2.0 - - - -
113B ALA* 5.2 8.1 - - - +
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Residues in contact with GLY 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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193A THR 3.1 12.6 + - - -
195A ARG* 1.3 79.3 - - - +
197A TYR* 1.3 69.8 + - - +
198A SER* 4.2 3.1 + - - -
74B ILE* 5.4 5.4 - - - +
111B PRO* 3.9 16.4 - - - -
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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
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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