Contacts of the helix formed by residues 206 - 216 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LYS 4.2 6.0 + - - -
203A CYS* 4.4 6.1 - - - -
204A PHE 3.3 5.1 - - - +
205A GLU* 1.3 78.1 - - - +
207A PRO* 1.3 60.6 - - - +
208A TRP* 3.2 17.1 + - - +
209A THR* 2.6 40.7 + - - +
280A ASP* 4.0 9.3 + - - +
283A GLN* 5.8 2.2 - - - +
284A ALA* 4.0 20.4 + - - +
287A LEU* 5.6 3.8 - - - -
437A PHE* 5.0 3.8 - - - -
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Residues in contact with PRO 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU 3.6 8.7 - - - +
206A SER* 1.3 80.1 - - - +
208A TRP* 1.3 59.6 + - - +
209A THR 3.2 0.7 - - - -
210A THR* 3.2 18.1 - - + +
211A LYS* 3.0 26.3 + - - +
277A ASP 6.3 0.9 - - - +
280A ASP* 3.3 26.7 - - + +
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Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A SER* 3.2 9.3 - - - +
207A PRO* 1.3 77.5 - - - +
209A THR* 1.3 70.1 + - + +
211A LYS* 3.5 31.5 - - - +
212A ALA* 2.8 43.8 + - + +
280A ASP* 3.2 27.7 + - + +
281A GLY 5.5 0.2 - - - +
284A ALA* 4.8 0.7 - - + -
288A PHE* 4.3 10.1 - + - -
436A VAL* 5.5 4.5 - - + -
437A PHE* 4.3 17.7 - + - -
442A SER* 3.1 40.6 - - - -
445A LYS* 4.6 9.8 - - + +
446A LEU* 3.5 49.9 - - + +
449A ILE* 5.5 6.4 - - + +
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A CYS 4.4 8.8 + - - +
204A PHE 5.1 1.7 + - - -
206A SER* 2.6 30.5 + - - +
208A TRP* 1.3 87.6 - - + +
210A THR* 1.3 63.7 + - - +
212A ALA* 3.4 2.1 + - - +
213A LEU* 2.9 37.6 + - - +
433A ARG* 3.9 30.8 - - - +
436A VAL* 5.7 4.3 - - + -
437A PHE* 3.7 32.5 - - + +
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A SER 5.1 0.2 - - - +
207A PRO* 3.2 27.6 - - + +
209A THR* 1.3 80.4 + - - +
211A LYS* 1.3 60.4 + - - +
213A LEU* 3.8 7.4 - - - +
214A SER* 2.9 28.1 + - - -
433A ARG* 5.5 1.1 - - - +
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Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO 3.0 18.3 + - - +
208A TRP* 3.2 32.6 + - - +
210A THR* 1.3 78.3 - - - +
212A ALA* 1.3 55.8 + - - +
214A SER* 2.3 28.0 + - - +
215A GLU* 2.9 14.0 + - + +
277A ASP* 3.5 32.9 + - - +
280A ASP* 5.4 2.8 + - - -
449A ILE* 4.9 14.0 - - - +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TRP* 2.8 49.1 + - + +
209A THR* 3.9 4.5 - - - +
211A LYS* 1.3 73.9 - - - +
213A LEU* 1.3 54.3 + - + +
215A GLU* 3.4 12.0 + - - +
216A THR* 2.6 37.5 + - - +
409A ILE* 5.4 0.6 - - + +
436A VAL* 5.5 3.4 - - + -
442A SER* 5.0 3.1 - - - +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A THR* 2.9 28.8 + - - +
210A THR* 3.9 8.5 - - - +
212A ALA* 1.3 77.2 - - + +
214A SER* 1.3 63.1 + - - +
215A GLU 3.2 0.4 - - - -
216A THR* 3.4 27.9 + - - +
407A SER 6.1 0.9 - - - +
409A ILE* 5.8 0.7 - - + -
432A LYS* 5.5 10.3 - - + -
433A ARG* 5.6 7.6 - - + -
436A VAL* 3.7 42.6 - - + -
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 2.9 15.6 + - - -
211A LYS* 2.3 34.0 + - - +
213A LEU* 1.3 76.5 - - - +
215A GLU* 1.3 59.2 + - - +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 2.9 12.6 + - - +
212A ALA* 3.6 12.4 - - - +
214A SER* 1.3 81.2 + - - +
216A THR* 1.3 70.0 + - - +
445A LYS* 6.0 3.0 - - - -
449A ILE* 5.9 2.8 - - - +
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA 2.6 23.9 + - - +
213A LEU* 3.4 34.1 - - - +
215A GLU* 1.3 85.2 + - - +
407A SER 4.8 1.8 - - - +
408A ASP* 3.6 31.4 - - + +
409A ILE* 3.4 36.4 - - + +
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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