Contacts of the strand formed by residues 212 - 219 (chain C) in PDB entry 1M6X
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 GLY 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C GLN* 3.4 5.0 + - - +
208C ASN* 2.9 28.0 + - - +
210C TYR 3.6 1.6 - - - -
211C LEU* 1.3 76.2 - - - +
213C VAL* 1.3 68.2 + - - +
381C ILE* 3.7 13.9 - - - +
384C TRP* 3.9 26.9 - - - -
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 4.6 16.2 - - + -
206C VAL 3.1 20.0 - - - +
207C GLN* 4.3 9.6 - - + +
208C ASN 4.4 0.9 - - - +
211C LEU* 3.1 9.8 + - - +
212C GLY* 1.3 82.2 - - - +
214C ILE* 1.3 69.9 + - - +
233C PHE* 5.0 2.4 - - - +
234C SER* 5.5 1.4 + - - -
384C TRP* 3.4 54.2 - - + +
414C TYR* 3.8 31.9 + - + +
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Residues in contact with ILE 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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205C LEU* 3.6 3.9 - - - -
206C VAL* 2.9 45.9 + - + +
207C GLN 5.5 0.9 - - - +
208C ASN* 4.2 18.6 - - + +
211C LEU* 4.0 18.6 - - + -
213C VAL* 1.3 81.6 - - - +
215C ILE* 1.3 64.4 + - - +
216C GLN 3.7 0.2 + - - -
231C TYR* 3.4 31.9 - - + -
232C PHE 3.8 9.2 - - - +
233C PHE* 3.6 21.1 - - + +
355C PHE* 3.8 27.1 - - + -
414C TYR* 5.6 1.6 - - - -
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Residues in contact with ILE 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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203C PHE* 3.4 35.9 - - + -
204C LYS 3.3 10.8 - - - +
205C LEU* 4.2 6.3 - - + +
214C ILE* 1.3 74.4 - - - +
216C GLN* 1.3 62.1 + - - +
230C ILE 4.5 0.2 - - - -
231C TYR* 3.2 8.5 - - - +
232C PHE* 2.8 43.6 + - + +
242C LEU* 3.7 17.5 - - + -
245C LEU* 3.6 26.0 - - + -
411C VAL* 4.2 17.0 - - + -
414C TYR* 4.2 26.7 - - + -
415C LEU* 4.5 6.5 - - + -
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Residues in contact with GLN 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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202C SER 3.3 4.9 - - - +
203C PHE* 3.5 0.6 - - - -
204C LYS* 2.9 52.3 + - - +
206C VAL* 3.7 31.4 - - + +
215C ILE* 1.3 77.4 - - - +
217C CYS* 1.3 63.3 + - - +
229C HIS* 3.4 50.6 + - + -
230C ILE 3.4 2.9 - - - +
231C TYR* 3.5 30.1 + - + -
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Residues in contact with CYS 217 (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 VAL* 3.4 30.7 - - + -
202C SER* 3.7 8.5 - - - +
203C PHE* 4.0 24.7 - - + -
216C GLN* 1.3 75.9 - - - +
218C LEU* 1.3 60.8 + - - +
229C HIS* 3.1 13.6 + - - -
230C ILE* 2.8 60.1 + - - -
232C PHE* 3.9 15.7 - - - -
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Residues in contact with LEU 218 (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 VAL* 3.5 2.0 - - - -
199C ASP* 3.0 31.7 + - + +
202C SER* 2.9 27.4 + - - +
217C CYS* 1.3 75.7 - - - +
219C VAL* 1.3 71.7 + - - +
220C THR* 4.0 14.7 + - - +
227C SER* 4.3 3.8 - - - -
228C ARG 3.5 15.9 - - - +
229C HIS* 3.7 16.2 - - + +
347C ILE* 3.6 26.0 - - + -
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Residues in contact with VAL 219 (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 SER 4.1 2.9 - - - +
194C ASP 3.0 30.7 - - - +
197C ASN* 3.5 32.5 - - + +
198C VAL* 3.7 4.7 - - + -
218C LEU* 1.3 75.9 - - - +
220C THR* 1.3 65.1 + - - +
221C GLU 4.5 1.3 - - - +
222C THR* 4.0 20.5 - - + +
227C SER* 3.3 5.9 - - - -
228C ARG* 2.9 38.0 + - + +
230C ILE* 3.4 26.7 - - + -
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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