Contacts of the helix formed by residues 197 - 209 (chain C) in PDB entry 2XMQ
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 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 4.6 8.5 - - - -
192C GLU 4.4 0.2 + - - -
195C GLY 3.3 4.4 + - - -
196C ASN* 1.3 82.1 - - - +
198C GLU* 1.3 65.4 + - - +
199C LEU* 3.3 9.9 + - - +
200C ILE* 3.3 27.3 + - - +
201C GLN* 3.1 20.2 + - - +
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Residues in contact with GLU 198 (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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28A SER* 5.6 2.6 + - - +
30A GLU* 3.7 33.8 + - + +
197C SER* 1.3 76.6 - - - +
199C LEU* 1.3 61.9 + - - +
201C GLN* 3.4 20.9 + - - +
202C LYS* 3.2 21.5 + - - +
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Residues in contact with LEU 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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188C PHE* 4.6 15.0 - - + -
192C GLU* 5.9 0.2 - - - +
197C SER* 3.3 8.3 + - - +
198C GLU* 1.3 77.1 - - - +
200C ILE* 1.3 69.2 + - + +
202C LYS* 3.0 13.6 + - + +
203C TYR* 2.9 50.7 + - + +
283C LEU* 4.5 24.2 - - + +
284C THR* 4.1 26.9 - - + -
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Residues in contact with ILE 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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184C LEU* 5.1 1.5 - - + +
188C PHE* 3.5 43.3 - - + -
192C GLU* 3.3 42.0 - - + +
193C LEU* 4.0 15.9 - - + +
196C ASN* 3.8 7.2 - - - +
197C SER* 3.3 24.0 + - - +
199C LEU* 1.3 79.5 - - + +
201C GLN* 1.3 57.7 + - - +
203C TYR* 4.1 3.9 - - - +
204C ARG* 2.9 51.4 + - + +
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Residues in contact with GLN 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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196C ASN* 2.9 44.7 + - - +
197C SER 3.1 16.8 + - - +
198C GLU* 3.6 21.0 + - - +
199C LEU 3.1 0.2 - - - -
200C ILE* 1.3 75.5 - - - +
202C LYS* 1.3 62.1 + - - +
204C ARG* 3.6 7.2 + - - +
205C ASN* 3.2 23.4 + - - +
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Residues in contact with LYS 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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67C PRO* 6.2 2.2 - - - +
198C GLU 3.2 11.0 + - - +
199C LEU* 3.2 15.8 - - + +
201C GLN* 1.3 79.3 - - - +
203C TYR* 1.3 80.1 + - + +
205C ASN* 3.2 8.8 + - - +
206C ILE* 2.9 40.0 + - + +
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Residues in contact with TYR 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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59C LEU* 3.9 26.5 - - + -
63C SER* 2.7 38.0 + - - -
67C PRO* 4.9 3.5 - - - +
184C LEU* 4.0 4.5 - - + -
188C PHE* 3.9 31.4 - + + -
199C LEU* 2.9 45.2 + - + +
200C ILE 4.1 2.7 - - - +
202C LYS* 1.3 95.4 + - + +
204C ARG* 1.3 65.9 + - - +
205C ASN 3.0 1.3 - - - -
206C ILE* 4.1 14.4 - - + +
207C ILE* 3.0 31.3 + - + +
283C LEU* 3.2 25.5 - - + +
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Residues in contact with ARG 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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181C GLU* 3.2 33.5 + - - +
184C LEU* 3.8 19.2 - - + +
193C LEU* 4.1 31.0 + - - +
196C ASN* 3.5 23.6 + - - -
200C ILE* 2.9 34.4 + - - +
201C GLN* 3.7 7.4 - - - +
203C TYR* 1.3 71.2 - - - +
205C ASN* 1.3 58.8 + - - +
207C ILE* 4.3 0.3 - - - +
208C THR* 2.8 46.8 + - - +
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Residues in contact with ASN 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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201C GLN 3.2 11.1 + - - +
202C LYS* 3.2 12.4 + - - +
203C TYR 3.0 0.6 - - - -
204C ARG* 1.3 78.8 - - + +
206C ILE* 1.3 69.2 + - - +
207C ILE 3.1 1.3 - - - -
208C THR* 4.7 0.2 - - - -
209C HIS* 3.0 51.2 + - - +
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Residues in contact with ILE 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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58C GLY 4.3 10.8 - - - +
59C LEU* 5.2 2.7 - - + -
63C SER* 4.1 21.1 - - - +
202C LYS* 2.9 35.6 + - + +
203C TYR* 3.3 38.3 + - + +
205C ASN* 1.3 76.6 + - - +
207C ILE* 1.3 68.0 + - + +
209C HIS 3.9 0.6 - - - -
210C ALA* 3.1 31.2 + - + +
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Residues in contact with ILE 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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58C GLY* 3.9 22.7 - - - +
59C LEU* 4.4 4.9 - - + -
180C PRO* 4.1 25.8 - - + +
183C ILE* 4.0 20.9 - - + -
184C LEU* 4.1 14.4 - - + -
187C LEU* 3.5 32.1 - - + -
203C TYR* 3.0 19.2 + - + +
204C ARG 4.3 0.9 - - - +
206C ILE* 1.3 80.2 - - + +
208C THR* 1.4 66.5 + - - +
210C ALA* 3.2 18.5 + - - +
213C LEU* 3.8 17.9 - - + +
216C ILE* 5.3 2.5 - - + -
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Residues in contact with THR 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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180C PRO* 3.7 27.5 - - + +
181C GLU* 4.8 3.5 + - - -
184C LEU* 4.6 1.9 - - - +
204C ARG* 2.8 39.3 + - - +
207C ILE* 1.4 75.0 - - - +
209C HIS* 1.3 81.3 + - + +
210C ALA 3.7 0.9 + - - +
213C LEU* 4.3 12.6 - - - +
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Residues in contact with HIS 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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205C ASN* 3.0 47.5 + - - +
206C ILE 3.9 2.0 - - - -
208C THR* 1.3 91.7 + - + +
210C ALA* 1.3 66.2 + - - +
211C PRO* 3.1 9.0 - - - +
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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