Contacts of the helix formed by residues 197 - 208 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C GLU 4.7 2.7 - - - +
191C GLY* 4.1 2.5 - - - -
195C GLY 3.4 8.3 - - - +
196C VAL* 1.3 92.1 - - + +
198C PRO* 1.3 78.3 - - + +
199C GLY 3.3 2.9 - - - +
200C GLU* 3.3 16.3 + - + +
201C CYS* 3.0 18.8 + - - -
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Residues in contact with PRO 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ILE* 4.5 4.3 - - + -
188C GLY 3.7 16.2 - - - +
189C PRO* 3.5 28.0 - - + +
190C GLU 4.5 0.2 - - - -
191C GLY* 3.9 6.3 - - - +
196C VAL 3.9 0.4 - - - -
197C PRO* 1.3 88.7 - - + +
199C GLY* 1.3 57.4 + - - +
201C CYS* 3.1 10.8 + - + +
202C ALA* 2.9 30.7 + - - +
227C THR* 4.1 9.4 - - + +
230C LEU* 3.9 24.2 - - + -
231C MET* 3.7 24.2 - - + +
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Residues in contact with GLY 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C PRO* 3.3 3.4 - - - +
198C PRO* 1.3 80.1 - - - +
200C GLU* 1.3 58.7 + - - +
202C ALA* 3.3 3.6 + - - +
203C VAL* 3.0 30.7 + - - +
230C LEU* 3.3 23.1 + - - +
231C MET* 4.1 2.2 - - - -
234C GLY* 3.8 16.5 - - - -
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 4.1 12.3 - - + -
197C PRO* 3.3 19.0 + - + +
199C GLY* 1.3 73.0 - - - +
201C CYS* 1.3 65.3 + - - +
203C VAL* 4.0 21.3 - - - +
204C ARG* 3.0 51.9 + - - +
207C LYS* 4.5 5.2 + - - -
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Residues in contact with CYS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL* 3.8 24.5 - - + +
185C MET* 4.0 15.7 - - - -
187C ILE* 3.9 19.7 - - + -
192C ASP* 4.0 6.7 - - - -
196C VAL* 3.7 27.1 - - - -
197C PRO 3.0 17.6 + - - +
198C PRO* 3.1 11.4 + - + +
200C GLU* 1.3 76.4 - - - +
202C ALA* 1.3 62.4 + - - +
204C ARG* 3.2 4.0 + - - +
205C LEU* 3.1 29.0 + - - +
231C MET* 4.8 2.9 - - + -
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PRO 2.9 12.2 + - - +
199C GLY 3.5 8.5 - - - +
201C CYS* 1.3 74.9 - - - +
203C VAL* 1.3 64.6 + - - +
205C LEU* 3.2 9.9 + - - +
206C VAL* 3.0 27.4 + - - +
213C ILE* 3.8 17.3 - - + -
231C MET* 3.8 35.6 - - + +
235C LEU* 3.8 8.1 - - + -
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLY 3.0 20.5 + - - +
200C GLU* 3.7 24.0 - - - +
201C CYS 3.3 0.2 - - - -
202C ALA* 1.3 77.1 - - - +
204C ARG* 1.3 57.0 + - - +
206C VAL* 3.5 1.6 + - - +
207C LYS* 3.0 53.6 + - + +
234C GLY* 3.4 26.5 - - - +
235C LEU* 4.0 9.6 - - + -
238C ALA* 3.6 17.7 - - + -
240C LEU* 4.0 12.3 - - + +
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Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL* 3.8 32.5 - - + +
165C GLU* 4.8 12.9 - - - +
168C VAL* 3.9 19.7 - - + +
196C VAL* 4.1 18.8 - - - +
200C GLU* 3.0 43.6 + - - +
201C CYS 3.9 3.1 - - - +
203C VAL* 1.3 76.2 - - - +
205C LEU* 1.3 57.1 + - - +
207C LYS* 3.5 16.4 + - - +
208C ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL* 4.5 3.1 - - + -
167C ALA* 3.7 36.3 - - + -
168C VAL* 4.1 8.3 - - + +
171C VAL* 4.1 14.0 - - + +
183C ALA* 4.2 20.4 - - + +
184C THR* 5.5 0.2 - - - -
185C MET* 4.0 27.6 - - + -
201C CYS* 3.1 18.9 + - + +
202C ALA* 3.2 8.5 + - - +
204C ARG* 1.3 74.5 - - - +
206C VAL* 1.3 63.2 + - - +
208C ALA* 3.2 7.3 + - - +
209C GLY 3.2 6.4 + - - -
210C ALA* 2.9 28.1 + - + +
213C ILE* 3.8 16.8 - - + -
214C GLY 5.5 1.8 - - - +
231C MET* 5.6 3.4 - - + -
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ALA 3.0 17.0 + - - +
203C VAL 3.9 2.9 - - - +
205C LEU* 1.3 76.5 - - - +
207C LYS* 1.3 64.1 + - - +
209C GLY* 2.9 16.5 + - - -
210C ALA 3.5 16.8 + - - +
213C ILE* 4.0 11.0 - - + -
235C LEU* 3.7 14.6 - - + -
240C LEU* 4.0 30.5 - - + -
241C LYS 4.3 12.6 - - - +
242C ALA* 3.6 26.0 - - + -
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Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLU* 4.5 4.8 + - - -
203C VAL* 3.0 46.3 + - + +
204C ARG* 3.8 19.5 - - - +
206C VAL* 1.3 76.6 - - - +
208C ALA* 1.3 61.1 + - - +
209C GLY* 3.2 2.1 + - - -
240C LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C VAL* 3.9 24.7 - - + -
171C VAL* 3.5 22.7 - - + +
172C GLU* 4.3 13.7 - - + +
175C ILE* 3.3 21.0 - - - +
204C ARG 2.9 19.0 + - - +
205C LEU* 3.5 9.0 - - - +
206C VAL 3.2 0.2 - - - -
207C LYS* 1.3 75.6 - - - +
209C GLY* 1.3 55.4 + - - +
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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