Contacts of the helix formed by residues 213 - 220 (chain A) in PDB entry 5LCM
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 CYS 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A CYS* 3.4 10.4 - - + +
194A CYS* 4.0 0.2 - - - -
197A ASN* 3.3 32.8 - - + +
199A GLU 3.5 17.0 - - - +
200A MET* 4.0 0.6 - - - +
201A ASP* 3.7 7.0 - - - +
212A VAL* 1.3 81.9 - - - +
214A LYS* 1.3 60.9 + - - +
215A GLN* 3.7 6.1 - - - +
216A CYS* 3.4 18.6 + - - -
217A SER* 2.9 25.6 + - - -
401A ZN 2.3 35.7 - - - -
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Residues in contact with LYS 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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199A GLU 4.7 0.8 + - - -
200A MET 4.7 0.8 - - - -
201A ASP* 3.2 40.4 + - + +
202A PRO* 5.3 4.5 - - + -
213A CYS* 1.3 73.9 - - - +
215A GLN* 1.3 62.1 + - - +
217A SER* 2.4 28.0 + - - +
218A LYS* 3.2 35.0 + - + +
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Residues in contact with GLN 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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197A ASN* 4.4 11.9 + - - +
213A CYS* 3.3 10.5 - - - +
214A LYS* 1.3 78.5 - - - +
216A CYS* 1.3 60.2 + - - +
218A LYS* 3.3 10.2 + - - +
219A GLU* 3.0 61.2 + - + +
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 3.7 25.1 - - + -
194A CYS* 3.4 18.8 - - - -
212A VAL* 4.0 7.9 - - + -
213A CYS* 3.4 8.0 - - - +
214A LYS 3.3 0.2 - - - -
215A GLN* 1.3 77.8 - - - +
217A SER* 1.3 65.2 + - - +
219A GLU* 3.2 14.9 + - - -
220A HIS* 3.0 30.8 + - + +
224A TYR* 3.9 0.4 - - - -
401A ZN 2.3 36.1 - - - -
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Residues in contact with SER 217 (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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201A ASP* 4.9 1.8 - - - -
204A LEU* 3.3 33.4 - - - +
212A VAL* 4.0 1.5 - - - +
213A CYS 2.9 11.8 + - - -
214A LYS* 2.4 30.0 + - - +
216A CYS* 1.3 78.9 - - - +
218A LYS* 1.3 68.7 + - - +
220A HIS 3.3 18.2 + - - +
221A PRO* 3.7 3.5 - - - +
224A TYR* 3.7 21.0 - - - +
225A ALA* 5.8 0.2 - - - -
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Residues in contact with LYS 218 (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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214A LYS* 3.2 41.6 + - + +
215A GLN* 3.7 9.2 - - - +
217A SER* 1.3 84.1 + - - +
219A GLU* 1.3 63.1 + - + +
221A PRO* 3.4 15.9 - - - +
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Residues in contact with GLU 219 (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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215A GLN* 3.0 52.8 + - + +
216A CYS* 3.2 17.5 + - - +
218A LYS* 1.3 78.6 - - + +
220A HIS* 1.3 79.8 + - + +
221A PRO* 3.5 6.2 - - - +
222A GLU* 4.2 1.6 - - - +
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Residues in contact with HIS 220 (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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193A GLU* 4.0 31.7 + - + +
216A CYS* 3.0 22.0 + - + +
217A SER 3.3 4.4 + - - -
219A GLU* 1.3 95.2 + - + +
221A PRO* 1.4 62.5 - - - +
222A GLU* 2.9 30.3 + - - +
223A LYS* 3.0 17.9 + - + -
224A TYR* 3.1 23.9 + - + -
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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