Contacts of the helix formed by residues 198 - 212 (chain C) in PDB entry 5H1C
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 ASP 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ASN* 3.1 7.9 - - + +
197C THR* 1.3 87.0 + - - +
199C HIS* 1.3 61.9 + - - +
201C THR* 2.2 38.3 + - - +
202C GLN* 3.6 4.7 + - - +
232C TYR* 4.7 2.9 + - - -
244C HIS* 3.6 20.1 + - - -
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Residues in contact with HIS 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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193C ARG 3.4 22.2 - - - -
194C ALA* 3.3 6.7 - - + -
195C PHE* 3.3 25.4 + + - +
196C ASN* 3.1 28.6 + - + +
198C ASP* 1.3 80.2 - - - +
200C GLN* 1.3 62.6 + - - +
202C GLN* 3.1 24.5 + - + -
203C LEU* 3.0 42.9 + - + +
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Residues in contact with GLN 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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160C ILE* 5.4 5.7 - - + +
162C THR* 3.4 18.9 - - + +
194C ALA* 4.0 15.9 - - + -
196C ASN 4.1 0.4 - - - +
197C THR 3.7 9.2 - - - +
198C ASP 3.2 0.6 - - - -
199C HIS* 1.3 78.0 - - - +
201C THR* 1.3 56.6 + - - +
203C LEU* 3.3 11.4 + - + +
204C LEU* 2.9 32.8 + - - +
221C VAL* 5.2 1.8 - - - +
223C SER 3.9 3.4 + - - -
224C ALA* 3.7 18.5 + - - +
227C LEU* 3.3 29.0 - - + +
228C TYR* 3.6 27.7 + - - -
248C PHE* 3.9 24.4 - - + -
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Residues in contact with THR 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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197C THR 4.3 0.2 - - - +
198C ASP* 2.2 31.8 + - - +
200C GLN* 1.3 76.2 - - + +
202C GLN* 1.3 68.4 + - - +
204C LEU* 2.8 25.8 + - + +
205C TYR* 2.9 32.7 + - - -
244C HIS* 3.8 33.2 - - + +
248C PHE* 5.2 7.0 - - + -
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Residues in contact with GLN 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 ASP 4.3 5.4 - - - +
199C HIS* 3.1 25.1 + - + +
201C THR* 1.3 87.6 + - - +
203C LEU* 1.3 59.0 + - + +
205C TYR* 3.3 11.0 + - + +
206C GLN* 2.9 39.9 + - + +
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Residues in contact with LEU 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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160C ILE* 4.2 27.0 - - + +
192C ALA* 4.5 18.2 - - + -
193C ARG 4.6 2.0 - - - +
194C ALA* 3.6 35.4 - - + +
199C HIS* 3.0 40.8 + - + +
200C GLN* 3.5 9.9 - - - +
201C THR 3.1 0.2 - - - -
202C GLN* 1.3 78.5 - - + +
204C LEU* 1.3 57.4 + - - +
206C GLN* 3.6 20.5 + - - +
207C ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 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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160C ILE* 4.6 16.8 - - + -
200C GLN 2.9 17.3 + - - +
201C THR* 2.8 14.7 + - + +
203C LEU* 1.3 75.6 - - - +
205C TYR* 1.3 68.1 + - + +
207C ALA* 3.0 6.2 + - + +
208C SER* 2.9 23.0 + - - -
219C LEU* 5.2 2.2 - - + -
221C VAL* 6.3 0.4 - - + -
248C PHE* 3.6 36.3 - - + +
251C MET* 3.8 36.3 - - + -
252C LEU* 3.8 23.3 - - + -
255C LEU* 4.4 16.6 - - + +
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Residues in contact with TYR 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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44C ALA 3.4 25.8 - - - -
45C GLY* 3.8 14.7 - - - -
47C HIS* 4.7 2.4 + - - -
59C GLU* 4.7 9.7 + - - -
201C THR* 2.9 42.2 + - - -
202C GLN* 3.3 8.5 + - + +
204C LEU* 1.3 77.5 - - + +
206C GLN* 1.3 58.7 + - + +
208C SER* 2.5 23.0 + - - -
209C ALA* 2.9 13.9 + - - +
251C MET* 4.5 30.4 - - + +
254C ARG* 5.0 5.4 - - - -
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Residues in contact with GLN 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 GLN* 2.9 24.7 + - + +
203C LEU* 3.9 22.5 - - + +
205C TYR* 1.3 73.2 - - + +
207C ALA* 1.3 61.2 + - - +
209C ALA* 3.2 10.2 + - - +
210C MET* 2.9 33.7 + - + +
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Residues in contact with ALA 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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158C MET* 4.8 15.5 - - - -
160C ILE* 5.4 2.7 - - + -
203C LEU 2.9 16.4 + - - +
204C LEU* 3.0 13.9 + - + +
206C GLN* 1.3 77.1 - - - +
208C SER* 1.3 59.0 + - - +
210C MET* 2.8 24.3 + - - +
211C MET* 2.9 19.3 + - + +
219C LEU* 4.8 10.8 - - + -
255C LEU* 4.7 12.1 - - + -
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Residues in contact with SER 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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45C GLY 3.3 21.7 + - - -
47C HIS* 3.8 8.7 - - - +
48C THR* 5.9 0.2 - - - +
204C LEU 2.9 9.2 + - - -
205C TYR* 2.5 29.3 + - - -
207C ALA* 1.3 75.6 - - - +
209C ALA* 1.3 61.2 + - - +
211C MET* 3.3 23.9 + - - +
212C VAL* 3.9 7.4 - - - +
251C MET* 6.4 2.0 - - - -
254C ARG* 6.6 0.2 - - - -
255C LEU* 3.9 18.3 - - - +
259C PHE* 5.1 4.0 - - - -
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C HIS* 3.5 26.6 - - + +
205C TYR 2.9 13.4 + - - +
206C GLN* 3.3 13.9 - - - +
208C SER* 1.3 80.0 + - - +
210C MET* 1.3 63.3 + - + +
211C MET 3.5 0.5 + - - -
212C VAL* 3.8 14.7 + - - +
213C GLU* 4.7 6.9 - - - +
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Residues in contact with MET 210 (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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158C MET* 5.1 2.2 - - + -
206C GLN* 2.9 17.9 + - + +
207C ALA* 2.8 12.1 + - - +
209C ALA* 1.3 76.1 - - + +
211C MET* 1.3 65.6 + - - +
212C VAL 3.1 3.8 + - - -
213C GLU* 3.5 38.4 + - + +
214C SER* 4.2 7.4 + - - +
216C TYR* 4.6 29.8 - - + +
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Residues in contact with MET 211 (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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158C MET* 3.2 38.1 - - + +
207C ALA* 2.9 20.1 + - - +
208C SER* 3.5 16.4 - - - +
209C ALA 3.3 0.8 - - - -
210C MET* 1.3 79.1 - - - +
212C VAL* 1.3 61.7 + - - +
213C GLU 3.2 0.6 + - - -
214C SER 4.0 14.1 + - - +
215C ARG* 4.8 2.6 + - - +
216C TYR* 4.2 7.6 - - + +
219C LEU* 5.8 5.6 - - + -
255C LEU* 4.7 10.3 - - + -
259C PHE* 3.4 57.7 - - + -
261C VAL* 4.1 18.8 - - + -
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Residues in contact with VAL 212 (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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24C PRO* 4.8 15.5 - - + -
47C HIS* 3.5 42.0 - - + +
48C THR* 4.4 12.1 - - + -
208C SER 3.9 4.7 - - - +
209C ALA 3.9 14.1 - - - +
210C MET 3.1 0.6 - - - -
211C MET* 1.3 79.2 - - + +
213C GLU* 1.3 67.7 + - + +
259C PHE* 6.0 0.2 - - - -
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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