Contacts of the helix formed by residues 197 - 208 (chain D) in PDB entry 4M3P
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 PRO 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D GLU 4.7 2.0 - - - +
191D GLY* 4.1 2.7 - - - -
195D GLY 3.2 10.5 - - - +
196D VAL* 1.3 86.3 - - + +
198D PRO* 1.4 63.6 - - + +
199D GLY 3.4 3.6 - - - +
200D GLU* 3.1 29.7 + - + +
201D CYS* 2.9 29.9 + - - -
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Residues in contact with PRO 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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187D ILE* 4.4 5.4 - - + -
188D GLY 3.6 16.4 - - - +
189D PRO 3.4 27.1 - - - +
190D GLU 4.4 0.4 - - - -
191D GLY* 3.6 8.1 - - - +
196D VAL 3.8 0.2 - - - -
197D PRO* 1.4 84.8 - - + +
199D GLY* 1.3 57.1 + - - +
201D CYS* 3.5 10.1 - - + +
202D ALA 2.8 30.1 + - - -
227D THR* 4.0 9.6 - - + +
230D LEU* 3.9 22.0 - - + -
231D MET* 3.5 27.1 - - + +
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Residues in contact with GLY 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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197D PRO* 3.4 3.0 - - - +
198D PRO* 1.3 77.6 - - - +
200D GLU* 1.3 57.1 + - - +
202D ALA* 3.3 4.0 + - - +
203D VAL* 3.0 31.9 + - - +
230D LEU* 3.4 24.7 + - - +
231D MET* 3.9 3.4 - - - -
234D GLY* 3.6 17.5 - - - -
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Residues in contact with GLU 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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196D VAL* 3.6 22.3 - - + +
197D PRO* 3.1 29.8 + - + +
199D GLY* 1.3 74.1 - - - +
201D CYS* 1.3 65.8 + - - +
203D VAL* 3.3 9.0 + - + +
204D ARG* 3.0 46.1 + - + +
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Residues in contact with CYS 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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164D VAL* 3.7 29.2 - - + +
185D MET* 4.0 10.8 - - - -
187D ILE* 3.9 13.5 - - + -
192D ASP* 3.9 11.9 - - - -
196D VAL* 3.5 29.2 - - - -
197D PRO 2.9 19.2 + - - -
198D PRO* 3.1 9.6 + - + +
200D GLU* 1.3 76.4 - - - +
202D ALA* 1.3 63.1 + - - +
204D ARG* 3.4 3.4 + - - +
205D LEU* 3.1 27.6 + - - +
231D MET* 4.8 2.5 - - + -
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Residues in contact with ALA 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 PRO 2.8 19.6 + - - +
199D GLY 3.5 3.4 - - - +
201D CYS* 1.3 70.5 - - - +
203D VAL* 1.3 66.5 + - - +
205D LEU* 3.1 12.0 + - - +
206D VAL* 3.0 27.0 + - - +
213D ILE* 3.9 13.2 - - + +
231D MET* 3.6 27.3 - - + +
235D LEU* 3.4 20.2 - - + -
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Residues in contact with VAL 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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199D GLY 3.0 18.1 + - - +
200D GLU* 3.3 11.2 + - + +
202D ALA* 1.3 74.0 - - - +
204D ARG* 1.3 67.9 + - + +
206D VAL* 3.1 6.1 + - - +
207D LYS* 2.9 43.1 + - + +
234D GLY* 3.5 22.4 - - - +
235D LEU* 3.5 12.1 - - + +
238D ALA* 4.0 17.0 - - + -
240D LEU* 4.5 10.0 - - + +
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Residues in contact with ARG 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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164D VAL* 4.0 28.8 - - + +
165D GLU* 4.1 19.2 - - - +
168D VAL* 3.7 24.3 - - + +
196D VAL* 4.3 7.3 - - - +
200D GLU* 3.0 42.5 + - + +
201D CYS* 3.5 8.7 - - - +
203D VAL* 1.3 80.1 - - + +
205D LEU* 1.3 59.5 + - - +
207D LYS* 3.7 11.0 + - - +
208D ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 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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164D VAL* 4.3 3.4 - - + -
167D ALA* 3.8 37.5 - - + -
168D VAL* 4.1 8.3 - - + +
171D VAL* 4.1 13.4 - - + +
183D ALA* 3.9 24.9 - - + +
185D MET* 4.1 23.1 - - + -
201D CYS* 3.1 20.6 + - + +
202D ALA* 3.1 10.2 + - - +
204D ARG* 1.3 74.6 - - - +
206D VAL* 1.3 67.6 + - - +
208D ALA* 3.3 6.7 + - - +
209D GLY 3.3 5.2 + - - -
210D ALA* 3.1 25.7 + - + +
213D ILE* 4.1 16.4 - - + -
214D GLY 5.4 1.6 - - - +
231D MET* 5.5 2.7 - - + -
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Residues in contact with VAL 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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202D ALA 3.0 16.9 + - - +
203D VAL* 3.7 6.1 - - - +
205D LEU* 1.3 75.0 - - - +
207D LYS* 1.3 58.8 + - - +
209D GLY* 2.8 22.3 + - - -
210D ALA 3.6 12.3 + - - +
213D ILE* 4.0 13.0 - - + -
235D LEU* 4.1 13.5 - - + -
240D LEU* 3.8 34.5 - - + -
241D LYS 4.0 13.7 - - - +
242D ALA* 3.5 25.4 - - + -
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Residues in contact with LYS 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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203D VAL* 2.9 39.1 + - + +
204D ARG* 3.9 11.7 - - - +
206D VAL* 1.3 76.7 - - - +
208D ALA* 1.3 57.9 + - - +
209D GLY* 2.9 6.8 + - - -
240D LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 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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168D VAL* 4.1 25.6 - - + +
171D VAL* 3.5 24.0 - - + +
172D GLU* 4.2 11.7 - - + +
175D ILE* 3.2 24.7 - - - +
204D ARG 3.2 15.5 + - - +
205D LEU* 3.7 7.4 - - - +
206D VAL 3.3 0.6 - - - -
207D LYS* 1.3 76.8 - - - +
209D GLY* 1.3 57.3 + - - +
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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