Contacts of the helix formed by residues 191 - 206 (chain A) in PDB entry 2A79
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ARG 4.2 0.6 + - - -
190A TRP* 1.3 77.4 - - - +
192A SER* 1.3 64.6 + - - +
193A MET* 3.8 8.8 + - - +
194A GLU* 2.6 39.4 + - - +
195A ILE* 3.0 20.0 + - - +
224A LYS* 5.1 2.9 - - - +
228A GLN* 5.5 2.2 - - - -
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Residues in contact with SER 192 (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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190A TRP 4.0 0.2 + - - -
191A SER* 1.3 72.8 - - - +
193A MET* 1.3 54.0 + - - +
195A ILE* 3.1 4.0 + - - +
196A MET* 2.8 37.0 + - - +
224A LYS* 5.7 1.6 - - - +
228A GLN* 3.4 41.4 + - - +
229A LEU* 4.8 2.7 - - - +
231A GLU* 6.1 0.9 - - - -
232A LEU* 3.8 29.9 - - - +
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Residues in contact with MET 193 (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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191A SER* 3.2 7.1 - - - +
192A SER* 1.3 78.9 - - - +
194A GLU* 1.3 53.0 + - + +
196A MET* 3.3 6.8 + - - +
197A GLU* 2.7 36.0 + - + +
33B GLU* 4.3 26.5 - - + +
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Residues in contact with GLU 194 (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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160A PRO* 3.5 26.9 - - - +
166A MET* 4.4 2.2 - - - +
190A TRP* 3.2 31.6 - - + -
191A SER* 2.6 44.5 + - - +
193A MET* 1.3 77.5 - - + +
195A ILE* 1.3 65.3 + - - +
197A GLU* 3.2 14.7 + - - +
198A ALA 3.0 18.0 + - - -
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Residues in contact with ILE 195 (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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187A THR* 3.7 12.3 - - - +
190A TRP* 3.7 26.7 - - + +
191A SER 3.0 17.2 + - - +
192A SER* 3.6 4.7 - - - +
194A GLU* 1.3 74.0 - - - +
196A MET* 1.3 64.5 + - - +
198A ALA* 3.1 5.7 + - - +
199A TYR* 2.9 21.4 + - - +
210A PRO* 4.8 9.0 - - + +
213A GLU* 3.6 33.9 - - + +
229A LEU* 4.6 4.7 - - + -
232A LEU* 3.8 25.6 - - + -
236A ILE* 4.4 4.7 - - + -
238A VAL* 4.2 25.1 - - + -
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Residues in contact with MET 196 (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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192A SER 2.8 17.2 + - - +
193A MET* 3.5 8.1 - - - +
195A ILE* 1.3 77.5 - - - +
197A GLU* 1.3 56.2 + - - +
199A TYR* 3.3 34.0 + - + +
200A SER* 2.8 35.2 + - - -
232A LEU* 4.2 12.5 - - + +
235A LYS* 3.7 33.9 - - - +
236A ILE* 4.1 23.8 - - + -
33B GLU* 3.4 25.6 - - - +
74B ASN* 3.7 13.0 - - - +
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Residues in contact with GLU 197 (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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166A MET* 3.0 35.1 + - + +
193A MET* 2.7 17.6 + - + +
194A GLU* 3.4 16.8 - - - +
195A ILE 3.2 0.2 - - - -
196A MET* 1.3 73.6 - - - +
198A ALA* 1.3 56.3 + - - +
200A SER* 3.3 7.1 - - - -
201A VAL* 2.9 42.4 + - + +
33B GLU* 5.6 0.2 + - - -
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Residues in contact with ALA 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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166A MET* 3.7 32.0 - - + +
170A VAL* 4.0 5.8 - - + +
185A TRP* 4.1 4.7 - - + -
190A TRP* 3.8 9.0 - - + -
194A GLU 3.0 10.7 + - - +
195A ILE* 3.1 9.2 + - - +
197A GLU* 1.3 75.4 - - - +
199A TYR* 1.3 64.3 + - - +
201A VAL* 3.2 4.0 + - - +
202A ALA* 2.9 22.9 + - - +
210A PRO* 3.9 20.6 - - + -
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Residues in contact with TYR 199 (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 ILE 2.9 12.7 + - - +
196A MET* 3.5 28.0 - - + +
198A ALA* 1.3 74.8 - - - +
200A SER* 1.3 75.2 + - - +
202A ALA* 3.1 5.7 + - - +
203A ARG* 3.0 43.6 + - + +
209A PRO* 4.0 16.4 - - + -
210A PRO* 4.1 14.5 - - + +
236A ILE* 3.7 43.1 - - + -
69B PHE* 3.9 1.4 - + - -
71B PRO* 2.5 38.6 + - + +
74B ASN* 3.2 43.0 - - + +
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Residues in contact with SER 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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196A MET* 2.8 25.4 + - - -
197A GLU* 3.3 10.9 - - - +
199A TYR* 1.3 81.7 - - - +
201A VAL* 1.3 50.9 + - - +
203A ARG* 3.2 4.9 + - - +
204A GLN* 2.8 35.1 + - - +
74B ASN* 3.8 20.4 + - - +
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Residues in contact with VAL 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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166A MET* 3.9 19.7 - - + -
167A GLU* 3.8 28.7 - - + +
170A VAL* 4.2 13.7 - - + -
197A GLU* 2.9 31.5 + - + +
198A ALA 3.6 4.5 - - - +
200A SER* 1.3 70.0 - - - +
202A ALA* 1.3 67.9 + - - +
204A GLN* 3.2 9.6 + - + +
205A PHE* 2.8 40.6 + - + +
207A LEU* 4.8 1.1 - - + -
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Residues in contact with ALA 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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170A VAL* 4.0 6.5 - - + +
198A ALA 2.9 12.2 + - - +
199A TYR 3.1 8.9 + - - +
201A VAL* 1.3 78.9 - - - +
203A ARG* 1.3 58.2 + - - +
206A ASN* 2.7 27.5 + - - -
207A LEU* 2.9 35.6 + - - +
208A ILE 3.9 5.4 - - - +
209A PRO* 3.7 25.8 - - + -
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Residues in contact with ARG 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 TYR* 3.0 42.3 + - + +
200A SER 3.7 5.8 - - - +
202A ALA* 1.3 76.4 - - - +
204A GLN* 1.3 64.8 + - - +
206A ASN* 3.3 12.6 + - - +
207A LEU 4.7 4.6 + - - -
209A PRO* 3.8 29.0 - - - +
71B PRO* 3.0 31.3 + - - +
72B LEU* 3.4 31.4 + - - +
73B ARG* 4.8 5.2 - - - +
74B ASN* 4.1 15.9 - - + +
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Residues in contact with GLN 204 (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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200A SER* 2.8 15.2 + - - +
201A VAL* 3.2 14.8 + - + +
203A ARG* 1.3 79.4 - - - +
205A PHE* 1.3 84.6 + - + +
206A ASN 3.8 0.3 + - - -
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Residues in contact with PHE 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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167A GLU* 3.5 37.5 - - + -
171A ARG* 3.2 27.0 + - - +
201A VAL* 2.8 38.4 + - + +
204A GLN* 1.3 94.4 - - + +
206A ASN* 1.3 73.9 + - - +
207A LEU* 3.4 21.1 + - + +
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Residues in contact with ASN 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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174A THR* 5.5 0.3 - - - +
202A ALA 2.7 13.3 + - - -
203A ARG* 3.3 10.7 + - - +
204A GLN 3.4 0.6 + - - -
205A PHE* 1.3 77.3 - - - +
207A LEU* 1.3 63.3 + - - +
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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