Contacts of the helix formed by residues 203 - 210 (chain M) in PDB entry 6G0L
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 203 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201M VAL* 3.4 7.9 + - + +
202M PRO* 1.3 75.9 - - - +
204M LEU* 1.3 64.8 + - - +
205M ASN* 3.0 31.7 + - - +
206M ASN* 2.8 26.2 + - - +
207M CYS* 3.2 21.8 + - - -
250M ILE* 4.2 7.6 - - - -
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Residues in contact with LEU 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ASP* 1.3 74.9 + - - +
205M ASN* 1.3 63.3 + - - +
207M CYS* 3.1 11.2 + - + +
208M LYS* 2.9 59.7 + - + +
230M TYR* 3.9 16.6 - - + -
243M ASP* 4.6 20.9 - - + +
246M CYS* 6.2 5.2 - - + -
250M ILE* 4.6 4.2 - - + +
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Residues in contact with ASN 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ASP* 3.0 20.3 + - - +
204M LEU* 1.3 79.6 - - - +
206M ASN* 1.3 58.7 + - - +
208M LYS* 3.0 30.7 + - - +
209M GLU* 2.9 32.6 + - + +
210M ASN* 4.5 0.2 - - - +
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Residues in contact with ASN 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M LYS* 3.5 24.9 - - - +
202M PRO* 3.8 16.4 - - + -
203M ASP* 2.8 30.4 + - - +
204M LEU 3.3 0.2 - - - -
205M ASN* 1.3 78.5 - - - +
207M CYS* 1.3 57.3 + - - +
210M ASN* 2.6 56.8 + - + +
211M TYR* 3.2 6.6 - - + -
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Residues in contact with CYS 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M PRO* 4.7 3.8 - - - -
203M ASP 3.2 17.0 + - - -
204M LEU* 3.1 15.1 + - + +
206M ASN* 1.3 77.4 - - - +
208M LYS* 1.3 59.2 + - + +
211M TYR* 2.9 39.3 - - - +
213M PHE* 3.3 29.0 - - + -
229M THR* 4.9 0.3 - - - +
230M TYR* 6.2 1.8 - - + -
246M CYS* 4.7 13.9 - - + -
249M PHE* 5.1 8.3 - - - -
250M ILE* 4.3 21.8 - - - -
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Residues in contact with LYS 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LYS* 2.5 29.8 + - - -
204M LEU* 2.9 30.4 + - + +
205M ASN* 3.0 39.1 + - - +
207M CYS* 1.3 81.5 - - - +
209M GLU* 1.3 65.0 + - + +
210M ASN 3.3 1.3 - - - -
211M TYR 4.0 2.9 - - - +
229M THR* 4.2 6.4 - - - +
230M TYR* 3.5 34.5 - - + -
231M GLU* 3.5 15.8 - - - +
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Residues in contact with GLU 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LYS* 3.5 17.0 + - - +
189M THR* 3.4 14.7 - - - +
205M ASN* 2.9 15.4 + - + +
208M LYS* 1.3 91.0 + - + +
210M ASN* 1.3 74.3 + - - +
231M GLU* 4.1 20.1 - - - +
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Residues in contact with ASN 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M LEU* 3.7 4.7 - - - +
188M LYS* 3.1 20.2 + - - -
189M THR* 2.9 32.7 + - - +
205M ASN 4.5 0.3 - - - +
206M ASN* 2.6 46.6 + - + +
208M LYS 3.3 0.6 - - - -
209M GLU* 1.3 88.0 + - - +
211M TYR* 1.3 79.2 + - + +
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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