Contacts of the helix formed by residues 183 - 199 (chain A) in PDB entry 6XAV
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 GLY 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LYS* 3.8 1.2 - - - +
182A ALA* 1.3 79.7 - - - +
184A LYS* 1.3 62.5 + - - +
185A THR* 3.2 3.6 - - - -
186A MET* 3.6 7.8 + - - +
187A LEU* 3.0 31.3 + - - +
345A LEU* 4.8 4.2 - - - +
355A PHE* 4.1 19.7 - - - -
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Residues in contact with LYS 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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176A ILE* 5.6 3.4 - - + -
178A ALA* 3.7 37.5 - - + +
179A PRO 3.5 16.3 + - - +
180A PRO* 3.8 13.3 - - - +
181A LYS 3.8 6.9 - - - +
182A ALA 4.4 2.4 - - - +
183A GLY* 1.3 81.0 - - - +
185A THR* 1.3 58.3 - - - +
187A LEU* 4.0 7.7 - - - +
188A LEU* 3.0 31.7 + - - +
318A THR* 4.8 24.7 - - + +
319A ALA 4.9 1.1 - - - +
320A LEU* 3.7 22.4 - - + +
345A LEU* 4.8 3.1 - - + -
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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
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183A GLY* 3.2 1.4 - - - -
184A LYS* 1.3 79.6 - - - +
186A MET* 1.3 69.0 + - - +
188A LEU* 3.3 5.6 + - - +
189A GLN* 3.1 49.6 + - + +
215A GLU* 5.4 8.4 + - + -
218A GLU* 5.8 2.7 - - - +
219A MET* 5.0 6.2 - - - +
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Residues in contact with MET 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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158A THR* 5.5 0.6 - - - +
183A GLY* 3.6 10.1 + - - +
184A LYS 3.5 0.2 - - - -
185A THR* 1.3 83.1 - - - +
187A LEU* 1.3 62.1 + - - +
189A GLN* 3.5 21.6 + - + +
190A ASN* 3.1 23.9 + - - +
355A PHE* 5.1 19.5 - - + -
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Residues in contact with LEU 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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158A THR* 4.6 16.8 - - + -
162A LEU* 5.3 2.5 - - + -
176A ILE* 4.2 23.1 - - + -
183A GLY 3.0 19.5 + - - +
184A LYS* 4.0 6.1 - - - +
186A MET* 1.3 77.1 - - - +
188A LEU* 1.3 67.9 + - + +
190A ASN* 3.5 5.8 + - - +
191A ILE* 3.1 49.7 + - + +
343A LEU* 4.4 14.1 - - + -
345A LEU* 4.2 30.3 - - + -
356A PRO* 5.1 4.3 - - + -
358A ILE* 4.5 14.8 - - + -
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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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176A ILE* 6.2 0.7 - - + -
184A LYS 3.0 18.1 + - - +
185A THR* 3.7 6.3 - - - +
186A MET 3.3 0.2 - - - -
187A LEU* 1.3 79.4 - - + +
189A GLN* 1.3 59.7 - - - +
191A ILE* 3.2 10.5 + - + +
192A ALA* 2.9 28.2 + - + +
206A VAL* 4.4 11.2 - - + -
219A MET* 4.1 20.9 - - + -
263A LEU* 3.7 32.8 - - + -
265A ASP* 3.2 39.0 - - - +
316A ILE* 5.6 5.2 - - + +
318A THR* 4.6 9.9 - - + -
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Residues in contact with GLN 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* 3.1 32.0 + - - +
186A MET* 3.9 23.2 - - + +
187A LEU 3.4 0.2 - - - -
188A LEU* 1.3 74.6 - - - +
190A ASN* 1.3 57.7 + - - +
192A ALA* 4.0 4.9 - - - +
193A GLN* 2.9 40.8 + - - +
218A GLU* 4.0 19.8 + - - +
219A MET* 3.5 36.6 - - + -
222A LEU* 3.8 32.8 - - + +
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Residues in contact with ASN 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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149A ARG* 6.0 3.0 - - - +
155A GLU* 2.7 37.4 + - - +
156A ASP* 4.7 1.4 - - - +
158A THR* 3.5 21.9 + - + +
159A ALA* 3.3 27.8 + - - +
186A MET 3.1 17.4 + - - +
187A LEU 3.7 5.2 - - - +
188A LEU 3.2 0.2 - - - -
189A GLN* 1.3 78.7 - - - +
191A ILE* 1.3 56.8 + - - +
193A GLN* 4.1 8.1 + - - +
194A SER* 2.7 41.5 + - - -
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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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147A MET* 3.5 21.9 - - + +
158A THR* 6.0 0.7 - - + -
162A LEU* 3.8 27.1 - - + -
168A ILE* 5.4 8.1 - - + -
176A ILE* 5.3 4.5 - - + -
187A LEU* 3.1 38.5 + - + +
188A LEU* 3.7 9.9 - - + +
190A ASN* 1.3 79.5 - - - +
192A ALA* 1.3 61.0 + - - +
194A SER 3.2 0.5 + - - -
195A ILE* 2.9 43.6 + - + +
263A LEU* 3.8 20.2 - - + -
316A ILE* 5.2 16.2 - - + -
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Residues in contact with ALA 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 LEU* 2.9 21.4 + - + +
189A GLN 4.0 1.8 - - - +
191A ILE* 1.3 78.2 - - - +
193A GLN* 1.3 62.7 + - - +
195A ILE* 3.9 2.0 - - - +
196A ALA* 3.1 24.4 + - - +
204A LEU* 3.8 24.4 - - + +
206A VAL* 5.0 2.9 - - + -
223A VAL* 3.7 29.9 - - + +
224A LYS 5.6 0.5 + - - -
263A LEU* 4.5 11.4 - - + +
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Residues in contact with GLN 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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149A ARG* 3.3 25.2 + - - +
155A GLU* 5.7 5.9 - - - +
189A GLN* 2.9 25.3 + - - +
190A ASN* 4.1 6.2 + - - +
192A ALA* 1.3 76.5 - - + +
194A SER* 1.3 59.0 + - - +
196A ALA* 3.6 4.9 + - - +
197A TYR* 3.1 29.5 + - - +
222A LEU* 3.4 43.6 + - + +
223A VAL* 5.5 3.4 - - + +
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Residues in contact with SER 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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147A MET* 3.4 42.5 + - - -
149A ARG* 3.6 19.9 + - - +
159A ALA* 3.8 5.0 - - - +
190A ASN* 2.7 33.9 + - - -
191A ILE 3.2 0.2 + - - -
193A GLN* 1.3 75.1 - - - +
195A ILE* 1.3 59.3 + - - +
198A ASN* 2.9 36.4 + - - +
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Residues in contact with ILE 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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147A MET* 3.6 20.0 - - + -
191A ILE* 2.9 36.5 + - + +
192A ALA* 3.9 4.9 - - - +
193A GLN 3.3 0.2 - - - -
194A SER* 1.3 77.2 - - - +
196A ALA* 1.3 58.1 + - - +
199A HIS* 2.8 54.6 + - + +
202A CYS* 4.7 5.4 - - + +
204A LEU* 4.4 20.2 - - + -
261A ILE* 4.1 41.3 - - + -
263A LEU* 4.4 8.3 - - + -
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Residues in contact with ALA 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 ALA 3.1 18.4 + - - +
193A GLN* 4.1 4.9 - - - +
195A ILE* 1.3 77.8 - - - +
197A TYR* 1.3 59.6 + - - +
199A HIS 4.4 4.0 - - - -
200A PRO* 3.7 21.9 - - - +
204A LEU* 5.1 3.8 - - + +
224A LYS* 4.1 37.7 - - + +
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Residues in contact with TYR 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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149A ARG* 3.6 50.3 - - + +
150A GLY 6.0 0.3 - - - -
151A ASN* 4.8 16.2 + - - +
193A GLN 3.1 18.9 + - - +
196A ALA* 1.3 78.7 - - - +
198A ASN* 1.3 82.4 + - - +
200A PRO* 4.2 5.7 - - - +
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Residues in contact with ASN 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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146A ARG* 2.9 22.4 + - - +
147A MET 3.3 5.5 - - - -
148A GLU 2.5 35.2 + - - +
149A ARG* 3.9 5.6 - - - -
194A SER 2.9 18.1 + - - +
197A TYR* 1.3 99.4 - - - +
199A HIS* 1.3 78.4 + - + +
200A PRO* 3.3 7.9 - - - +
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Residues in contact with HIS 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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144A ARG 4.2 4.9 - - - -
145A LEU* 3.6 37.9 - - + +
146A ARG* 3.4 28.9 + - + +
147A MET* 5.6 3.6 - - - -
170A ARG* 4.3 9.1 + - - -
195A ILE* 2.8 35.4 + - + +
196A ALA* 4.4 1.0 - - - -
198A ASN* 1.3 87.9 + - + +
200A PRO* 1.3 64.6 - - - +
201A ASP* 3.2 8.6 + - - +
202A CYS* 3.5 31.3 + - + +
261A ILE* 6.0 0.2 - - + -
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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
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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