Contacts of the helix formed by residues 197 - 213 (chain A) in PDB entry 3E2A
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A TRP* 3.4 22.8 - - - -
195A ALA* 4.0 0.2 - - - +
196A THR* 1.3 79.9 + - - +
198A ARG* 1.3 65.0 + - - +
199A GLU* 3.8 6.8 + - - +
200A THR* 2.8 34.8 + - - +
201A LEU* 3.0 22.7 + - - +
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Residues in contact with ARG 198 (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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156A TYR* 4.6 0.6 + - - -
159A GLY 3.3 23.5 + - - -
160A ARG* 3.9 5.8 - - - +
165A LYS* 3.5 32.3 - - + +
168A TRP* 3.4 17.6 - - + +
197A SER* 1.3 73.9 - - - +
199A GLU* 1.3 62.5 + - - +
201A LEU* 3.3 18.9 + - - +
202A GLU* 3.1 41.2 + - - +
231B SO4 3.1 33.9 + - - -
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Residues in contact with GLU 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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197A SER* 3.3 6.8 + - - +
198A ARG* 1.3 75.4 - - - +
200A THR* 1.3 67.8 + - + +
202A GLU* 3.3 7.4 + - + +
203A ILE* 3.1 35.5 + - + +
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Residues in contact with THR 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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194A MET* 4.4 6.5 - - - -
195A ALA* 4.4 1.6 - - - -
196A THR* 2.9 36.5 + - - +
197A SER* 2.8 24.4 + - - +
199A GLU* 1.3 81.4 - - + +
201A LEU* 1.3 56.5 + - - +
203A ILE* 4.2 4.7 - - - +
204A SER* 2.9 35.5 + - - -
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Residues in contact with LEU 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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155A VAL* 4.0 8.1 - - + +
156A TYR* 3.8 39.5 - - + +
159A GLY* 3.5 36.1 - - - +
160A ARG* 4.0 0.7 - - + +
168A TRP* 4.4 0.9 - - + -
176A LEU* 4.8 0.2 - - + -
193A VAL* 4.4 11.4 - - + +
195A ALA* 3.5 23.1 - - + -
197A SER 3.0 15.1 + - - +
198A ARG* 3.3 31.9 - - - +
199A GLU 3.1 0.2 - - - -
200A THR* 1.3 77.2 + - - +
202A GLU* 1.3 57.3 + - - +
204A SER* 4.0 1.0 - - - -
205A TYR* 2.9 33.6 + - - +
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Residues in contact with GLU 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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156A TYR* 2.3 38.9 + - - -
198A ARG* 3.1 28.3 + - - +
199A GLU* 3.3 9.4 + - + +
201A LEU* 1.3 77.4 - - - +
203A ILE* 1.3 68.1 + - + +
205A TYR* 3.9 2.6 - - - +
206A ARG* 2.9 77.8 + - - +
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Residues in contact with ILE 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 GLU* 3.1 29.3 + - + +
200A THR* 4.2 4.3 - - - +
202A GLU* 1.3 78.1 - - + +
204A SER* 1.3 59.6 + - - +
206A ARG* 3.3 20.6 + - - +
207A ASN* 2.9 56.3 + - - +
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Residues in contact with SER 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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192A GLY 2.9 17.3 + - - +
193A VAL* 4.2 2.5 - - - -
194A MET* 2.8 39.4 + - - +
200A THR* 2.9 21.6 + - - -
201A LEU 4.0 2.2 - - - -
203A ILE* 1.3 77.9 - - - +
205A TYR* 1.3 63.3 + - - +
207A ASN* 3.5 7.4 + - - +
208A ALA* 3.0 25.6 + - - +
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Residues in contact with TYR 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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129A LYS* 2.8 21.0 + - - -
130A HIS* 4.0 2.9 + - - -
152A ALA 3.9 12.6 - - - -
153A GLU* 2.7 38.2 + - - -
156A TYR* 3.8 53.2 - + + -
193A VAL* 3.9 16.1 - - + +
201A LEU 2.9 21.4 + - - +
202A GLU* 3.9 2.9 - - - +
204A SER* 1.3 76.3 - - - +
206A ARG* 1.3 75.6 + - + +
208A ALA* 3.2 3.1 + - - +
209A ILE* 3.1 52.6 + - + +
128B PHE* 6.2 4.0 - + - -
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Residues in contact with ARG 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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202A GLU* 2.9 51.0 + - - +
203A ILE* 3.8 20.1 - - - +
205A TYR* 1.3 87.2 - - + +
207A ASN* 1.3 64.1 + - - +
209A ILE* 3.5 4.9 + - - +
210A ALA* 3.1 24.9 + - - +
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Residues in contact with ASN 207 (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 GLY 6.0 0.7 - - - +
203A ILE* 2.9 41.1 + - - +
204A SER* 3.7 7.8 - - - +
206A ARG* 1.3 77.0 - - - +
208A ALA* 1.3 58.7 + - - +
210A ALA* 3.3 6.9 + - - +
211A ARG* 2.9 29.9 + - - +
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Residues in contact with ALA 208 (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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152A ALA* 5.0 4.5 - - + -
191A GLN 3.6 19.1 - - - +
192A GLY* 4.1 3.6 - - - -
193A VAL* 3.5 27.8 - - + +
204A SER 3.0 18.4 + - - +
205A TYR 3.2 1.3 + - - +
207A ASN* 1.3 76.7 - - - +
209A ILE* 1.3 58.6 + - - +
211A ARG* 3.1 7.7 + - - +
212A LEU* 2.8 36.6 + - + +
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Residues in contact with ILE 209 (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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130A HIS* 3.6 37.5 - - + +
149A ILE* 4.7 6.7 - - + -
152A ALA* 4.2 17.7 - - + -
153A GLU* 4.2 1.1 - - - +
205A TYR* 3.1 49.3 + - + +
206A ARG* 3.9 5.2 - - - +
208A ALA* 1.3 75.9 - - - +
210A ALA* 1.3 58.6 + - - +
212A LEU* 3.3 12.2 + - + +
213A SER* 2.7 39.7 + - - +
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Residues in contact with ALA 210 (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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206A ARG 3.1 18.8 + - - +
207A ASN* 3.6 7.0 - - - +
208A ALA 3.3 0.2 - - - -
209A ILE* 1.3 77.4 - - - +
211A ARG* 1.3 61.6 + - - +
213A SER* 3.3 17.5 + - - -
214A ILE* 3.7 12.2 + - - +
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Residues in contact with ARG 211 (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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207A ASN 2.9 17.1 + - - +
208A ALA* 3.6 7.2 - - - +
210A ALA* 1.3 76.3 - - - +
212A LEU* 1.3 69.7 + - + +
213A SER 3.2 0.7 + - - -
214A ILE* 3.3 40.7 + - - +
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Residues in contact with LEU 212 (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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133A LEU* 4.5 1.4 - - - +
145A MET* 3.3 40.9 - - + +
148A LYS* 3.3 36.1 - - + +
149A ILE* 4.1 33.2 - - + +
152A ALA* 4.7 6.3 - - + -
191A GLN* 4.4 15.7 - - + +
208A ALA 2.8 27.8 + - - +
209A ILE* 3.6 12.1 - - + +
211A ARG* 1.3 79.2 - - + +
213A SER* 1.3 61.0 + - - +
214A ILE 3.3 5.8 + - - +
215A LEU* 4.3 1.2 - - - +
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Residues in contact with SER 213 (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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130A HIS* 5.6 1.2 + - - -
133A LEU* 3.3 38.1 - - - +
209A ILE* 2.7 31.9 + - - +
210A ALA* 3.5 10.0 - - - -
211A ARG 3.1 1.0 - - - -
212A LEU* 1.3 77.2 - - - +
214A ILE* 1.3 58.5 + - - +
215A LEU* 3.3 8.0 + - - +
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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