Contacts of the helix formed by residues 183 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D LYS* 3.8 0.8 - - - +
182D ALA* 1.3 80.1 - - - +
184D LYS* 1.3 65.5 + - - +
185D THR* 3.2 3.6 - - - -
186D MET* 3.7 9.3 + - - +
187D LEU* 3.1 26.7 + - - +
345D LEU* 5.0 4.0 - - - -
355D PHE* 4.9 10.1 - - - -
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ARG* 6.2 0.2 - - - +
176D ILE* 5.1 4.9 - - + +
178D ALA* 3.7 34.3 - - + +
179D PRO 3.4 20.2 + - - +
180D PRO* 3.9 12.3 - - - +
181D LYS 4.1 5.7 - - - +
182D ALA 4.5 1.6 - - - +
183D GLY* 1.3 77.5 - - - +
185D THR* 1.3 60.7 + - - +
187D LEU* 4.0 7.3 - - - +
188D LEU* 3.0 30.5 + - - +
265D ASP* 4.5 9.1 - - - +
318D THR* 4.7 19.1 - - + +
319D ALA 4.4 7.9 - - - +
320D LEU* 4.7 19.9 - - - +
345D LEU* 4.7 4.9 - - + -
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ARG* 5.3 4.7 + - - -
367C LYS* 5.7 7.2 - - - +
183D GLY* 3.2 1.2 - - - -
184D LYS* 1.3 78.1 - - - +
186D MET* 1.3 68.5 + - - +
188D LEU* 3.3 4.5 + - - +
189D GLN* 3.1 49.2 + - + +
215D GLU* 4.7 20.6 + - + -
218D GLU* 5.6 3.8 - - - +
219D MET* 5.0 6.2 - - + +
265D ASP* 5.9 0.4 - - - -
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Residues in contact with MET 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C LYS* 3.5 28.3 - - - +
183D GLY* 3.7 10.7 + - - +
184D LYS 3.5 0.2 - - - -
185D THR* 1.3 81.7 - - - +
187D LEU* 1.3 61.0 + - - +
189D GLN* 3.5 23.9 + - + +
190D ASN* 3.1 23.7 + - - +
218D GLU* 5.7 0.2 - - - +
222D LEU* 6.2 0.4 - - + -
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D THR* 4.4 23.8 - - + -
162D LEU* 5.2 2.0 - - + -
176D ILE* 4.1 23.3 - - + -
183D GLY 3.1 18.9 + - - +
184D LYS* 4.0 6.1 - - - +
186D MET* 1.3 78.1 - - - +
188D LEU* 1.3 63.3 + - + +
190D ASN* 3.4 5.8 + - - +
191D ILE* 3.2 48.6 + - + +
343D LEU* 4.5 11.2 - - + -
345D LEU* 4.2 31.0 - - + -
356D PRO* 5.0 5.4 - - + -
358D ILE* 4.6 12.6 - - + -
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 5.0 5.6 - - + -
184D LYS 3.0 19.0 + - - +
185D THR* 3.3 4.9 + - - +
187D LEU* 1.3 75.4 - - + +
189D GLN* 1.3 62.7 + - + +
191D ILE* 3.3 12.4 + - + +
192D ALA* 2.9 26.2 + - + +
206D VAL* 4.5 19.1 - - + -
208D LEU* 5.5 0.2 - - + -
219D MET* 4.6 12.3 - - + -
263D LEU* 3.8 42.2 - - + -
265D ASP* 3.3 33.2 - - - +
316D ILE 5.3 1.3 - - - +
318D THR* 4.9 9.4 - - + -
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Residues in contact with GLN 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D THR* 3.1 36.1 + - - +
186D MET* 3.8 25.5 - - + +
187D LEU 3.3 0.2 - - - -
188D LEU* 1.3 78.6 - - - +
190D ASN* 1.3 56.5 + - - +
192D ALA* 3.3 6.9 + - - +
193D GLN* 2.9 37.0 + - - +
218D GLU* 4.1 18.9 + - - +
219D MET* 3.7 28.3 - - + +
222D LEU* 3.3 44.6 - - + +
223D VAL* 4.6 1.7 - - - +
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Residues in contact with ASN 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 6.1 0.2 - - - +
155D GLU* 2.9 34.0 + - - +
158D THR* 3.8 27.1 - - + +
159D ALA* 3.9 15.0 - - - +
186D MET 3.1 17.8 + - - +
187D LEU* 3.8 6.9 + - - +
188D LEU 3.3 0.2 - - - -
189D GLN* 1.3 75.7 - - - +
191D ILE* 1.3 62.9 + - - +
193D GLN* 3.5 11.3 + - - +
194D SER* 2.8 43.7 + - - -
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 3.7 23.7 - - + +
158D THR* 6.1 1.6 - - + -
162D LEU* 3.8 26.0 - - + -
168D ILE* 5.5 7.9 - - + -
176D ILE* 4.4 14.1 - - + -
187D LEU* 3.2 35.6 + - + +
188D LEU* 3.6 10.8 - - + +
189D GLN 3.3 0.2 - - - -
190D ASN* 1.3 80.0 - - - +
192D ALA* 1.3 59.6 + - - +
194D SER* 3.2 0.6 + - - -
195D ILE* 2.9 45.3 + - + +
263D LEU* 4.0 17.3 - - + -
316D ILE* 5.6 4.0 - - + -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 2.9 19.0 + - + +
189D GLN* 3.3 4.7 + - - +
191D ILE* 1.3 77.2 - - - +
193D GLN* 1.3 61.2 + - - +
196D ALA* 3.1 21.5 + - - +
204D LEU* 3.3 29.6 - - + +
206D VAL* 4.8 7.4 - - + -
223D VAL* 3.8 23.2 - - + +
263D LEU* 4.0 13.2 - - + -
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ARG* 3.0 27.3 + - - +
155D GLU* 5.4 8.0 - - - +
189D GLN* 2.9 22.7 + - - +
190D ASN* 3.9 10.7 - - - +
192D ALA* 1.3 76.2 - - - +
194D SER* 1.3 62.2 + - - +
196D ALA* 3.6 4.7 + - - +
197D TYR* 3.1 18.7 + - - +
222D LEU* 3.4 39.7 + - + +
223D VAL* 4.7 8.5 - - + +
224D LYS 6.4 0.2 - - - +
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Residues in contact with SER 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 3.7 41.1 + - - -
149D ARG* 3.4 21.1 + - - +
159D ALA* 4.3 3.1 - - - +
190D ASN* 2.8 34.1 + - - -
193D GLN* 1.3 75.9 - - - +
195D ILE* 1.3 59.9 + - - +
198D ASN* 2.9 35.0 + - - +
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 6.1 1.3 - - + -
147D MET* 3.7 21.3 - - + -
191D ILE* 2.9 36.5 + - + +
192D ALA 4.1 3.1 - - - +
194D SER* 1.3 77.0 - - - +
196D ALA* 1.3 58.5 + - - +
199D HIS* 2.8 53.6 + - + +
202D CYS* 4.4 4.9 - - + +
204D LEU* 4.3 23.1 - - + -
261D ILE* 3.7 48.7 - - + -
263D LEU* 4.6 2.5 - - + -
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ALA 3.1 19.0 + - - +
193D GLN* 4.2 4.3 - - - +
195D ILE* 1.3 78.6 - - - +
197D TYR* 1.3 59.8 + - - +
199D HIS 4.4 3.4 - - - -
200D PRO* 3.9 19.6 - - - +
204D LEU* 4.4 10.3 - - + +
224D LYS* 4.1 29.2 - - + +
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Residues in contact with TYR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ARG* 3.7 39.7 - - - +
151D ASN* 5.0 10.5 + - + +
193D GLN 3.1 18.8 + - - +
194D SER 4.0 0.2 - - - +
196D ALA* 1.3 79.7 - - - +
198D ASN* 1.3 81.8 + - - +
200D PRO* 4.1 7.3 - - - +
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Residues in contact with ASN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG 3.1 15.7 + - - +
147D MET 3.7 5.1 + - - -
148D GLU 2.7 34.8 + - - -
149D ARG* 3.2 15.9 + - - +
194D SER 2.9 14.0 + - - +
197D TYR* 1.3 97.6 - - - +
199D HIS* 1.3 77.9 + - + +
200D PRO* 3.3 8.6 - - - +
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Residues in contact with HIS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ARG 4.1 4.5 - - - -
145D LEU* 3.4 52.2 - - + +
146D ARG* 3.5 19.3 + - + -
147D MET* 5.5 3.1 - - - -
170D ARG* 4.2 9.2 + - - -
194D SER 4.9 0.2 - - - -
195D ILE* 2.8 34.5 + - + +
196D ALA* 4.4 1.0 - - - -
198D ASN* 1.3 91.9 + - + +
200D PRO* 1.3 64.9 - - - +
201D ASP* 3.2 8.0 + - - +
202D CYS* 3.3 33.3 + - + +
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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
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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