Contacts of the helix formed by residues 206 - 216 (chain C) in PDB entry 6M04
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 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B LYS* 5.5 2.9 + - - -
202C LYS 3.6 13.1 + - - -
204C PHE 3.2 6.0 + - - +
205C GLU* 1.3 77.0 - - - +
207C PRO* 1.3 68.1 - - - +
208C TRP* 3.3 16.1 + - - +
209C THR* 2.4 47.3 + - - +
210C THR* 3.7 4.5 + - - +
280C ASP* 5.4 1.7 + - - +
283C GLN* 6.0 1.7 - - - +
284C ALA* 4.6 10.4 + - - +
287C LEU* 4.8 9.4 - - - -
437C PHE* 5.6 0.2 - - - -
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Residues in contact with PRO 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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289B GLU* 4.5 15.4 - - - +
293B LYS* 5.5 4.0 - - - +
205C GLU 3.7 6.7 - - - +
206C SER* 1.3 86.7 - - - +
208C TRP* 1.3 60.1 + - - +
209C THR 3.2 0.2 - - - -
210C THR* 3.2 13.4 - - + +
211C LYS* 3.0 26.6 + - - +
280C ASP* 4.6 15.7 - - + -
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Residues in contact with TRP 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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206C SER* 3.3 8.9 + - - +
207C PRO* 1.3 78.8 - - - +
209C THR* 1.3 66.0 + - + +
211C LYS* 3.8 25.0 - - + +
212C ALA* 2.9 37.3 + - + +
280C ASP* 3.9 19.7 - - + +
284C ALA* 4.0 14.6 - - + -
288C PHE* 3.4 26.9 - + - -
437C PHE* 3.9 22.2 - + - -
442C SER* 3.1 45.8 - - - -
445C LYS* 4.2 13.5 - - + +
446C LEU* 3.4 42.3 - - + +
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Residues in contact with THR 209 (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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203C CYS 3.7 17.7 + - - +
204C PHE 4.3 3.8 + - - -
206C SER* 2.4 44.5 + - - +
208C TRP* 1.3 81.8 - - + +
210C THR* 1.3 59.7 + - - -
212C ALA* 3.3 4.7 + - - +
213C LEU* 2.9 36.5 + - - +
433C ARG* 4.2 21.2 - - - +
436C VAL* 6.4 0.2 - - - -
437C PHE* 3.6 34.5 - - + -
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Residues in contact with THR 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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289B GLU* 4.4 13.0 - - + +
293B LYS* 4.1 28.7 + - - +
206C SER 4.3 1.8 - - - +
207C PRO* 3.2 25.1 - - + +
209C THR* 1.3 81.7 + - - +
211C LYS* 1.3 61.1 + - - +
213C LEU* 3.6 9.3 - - - +
214C SER* 2.9 26.5 + - - -
433C ARG* 5.9 0.8 - - - +
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Residues in contact with LYS 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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289B GLU* 6.1 0.4 - - - +
207C PRO 3.0 17.8 + - - +
208C TRP* 3.6 24.6 - - - +
209C THR 3.2 0.2 - - - -
210C THR* 1.3 76.7 - - + +
212C ALA* 1.3 58.7 + - - +
214C SER* 2.4 30.3 + - - +
215C GLU* 3.0 12.8 + - - +
277C ASP* 2.5 36.0 + - - +
280C ASP* 3.2 13.8 + - - -
446C LEU* 5.2 3.2 - - - +
449C ILE* 5.8 2.8 - - - +
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Residues in contact with ALA 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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208C TRP* 2.9 31.2 + - + +
209C THR* 3.8 5.4 - - - +
211C LYS* 1.3 77.4 - - - +
213C LEU* 1.3 60.6 + - - +
215C GLU* 3.4 14.6 + - - +
216C THR* 3.4 18.4 + - - +
409C ILE* 5.2 3.1 - - - +
436C VAL* 4.6 11.7 - - + +
442C SER* 4.3 18.4 - - - +
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Residues in contact with LEU 213 (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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209C THR* 2.9 29.2 + - - +
210C THR* 3.8 9.0 - - - +
212C ALA* 1.3 78.1 - - - +
214C SER* 1.3 58.7 + - - +
216C THR 2.9 37.4 - - - +
407C SER* 4.7 5.4 - - - +
409C ILE* 6.1 0.2 - - + -
432C LYS* 5.5 7.0 - - + +
433C ARG* 4.8 20.9 - - + +
436C VAL* 3.8 42.2 - - + -
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Residues in contact with SER 214 (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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210C THR 2.9 14.6 + - - -
211C LYS* 2.4 35.0 + - - +
213C LEU* 1.3 74.3 - - - +
215C GLU* 1.3 65.0 + - - +
216C THR* 4.6 0.5 - - - -
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Residues in contact with GLU 215 (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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211C LYS 3.0 10.5 + - - +
212C ALA* 3.6 15.3 - - - +
213C LEU 3.3 0.4 - - - -
214C SER* 1.3 80.0 + - - +
216C THR* 1.3 67.0 + - - +
445C LYS* 5.1 14.9 - - - +
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Residues in contact with THR 216 (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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212C ALA 3.4 5.0 + - - -
213C LEU* 2.9 38.1 - - - +
214C SER 3.3 0.6 - - - -
215C GLU* 1.3 91.3 + - - +
407C SER* 3.6 25.6 + - - +
408C ASP* 4.1 17.1 + - + +
409C ILE* 3.9 19.6 - - + +
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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