Contacts of the helix formed by residues 196 - 211 (chain D) in PDB entry 5MR4
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 ASN 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D ILE* 4.5 7.3 + - + +
187D ARG 4.4 1.8 + - - -
189D ILE* 3.7 23.2 - - + +
193D GLU* 4.4 7.2 - - - -
195D CYS* 1.3 73.2 - - - +
197D ARG* 1.3 55.6 + - - +
198D ARG* 3.5 11.6 + - - +
199D LYS* 3.2 43.5 + - + +
200D CYS* 2.8 29.3 + - - +
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Residues in contact with ARG 197 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLU* 5.3 0.4 + - - -
195D CYS* 3.2 18.4 + - - +
196D ASN* 1.3 68.2 + - - +
198D ARG* 1.3 60.7 + - - +
200D CYS* 3.5 3.0 - - - +
201D HIS* 2.8 58.1 + - + +
241D CYS 3.0 27.9 + - - +
242D SER 3.3 21.6 + - - -
243D TYR* 3.4 15.0 + - - +
244D GLU 2.9 24.7 + - - -
245D ASP* 4.1 20.5 + - - +
303D PHE 5.7 0.2 + - - -
304D ASP* 5.3 7.5 + - - +
306D THR* 5.9 1.0 - - - -
322D TRP* 5.6 1.8 - - - +
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Residues in contact with ARG 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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196D ASN* 3.3 9.3 + - - +
197D ARG* 1.3 79.8 - - - +
199D LYS* 1.3 62.9 + - + +
201D HIS* 3.4 6.2 + - - +
202D LYS* 3.1 25.3 + - + +
205D ARG* 5.0 3.4 + - - +
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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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184D ILE* 3.7 37.7 - - + +
187D ARG* 5.6 3.0 - - - +
196D ASN* 3.2 33.9 + - + +
198D ARG* 1.3 79.0 - - + +
200D CYS* 1.3 62.3 + - - +
202D LYS* 3.2 20.3 + - + +
203D ALA* 3.0 24.6 + - - +
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Residues in contact with CYS 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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184D ILE* 3.5 7.9 - - + +
185D CYS* 2.1 52.8 - - - -
196D ASN 2.8 20.5 + - - +
197D ARG 3.5 3.8 - - - +
199D LYS* 1.3 69.1 - - - +
201D HIS* 1.3 67.3 + - - +
203D ALA* 3.2 4.8 + - - +
204D LEU* 2.9 22.6 + - - +
241D CYS* 3.2 24.2 - - - -
242D SER* 3.8 23.1 - - - -
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Residues in contact with HIS 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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197D ARG* 2.8 45.9 + - + +
198D ARG* 3.7 6.4 - - - +
200D CYS* 1.3 73.0 - - - +
202D LYS* 1.3 63.9 + - - +
204D LEU* 3.1 6.5 + - + +
205D ARG* 2.9 33.3 + - - +
242D SER* 2.8 47.5 + - - -
302D GLY* 3.2 32.1 + - - +
303D PHE* 3.6 24.8 + - - -
304D ASP* 4.9 2.2 - - - -
306D THR* 4.1 2.2 + - - -
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Residues in contact with LYS 202 (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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198D ARG* 3.1 16.8 + - + +
199D LYS* 3.5 23.7 - - + +
200D CYS 3.2 0.2 - - - -
201D HIS* 1.3 75.8 - - - +
203D ALA* 1.3 62.9 + - - +
205D ARG* 3.3 26.9 + - - +
206D GLN* 3.1 29.3 + - + +
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Residues in contact with ALA 203 (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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177D LEU 4.8 2.1 - - - +
180D SER* 4.5 4.5 - - - +
181D TYR* 3.6 31.3 - - + +
184D ILE* 3.9 19.1 - - + -
199D LYS 3.0 15.7 + - - +
200D CYS* 3.7 4.0 - - - +
202D LYS* 1.3 76.5 - - - +
204D LEU* 1.3 57.5 + - - +
206D GLN* 3.3 10.0 + - - +
207D PHE* 3.0 26.5 + - - +
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Residues in contact with LEU 204 (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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181D TYR* 3.6 39.9 - - + -
185D CYS* 4.3 0.7 - - - -
200D CYS* 2.9 23.2 + - - +
201D HIS* 3.5 13.5 - - + +
203D ALA* 1.3 73.8 - - - +
205D ARG* 1.3 64.6 + - - +
207D PHE* 3.3 3.6 + - - +
208D PHE* 3.0 44.6 + - + -
237D ILE* 3.7 25.8 - - + +
242D SER* 3.6 31.4 - - - +
301D ILE* 4.4 16.8 - - + -
302D GLY* 4.7 2.7 - - - -
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Residues in contact with ARG 205 (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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198D ARG* 5.0 3.0 + - - +
201D HIS* 2.9 22.5 + - - +
202D LYS* 3.5 29.5 - - - +
204D LEU* 1.3 76.1 - - - +
206D GLN* 1.3 57.9 + - + +
208D PHE* 3.3 4.5 + - - +
209D ASP* 2.8 45.4 + - - +
263D LEU* 4.6 12.7 - - - +
267D ARG* 5.4 4.0 - - - +
301D ILE 3.8 18.6 - - - +
302D GLY* 3.2 23.0 + - - -
303D PHE* 3.3 35.5 - - + -
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Residues in contact with GLN 206 (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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177D LEU* 3.9 11.4 - - + +
202D LYS* 3.1 23.1 + - + +
203D ALA* 3.5 11.7 - - - +
204D LEU 3.2 0.2 - - - -
205D ARG* 1.3 78.1 - - + +
207D PHE* 1.3 57.2 + - - +
209D ASP* 4.6 4.0 - - - +
210D ARG* 2.8 68.8 + - - +
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Residues in contact with PHE 207 (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 CYS* 3.8 21.8 - - - -
177D LEU* 3.8 7.5 + - - +
178D ARG* 3.7 30.7 - - + -
181D TYR* 3.7 30.3 - + + -
203D ALA 3.0 12.9 + - - +
204D LEU 3.4 7.9 - - - +
206D GLN* 1.3 75.5 - - - +
208D PHE* 1.3 86.3 + + - +
211D VAL* 3.1 46.6 + - + +
216D THR* 3.6 29.0 - - + +
219D MET* 3.8 27.4 - - + -
236D THR* 5.4 2.7 - - + -
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Residues in contact with PHE 208 (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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97D ARG* 5.0 7.3 + - - +
181D TYR* 5.9 0.4 - + - -
204D LEU* 3.0 40.8 + - + +
205D ARG* 4.2 4.0 - - - +
207D PHE* 1.3 94.5 - + - +
209D ASP* 1.3 64.5 + - - +
211D VAL 3.7 9.9 - - - +
216D THR* 3.8 37.7 + - + +
217D TYR* 5.3 2.2 - + - -
220D LEU* 3.8 28.7 - - + -
236D THR* 5.1 4.5 - - + -
237D ILE* 4.5 4.3 - - + -
298D ALA* 4.3 24.2 - - + +
301D ILE* 3.9 41.3 - - + +
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Residues in contact with ASP 209 (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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97D ARG* 3.0 31.8 + - - +
98D GLY* 5.0 18.8 + - - -
102D GLU* 4.8 4.2 - - - +
205D ARG* 2.8 33.5 + - - +
206D GLN* 4.0 5.1 - - - +
208D PHE* 1.3 74.2 - - - +
210D ARG* 1.3 66.0 + - + +
211D VAL 3.7 1.9 - - - +
267D ARG* 4.4 13.1 + - - -
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Residues in contact with ARG 210 (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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173D ASN* 3.0 24.6 + - - +
177D LEU* 3.5 15.1 - - + +
206D GLN* 2.8 57.8 + - - +
209D ASP* 1.3 81.9 - - + +
211D VAL* 1.3 62.3 + - - +
212D PRO* 4.2 2.5 - - - +
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Residues in contact with VAL 211 (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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173D ASN* 4.0 7.6 - - - +
174D CYS* 3.7 32.3 - - + -
177D LEU* 3.9 20.2 - - + -
207D PHE* 3.1 35.7 + - + +
208D PHE 3.7 14.6 - - - +
209D ASP 4.7 0.9 - - - +
210D ARG* 1.3 81.3 + - - +
212D PRO* 1.3 77.9 - - + +
213D SER 3.5 0.9 + - - -
215D TYR* 3.8 9.9 - - + -
216D THR* 3.6 20.3 + - + +
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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