Contacts of the helix formed by residues 189 - 196 (chain C) in PDB entry 2XMR
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C PHE* 1.3 76.2 - - - +
190C GLN* 1.3 59.5 + - - +
191C GLU* 3.6 8.6 + - - +
192C GLU* 2.8 39.7 + - - +
193C LEU* 3.1 27.0 + - - +
250C GLN 4.2 15.0 - - - -
251C ALA* 4.4 3.4 - - - -
252C PRO* 3.7 23.5 - - - +
278C GLY* 5.0 2.6 - - - -
279C GLY 4.2 2.2 - - - +
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Residues in contact with GLN 190 (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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185C GLY* 4.1 15.8 + - - -
188C PHE 4.8 0.2 + - - -
189C SER* 1.3 73.1 - - - +
191C GLU* 1.3 61.0 + - - +
193C LEU* 3.3 27.6 + - - +
194C SER* 3.0 34.8 + - - -
252C PRO* 5.4 0.6 - - - +
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Residues in contact with GLU 191 (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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189C SER* 3.6 7.4 + - - +
190C GLN* 1.3 77.7 - - - +
192C GLU* 1.3 56.7 + - + +
194C SER* 3.5 6.2 + - - +
195C GLY* 3.0 25.5 + - - -
250C GLN* 5.5 6.8 - - - +
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Residues in contact with GLU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C PHE* 3.4 17.5 - - + -
189C SER* 2.8 36.6 + - - +
191C GLU* 1.3 75.1 - - + +
193C LEU* 1.3 59.8 + - - +
195C GLY* 3.4 1.6 + - - -
196C ASN 3.0 23.4 + - - -
197C SER* 4.3 0.7 + - - -
199C LEU* 5.3 1.4 - - - +
200C ILE* 3.5 26.6 - - + +
277C SER 4.1 5.0 - - - +
278C GLY* 3.7 14.5 - - - -
279C GLY 2.8 28.1 + - - -
280C GLN 4.9 0.3 + - - -
284C THR* 4.5 10.4 - - - +
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Residues in contact with LEU 193 (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 5.3 1.1 - - - +
184C LEU* 3.9 41.7 - - + +
185C GLY* 4.0 7.0 - - - +
188C PHE* 4.0 15.5 - - + +
189C SER 3.1 21.2 + - - +
190C GLN* 3.3 31.6 + - - +
192C GLU* 1.3 76.7 - - - +
194C SER* 1.3 59.1 + - - +
196C ASN* 3.6 19.6 + - - +
200C ILE* 3.8 21.1 - - + -
204C ARG* 4.0 23.9 + - - +
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Residues in contact with SER 194 (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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190C GLN 3.0 18.6 + - - -
191C GLU* 3.5 8.1 + - - +
193C LEU* 1.3 73.8 - - - +
195C GLY* 1.3 68.3 + - - +
196C ASN* 3.0 8.0 + - - +
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Residues in contact with GLY 195 (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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191C GLU 3.0 18.2 + - - -
192C GLU* 3.8 1.6 - - - -
194C SER* 1.3 77.5 + - - +
196C ASN* 1.3 67.0 + - - +
197C SER* 3.6 3.2 + - - -
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Residues in contact with ASN 196 (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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192C GLU 3.0 13.3 + - - -
193C LEU 3.8 6.6 + - - +
194C SER 3.0 8.9 - - - +
195C GLY* 1.3 80.7 - - - +
197C SER* 1.3 58.1 + - - +
200C ILE* 3.9 7.8 - - - +
201C GLN* 2.9 47.3 + - - +
204C ARG* 3.1 29.9 - - - +
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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