Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 2G19
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 TYR 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.0 36.0 + - + +
195A LEU 3.4 1.2 - - - -
196A GLU* 1.3 83.9 - - + +
198A ILE* 1.3 66.2 + - - +
199A VAL 3.4 1.1 - - - -
200A PRO* 3.3 3.7 - - + +
201A CYS* 2.9 46.8 + - + +
208A CYS* 3.5 20.4 - - - -
209A VAL* 3.1 31.7 + - - +
210A VAL* 4.0 5.8 - - + -
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Residues in contact with ILE 198 (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 LEU* 3.0 34.9 + - + +
194A ALA* 3.8 17.0 - - + +
197A TYR* 1.3 71.9 - - - +
199A VAL* 1.3 59.4 + - - +
201A CYS* 3.7 0.3 - - - +
202A MET* 2.8 50.3 + - + +
208A CYS* 3.8 17.0 - - - -
210A VAL* 4.4 6.3 - - + -
279A LEU* 3.9 21.8 - - + -
280A ILE* 6.4 0.4 - - + -
283A CYS* 4.0 15.9 - - - -
287A LEU* 4.8 3.1 - - + -
365A PHE* 3.9 34.3 - - + -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 2.9 24.8 + - - +
195A LEU* 4.4 5.6 - - + +
198A ILE* 1.3 72.6 - - - +
200A PRO* 1.3 73.1 - - + +
202A MET* 3.9 0.5 - - - +
203A ASN* 3.0 46.4 + - - +
283A CYS* 3.8 25.8 - - + -
286A LYS* 3.6 41.5 - - + +
287A LEU* 4.5 7.4 - - + -
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Residues in contact with PRO 200 (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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195A LEU 3.3 16.4 - - - +
196A GLU 3.5 20.6 - - - +
197A TYR* 3.3 16.8 - - + +
199A VAL* 1.3 97.5 - - + +
201A CYS* 1.3 59.7 + - - +
203A ASN* 4.0 4.2 - - + +
204A LYS* 3.1 27.9 + - - +
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Residues in contact with CYS 201 (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 TYR* 2.9 40.8 + - + +
198A ILE 3.7 2.5 - - - +
200A PRO* 1.3 78.2 - - - +
202A MET* 1.3 57.4 + - - +
204A LYS* 4.7 0.2 - - - -
205A HIS* 2.8 52.4 + - - +
206A GLY 3.6 2.3 + - - -
207A ILE 3.3 23.7 - - - +
208A CYS* 3.8 21.5 - - + -
209A VAL 5.1 0.2 - - - -
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Residues in contact with MET 202 (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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198A ILE* 2.8 34.6 + - + +
199A VAL 3.9 0.4 - - - +
201A CYS* 1.3 74.3 - - - +
203A ASN* 1.3 58.8 + - - +
206A GLY* 2.8 36.5 + - - +
207A ILE 3.9 5.6 - - - -
208A CYS* 4.0 3.1 - - + -
287A LEU* 3.8 24.5 - - + -
324A VAL* 4.6 7.6 - - + -
365A PHE* 3.8 31.6 - - + +
366A PHE* 4.0 6.7 - - - +
367A TRP* 3.5 64.0 + - + +
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Residues in contact with ASN 203 (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 VAL* 3.0 33.4 + - - +
200A PRO* 4.3 4.0 - - + +
202A MET* 1.3 75.6 - - - +
204A LYS* 1.3 59.2 + - - +
286A LYS 2.9 21.9 + - - -
287A LEU* 3.9 2.5 - - - -
288A GLY* 2.9 31.4 + - - -
367A TRP* 4.2 6.2 + - - +
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO 3.1 18.8 + - - +
201A CYS 4.0 1.3 - - - +
202A MET 3.1 0.2 - - - -
203A ASN* 1.3 80.5 - - - +
205A HIS* 1.3 98.3 + - + +
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Residues in contact with HIS 205 (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 CYS* 2.8 37.2 + - - +
204A LYS* 1.3 115.9 + - + +
206A GLY* 1.3 60.7 - - - +
207A ILE* 3.0 26.2 + - + +
347A PRO* 4.8 8.1 - - - +
348A GLU* 5.0 7.0 - - - +
372A ASN* 5.0 1.6 - - - +
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Residues in contact with GLY 206 (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 CYS 3.6 0.8 + - - -
202A MET* 2.8 28.3 + - - -
203A ASN 4.8 0.2 - - - -
204A LYS 3.8 0.2 - - - -
205A HIS* 1.3 76.5 - - - +
207A ILE* 1.3 58.5 + - - +
348A GLU* 5.7 2.0 - - - -
366A PHE* 3.2 4.5 - - - -
367A TRP* 3.1 50.2 + - - -
372A ASN* 3.3 8.8 + - - -
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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