Contacts of the helix formed by residues 185 - 201 (chain D) in PDB entry 5GJQ
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 THR 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D ALA* 3.7 4.2 - - - +
41D ASP* 3.6 12.1 - - - +
183D GLU 4.0 5.6 + - - +
184D MET* 1.3 80.1 - - - +
186D LEU* 1.3 60.2 + - - +
187D LYS* 3.7 8.2 + - - +
188D SER* 2.7 49.4 + - - -
189D ALA* 2.9 18.7 + - - +
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Residues in contact with LEU 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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39D ALA* 4.5 2.0 - - + -
41D ASP* 2.9 26.9 + - - +
42D GLY* 4.6 2.0 - - - -
43D VAL* 4.4 21.3 - - - +
44D LEU* 4.7 8.5 - - + -
185D THR* 1.3 74.3 - - - +
187D LYS* 1.3 58.4 + - - +
189D ALA* 3.6 4.8 + - + +
190D LEU* 2.9 45.0 + - + +
215D THR* 3.8 30.1 - - + +
217D THR* 3.7 25.8 - - + -
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Residues in contact with LYS 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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185D THR* 3.2 7.3 - - - +
186D LEU* 1.3 79.7 - - - +
188D SER* 1.3 57.1 + - - +
190D LEU* 3.1 15.2 + - + +
191D ALA* 3.0 27.4 + - - +
236D LEU* 5.4 16.1 - - + +
239D LYS* 6.4 0.4 - - - +
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Residues in contact with SER 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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180D LYS* 2.6 32.5 + - - -
183D GLU 4.9 1.5 + - - -
184D MET* 4.1 0.2 - - - -
185D THR* 2.7 32.0 + - - -
187D LYS* 1.3 73.9 - - - +
189D ALA* 1.3 58.2 + - - +
191D ALA* 3.2 9.9 + - - +
192D LEU* 2.9 27.9 + - - +
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Residues in contact with ALA 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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37D ILE* 4.3 12.0 - - + +
38D LEU 5.0 2.2 - - - +
39D ALA* 4.8 9.2 - - + -
44D LEU* 3.7 25.9 - - + +
180D LYS* 3.7 10.7 - - - +
185D THR 2.9 19.1 + - - +
186D LEU* 3.8 6.3 - - + +
188D SER* 1.3 78.0 + - - +
190D LEU* 1.3 58.3 + - - +
192D LEU* 3.3 7.9 + - - +
193D ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 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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44D LEU* 4.1 15.9 - - + -
186D LEU* 2.9 37.0 + - + +
187D LYS* 3.1 15.0 + - + +
189D ALA* 1.3 73.3 - - - +
191D ALA* 1.3 64.5 + - - +
193D ALA* 3.2 4.5 + - + +
194D ILE* 3.0 23.2 + - - +
213D ILE* 3.8 34.5 - - + +
215D THR* 4.5 11.0 - - + -
228D LEU* 4.1 17.3 - - + -
236D LEU* 4.0 26.6 - - + +
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Residues in contact with ALA 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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187D LYS 3.0 11.2 + - - +
188D SER* 3.2 11.6 + - - +
190D LEU* 1.3 76.7 - - - +
192D LEU* 1.3 62.4 + - - +
194D ILE* 3.2 8.6 + - - +
195D LYS* 3.0 23.3 + - - +
236D LEU* 4.4 7.2 - - + +
240D HIS* 4.9 3.1 + - - +
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Residues in contact with LEU 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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35D LEU* 5.8 0.2 - - - -
37D ILE* 5.4 6.1 - - + -
174D MET 5.1 0.2 - - - +
175D LEU* 3.5 34.1 - - + -
178D ASP* 3.9 37.0 - - + +
179D TYR* 4.5 8.7 - - + -
180D LYS* 4.0 26.0 - - + -
188D SER 2.9 12.0 + - - +
189D ALA* 3.3 10.7 + - - +
191D ALA* 1.3 75.8 - - - +
193D ALA* 1.3 57.0 + - - +
195D LYS* 3.3 13.7 + - + +
196D VAL* 2.9 38.2 + - + +
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Residues in contact with ALA 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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35D LEU* 4.4 16.2 - - + +
37D ILE* 6.0 0.4 - - - +
44D LEU* 3.9 24.0 - - + -
46D ALA* 4.3 13.9 - - + -
189D ALA 2.9 14.0 + - - +
190D LEU* 3.4 10.1 - - - +
191D ALA 3.2 0.2 - - - -
192D LEU* 1.3 77.7 - - - +
194D ILE* 1.3 56.4 + - - +
196D VAL* 4.0 0.7 - - - +
197D LEU* 2.9 36.8 + - - +
213D ILE* 4.6 7.2 - - + -
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Residues in contact with ILE 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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190D LEU 3.0 12.9 + - - +
191D ALA* 3.2 10.5 + - - +
193D ALA* 1.3 75.7 - - - +
195D LYS* 1.3 57.4 + - - +
197D LEU* 3.9 4.6 - - - +
198D ASN* 2.9 31.2 + - - +
206D LEU* 4.3 6.3 - - + +
213D ILE* 5.2 6.2 - - + +
236D LEU* 4.5 21.8 - - + +
237D ILE* 5.1 6.7 - - + +
240D HIS* 4.5 20.7 - - + -
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Residues in contact with LYS 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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174D MET* 4.4 18.2 - - - -
178D ASP* 2.6 42.7 + - - +
191D ALA 3.0 14.1 + - - +
192D LEU* 3.4 18.6 - - + +
194D ILE* 1.3 73.8 - - - +
196D VAL* 1.3 64.9 + - - +
198D ASN* 3.0 6.1 + - - +
199D LYS* 3.0 22.3 + - + +
240D HIS* 3.7 28.3 + - + -
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Residues in contact with VAL 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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33D THR* 6.4 0.2 - - + -
35D LEU* 4.1 19.5 - - + -
171D ALA* 3.5 36.6 - - + +
174D MET* 4.0 26.7 - - + -
175D LEU* 4.0 14.4 - - + -
192D LEU* 2.9 43.5 + - + +
193D ALA 4.2 1.3 - - - +
195D LYS* 1.3 73.0 - - + +
197D LEU* 1.3 58.9 + - - +
199D LYS* 3.2 0.5 + - - +
200D THR* 2.8 36.7 + - + +
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Residues in contact with LEU 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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33D THR* 4.7 13.2 - - + -
35D LEU* 3.6 18.8 - - + +
46D ALA* 3.5 39.7 - - + +
47D ALA 4.4 2.2 - - - +
48D GLU* 4.7 13.2 - - + +
193D ALA 2.9 20.9 + - - +
194D ILE* 3.9 4.9 - - - +
196D VAL* 1.3 78.4 - - - +
198D ASN* 1.3 56.9 + - - +
200D THR* 3.5 9.4 + - - +
201D MET* 3.0 36.9 + - + +
206D LEU* 3.9 10.0 - - + +
211D VAL* 4.1 26.7 - - + -
213D ILE* 4.9 5.8 - - + -
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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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194D ILE 2.9 20.9 + - - +
195D LYS 3.0 4.4 + - - +
197D LEU* 1.3 77.2 - - - +
199D LYS* 1.3 62.4 + - - +
201D MET 4.0 8.8 - - - +
204D SER* 4.5 18.7 + - - -
205D LYS 5.0 2.3 + - - +
206D LEU* 4.0 33.6 - - + +
240D HIS* 3.8 27.4 + - + +
244D GLU* 4.2 9.7 + - - -
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Residues in contact with LYS 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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174D MET* 3.6 36.3 - - + -
195D LYS* 3.0 13.6 + - + +
196D VAL 3.9 0.9 - - - +
198D ASN* 1.3 81.9 - - - +
200D THR* 1.3 63.4 + - + +
201D MET 4.0 4.2 - - - +
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Residues in contact with THR 200 (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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33D THR* 4.3 14.7 + - + +
167D ASN* 3.0 44.0 + - + +
170D ALA* 4.6 6.3 - - + -
171D ALA* 3.8 36.8 - - + +
174D MET* 4.9 5.2 - - + -
196D VAL* 2.8 27.3 + - + +
197D LEU* 3.5 16.5 + - - +
199D LYS* 1.3 77.3 - - - +
201D MET* 1.3 67.0 + - - +
202D ASP* 3.3 1.4 + - - -
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Residues in contact with MET 201 (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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33D THR* 5.8 0.7 - - - -
48D GLU* 5.4 15.7 - - + +
197D LEU* 3.0 24.2 + - + +
198D ASN 4.0 7.2 - - - +
199D LYS 3.5 6.4 - - - +
200D THR* 1.3 78.5 + - - +
202D ASP* 1.3 66.4 + - - +
203D VAL* 4.1 11.3 - - + +
204D SER* 4.5 1.0 + - - -
206D LEU* 3.8 19.7 - - + -
210D LYS* 6.5 1.1 - - + -
211D VAL* 6.2 0.9 - - + -
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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