Contacts of the helix formed by residues 183 - 197 (chain D) in PDB entry 5M8L
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 183 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ALA 3.8 1.8 - - - -
152D LYS 3.3 23.4 + - - -
153D ARG 4.4 2.2 - - - -
154D THR 3.2 17.9 - - - -
155D THR* 4.0 2.2 - - - +
156D HIS* 3.9 0.7 - - - +
182D ILE* 1.3 82.0 - - - +
184D ILE* 1.3 59.5 + - - +
185D TYR 3.7 1.4 + - - -
186D ASN* 3.0 35.7 + - - +
187D TYR* 2.8 29.5 + - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ALA* 3.3 22.0 + - + +
154D THR* 2.9 26.2 + - + +
155D THR 4.2 0.2 - - - +
156D HIS* 3.8 28.0 - - + +
157D PRO* 4.3 10.3 - - + -
183D SER* 1.3 73.2 - - - +
185D TYR* 1.3 63.7 + - - +
187D TYR* 3.6 6.6 + - - +
188D PHE* 3.4 16.8 + - - +
231D LEU* 4.3 11.3 - - + +
234D ASP* 3.9 30.7 - - + +
235D MET* 4.7 3.1 - - + -
238D MET* 3.7 40.2 - - + -
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Residues in contact with TYR 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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148D LEU* 3.9 22.7 - - + -
151D ALA* 2.9 22.7 + - + +
152D LYS* 3.7 20.6 - - + +
184D ILE* 1.3 76.1 - - - +
186D ASN* 1.3 65.4 + - - +
188D PHE* 3.1 22.5 + + - +
189D VAL* 3.1 28.8 + - + +
231D LEU* 4.3 14.4 - - + -
286D TRP* 3.5 31.0 - + - -
395D PRO* 2.7 29.5 + - - +
396D ASN* 4.4 2.0 - - - -
397D ASP 4.0 0.3 + - - -
398D PRO* 3.4 17.8 - - + +
400D PHE* 4.8 0.3 - - - +
401D VAL* 3.5 26.5 - - + +
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Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LYS* 2.9 26.9 + - - +
182D ILE* 3.6 21.9 - - + +
183D SER* 3.0 25.5 + - - +
185D TYR* 1.3 74.5 - - - +
187D TYR* 1.3 55.3 + - - +
189D VAL* 3.2 11.0 + - - +
190D TRP* 2.7 34.0 + - - +
289D VAL* 3.7 27.2 - - + +
305D SER 4.9 3.2 + - - -
307D GLU* 2.7 29.5 + - - +
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Residues in contact with TYR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLN* 4.0 19.8 + - + -
156D HIS* 3.8 21.5 - + + -
159D PHE* 3.5 51.7 - + + -
161D ILE* 4.2 15.7 - - + -
182D ILE* 3.7 14.8 - - + +
183D SER 2.8 17.2 + - - +
184D ILE 3.7 4.9 - - - +
186D ASN* 1.3 76.6 - - - +
188D PHE* 1.3 65.7 + - + +
190D TRP* 3.6 4.4 - + - +
191D THR* 3.0 51.8 + - + +
230D ARG* 4.1 21.9 - - + +
234D ASP* 4.4 2.9 - - - -
443D PHE* 4.7 8.5 - + - -
444D TRP 4.9 3.6 + - - -
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Residues in contact with PHE 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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184D ILE 3.4 9.4 + - - +
185D TYR* 3.1 41.9 + + - +
187D TYR* 1.3 83.4 - - + +
189D VAL* 1.3 61.1 + - - +
191D THR* 3.5 4.7 + - - -
192D HIS* 3.8 1.6 + - - +
227D HIS* 2.7 78.8 + + - -
228D LEU* 4.6 8.7 - - + -
231D LEU* 3.5 38.4 - - + -
395D PRO* 3.9 6.7 - - + -
400D PHE* 3.6 29.8 - + - -
401D VAL* 4.0 8.7 - - + -
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D TYR* 3.1 38.5 + - + +
186D ASN* 3.2 11.4 + - - +
188D PHE* 1.3 75.0 - - - +
190D TRP* 1.3 64.5 + - - +
192D HIS* 3.4 4.3 + - - +
193D TYR* 3.1 19.9 + - - +
289D VAL* 3.7 18.8 - - + +
290D CYS* 4.6 4.3 - - + -
392D HIS 5.1 4.1 - - - +
393D LEU 4.7 0.2 - - - +
395D PRO* 3.9 29.3 - - + +
396D ASN* 3.6 33.0 - - - +
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Residues in contact with TRP 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLN* 3.3 40.6 - - + -
161D ILE* 3.5 30.6 - - + +
162D ALA* 3.5 20.6 - - + -
182D ILE* 4.2 6.7 - - + -
186D ASN 2.7 20.4 + - - +
187D TYR* 3.1 9.6 + - - +
189D VAL* 1.3 72.0 - - - +
191D THR* 1.3 76.5 + - + +
193D TYR* 3.0 5.9 + + - +
194D TYR* 2.8 58.9 + + + -
290D CYS* 4.4 6.5 - - - -
302D LEU* 4.3 7.0 - - + -
303D CYS* 2.8 48.6 + - + +
442D PRO* 4.0 10.5 - - + -
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLN 4.6 1.1 - - - +
187D TYR* 3.0 46.4 + - + +
188D PHE* 3.5 3.6 + - - -
190D TRP* 1.3 83.4 - - + +
192D HIS* 1.3 64.0 + - - +
195D SER* 3.0 25.5 + - - -
223D TRP* 4.1 1.8 - - - -
227D HIS* 3.4 25.6 + - - -
442D PRO* 3.6 28.9 - - + +
443D PHE* 4.0 13.8 - - + -
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Residues in contact with HIS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D PHE 3.8 6.7 + - - +
189D VAL 3.4 9.4 + - - +
190D TRP 3.2 0.4 - - - -
191D THR* 1.3 79.6 + - - +
193D TYR* 1.3 66.3 + - - +
195D SER* 2.9 17.4 + - - -
196D VAL* 3.4 10.0 + - - +
215D HIS* 3.3 15.1 + + - -
223D TRP* 3.7 20.0 - + - -
224D HIS* 3.7 7.0 - - - -
227D HIS* 4.0 2.9 - + + -
391D THR* 3.0 31.1 + - + -
392D HIS 5.0 1.0 + - - -
394D SER* 3.8 13.5 - - - -
395D PRO* 3.6 20.4 - - + +
400D PHE* 3.7 13.5 - + - -
518D ZN 2.1 37.1 - - - -
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Residues in contact with TYR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D VAL 3.1 10.4 + - - +
190D TRP* 3.0 14.9 + - - +
192D HIS* 1.3 79.7 + - - +
194D TYR* 1.3 82.8 + + + +
196D VAL* 3.0 7.1 + - - +
197D LYS* 2.9 57.8 + - + +
290D CYS* 3.9 20.0 - - + -
293D LEU* 3.9 21.3 - - + -
296D TYR* 3.6 27.0 - + - +
297D ASP* 5.3 0.6 + - - -
301D THR 4.2 0.5 + - - -
302D LEU* 3.8 8.7 - - + -
303D CYS* 3.5 36.7 + - + -
392D HIS* 3.8 31.4 + - + +
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Residues in contact with TYR 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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25D GLN* 5.3 2.7 - - - -
86D ASP* 3.6 26.7 + - - +
87D ARG* 2.8 53.9 + - + +
90D TRP* 4.1 12.8 - + - -
94D PHE* 4.3 5.2 - - - -
165D ARG* 6.3 0.4 - - + -
190D TRP* 2.8 50.7 + + + +
191D THR 3.8 3.8 - - - +
193D TYR* 1.3 81.6 - + - +
195D SER* 1.3 57.3 + - - +
197D LYS* 3.5 16.6 - - + +
302D LEU* 3.8 30.1 - - + -
441D VAL* 4.0 3.8 - - + -
442D PRO* 3.6 31.9 - - + -
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Residues in contact with SER 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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87D ARG* 3.5 9.0 + - - +
191D THR 3.0 15.0 + - - -
192D HIS* 2.9 14.7 + - - -
193D TYR 3.1 0.2 - - - -
194D TYR* 1.3 79.2 - - - +
196D VAL* 1.3 56.2 + - - +
212D ASP* 4.1 0.2 - - - -
213D PHE* 3.0 36.7 + - - +
214D SER* 2.5 29.3 + - - -
223D TRP* 3.5 11.6 - - - -
441D VAL* 3.5 22.4 - - - -
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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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87D ARG* 4.0 0.4 - - - -
192D HIS* 3.5 12.3 - - + +
193D TYR 3.0 11.3 + - - +
195D SER* 1.3 76.6 - - - +
197D LYS* 1.3 70.2 + - - +
198D LYS* 3.8 2.4 + - - +
211D VAL 4.1 10.0 - - - +
212D ASP* 3.6 17.3 - - - +
214D SER* 3.5 9.0 - - - +
215D HIS* 3.4 39.0 - - + +
391D THR* 3.9 11.4 - - + +
392D HIS* 3.9 31.2 - - + +
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Residues in contact with LYS 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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85D ASP* 4.9 4.1 + - - -
87D ARG* 2.8 35.4 + - - +
165D ARG* 4.7 12.3 - - - +
193D TYR* 2.9 50.9 + - + +
194D TYR* 3.5 26.9 - - + +
196D VAL* 1.3 82.2 - - - +
198D LYS* 1.3 84.2 + - - +
199D THR* 4.5 1.4 - - - +
200D PHE* 4.3 10.7 - - - +
211D VAL* 4.4 4.5 - - - +
293D LEU* 5.9 2.2 - - + -
296D TYR* 5.9 1.6 + - - +
297D ASP* 5.4 5.5 + - - +
301D THR 5.2 2.2 + - - -
302D LEU* 3.5 27.5 - - + +
392D HIS* 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
------------------------------------------------------------
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