Contacts of the helix formed by residues 191 - 205 (chain A) in PDB entry 3DL2
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 GLY 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 GLY* 3.5 3.4 - - - -
190A GLY* 1.3 79.4 - - - +
192A GLU* 1.3 67.0 + - - -
193A LEU 3.2 2.7 - - - -
194A GLY 3.0 3.7 + - - +
195A ILE* 2.9 22.0 + - - +
252A THR* 5.4 0.4 + - - -
388B TRP* 5.7 0.9 - - - -
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Residues in contact with GLU 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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191A GLY* 1.3 70.2 - - - +
193A LEU* 1.3 57.5 + - - +
195A ILE* 3.3 7.9 + - - +
196A ALA* 2.9 30.0 + - - +
387A SER* 4.1 20.6 + - - +
192B GLU* 4.2 21.3 - - - +
386B ARG* 3.0 49.9 + - - +
387B SER* 5.2 2.4 + - - -
388B TRP* 4.0 20.1 - - + +
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Residues in contact with LEU 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 GLY 3.2 1.2 - - - -
192A GLU* 1.3 77.9 - - - +
194A GLY* 1.3 58.5 + - - +
196A ALA* 3.3 1.1 + - - +
197A CYS* 2.9 39.9 + - - -
252A THR* 3.8 34.1 - - + +
254A ASN* 5.7 3.8 - - - +
292A ALA* 4.0 28.0 - - + +
387A SER* 3.7 31.7 + - - +
390A VAL* 3.7 29.4 - - + -
391A GLY 4.0 5.8 - - - +
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Residues in contact with GLY 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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187A VAL* 3.5 11.7 - - - +
189A GLY 3.3 26.0 - - - -
191A GLY* 3.0 6.9 + - - +
193A LEU* 1.3 77.7 - - - +
195A ILE* 1.3 56.6 + - - +
197A CYS 3.5 0.3 + - - -
198A THR* 2.8 33.2 + - - -
212A LEU* 4.3 2.5 - - - -
252A THR* 3.5 14.3 + - - -
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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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190A GLY 3.7 15.0 - - - +
191A GLY 2.9 17.8 + - - +
192A GLU* 3.6 8.1 - - - +
194A GLY* 1.3 75.2 - - - +
196A ALA* 1.3 59.8 + - - +
198A THR* 3.2 5.3 + - - -
199A LEU* 2.9 44.0 + - + +
212A LEU* 4.0 11.2 - - + -
223A THR* 4.4 4.0 - - + -
226A LEU* 3.8 29.8 - - + -
388B TRP* 3.6 61.7 - - + +
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Residues in contact with ALA 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 GLU 2.9 18.1 + - - +
193A LEU 3.6 3.8 - - - +
195A ILE* 1.3 77.6 - - - +
197A CYS* 1.3 57.6 + - - +
199A LEU* 3.5 5.4 + - - +
200A ALA* 3.0 31.7 + - - +
387A SER* 3.5 31.4 - - - +
388A TRP* 4.0 10.7 - - + +
391A GLY* 4.0 5.6 - - - -
199B LEU* 4.7 7.4 - - + +
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Residues in contact with CYS 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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187A VAL* 4.2 15.7 - - + -
193A LEU* 2.9 27.5 + - - +
194A GLY 3.7 4.7 - - - +
196A ALA* 1.3 75.9 - - - +
198A THR* 1.3 57.8 + - - +
200A ALA* 3.4 0.9 + - - +
201A ILE* 2.9 40.7 + - + +
250A ILE* 4.5 1.6 - - + -
252A THR* 3.9 19.3 - - - -
391A GLY* 4.0 15.3 - - - -
394A VAL* 3.8 36.1 - - + -
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Residues in contact with THR 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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187A VAL* 3.9 8.3 - - - +
194A GLY 2.8 18.1 + - - -
195A ILE* 3.5 11.4 - - - -
197A CYS* 1.3 76.2 - - - +
199A LEU* 1.3 54.2 + - - +
201A ILE* 3.9 1.4 - - - +
202A SER* 2.7 44.1 + - - +
210A LEU* 3.9 27.7 - - + +
212A LEU* 3.5 19.1 - - + +
226A LEU* 4.1 22.4 - - + -
231A LEU* 4.8 4.7 - - + -
234A VAL* 4.3 11.0 - - + -
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Residues in contact with LEU 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 38.8 + - + +
196A ALA* 4.1 4.5 - - - +
198A THR* 1.3 71.0 - - - +
200A ALA* 1.3 57.1 + - - +
202A SER* 3.4 2.2 + - - -
203A ALA* 2.7 36.5 + - - +
226A LEU* 4.6 5.2 - - + -
229A PHE* 5.0 0.2 - - + -
231A LEU* 4.1 20.9 - - + -
196B ALA* 4.8 7.9 - - - +
199B LEU* 4.1 25.9 - - + +
200B ALA* 4.3 9.6 - - - +
203B ALA* 4.1 15.3 - - + +
388B TRP* 5.1 8.7 - - + +
392B LEU* 4.0 31.0 - - + -
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Residues in contact with ALA 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 ALA 3.0 19.0 + - - +
197A CYS 3.9 0.7 - - - +
199A LEU* 1.3 72.6 - - - +
201A ILE* 1.3 64.9 + - - +
203A ALA* 3.5 6.7 + - - +
204A LYS* 3.4 16.8 + - - +
391A GLY 3.7 20.9 - - - +
392A LEU* 3.8 23.3 - - + -
395A ALA* 3.7 10.3 - - + -
199B LEU* 4.3 8.6 - - + +
229B PHE* 3.5 14.2 - - + -
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Residues in contact with ILE 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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185A ILE* 4.3 9.9 - - + -
187A VAL* 4.4 1.6 - - + -
197A CYS* 2.9 29.2 + - + +
198A THR 3.9 2.9 - - - +
200A ALA* 1.3 74.8 - - - +
202A SER* 1.3 62.4 + - - +
204A LYS 3.4 1.9 + - - -
205A GLY 3.2 3.1 + - - -
206A ILE* 3.2 37.9 + - + +
207A ALA* 3.7 26.4 + - + +
210A LEU* 3.6 25.6 - - + -
250A ILE* 3.8 29.6 - - + -
394A VAL* 5.0 0.7 - - + -
395A ALA* 3.7 23.3 - - + -
398A VAL* 4.3 9.9 - - + -
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Residues in contact with SER 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 THR* 2.7 23.8 + - - +
199A LEU* 3.8 4.5 - - - -
201A ILE* 1.3 75.9 - - - +
203A ALA* 1.3 64.6 + - - +
205A GLY* 3.1 14.5 + - - +
207A ALA* 6.0 1.1 - - - +
210A LEU* 4.6 3.5 - - - +
231A LEU* 4.1 10.2 - - - +
234A VAL* 3.7 23.8 - - - +
202B SER 4.8 0.2 - - - +
203B ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 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 LEU 2.7 22.4 + - - +
200A ALA 3.6 7.0 - - - +
201A ILE 3.4 0.2 - - - -
202A SER* 1.3 73.3 - - - +
204A LYS* 1.3 58.3 + - - +
199B LEU* 4.1 13.2 - - + +
202B SER* 3.8 24.7 - - - +
203B ALA* 3.6 15.6 - - - +
231B LEU* 3.7 25.8 - - + +
232B PRO* 5.4 2.8 - - - +
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Residues in contact with LYS 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 ALA 3.4 5.2 + - - +
201A ILE 3.4 0.2 + - - -
202A SER 3.2 0.4 - - - -
203A ALA* 1.3 77.3 - - - +
205A GLY* 1.3 64.1 + - - +
206A ILE* 3.3 28.4 - - + +
396A ASP* 4.7 9.1 + - - +
399A ASP* 4.4 15.2 + - - +
405A LYS* 5.7 1.6 - - - +
229B PHE* 2.7 55.1 + - + -
230B ASN* 3.8 14.3 + - - +
231B LEU* 3.8 17.5 - - + +
232B PRO* 4.8 11.2 - - + -
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Residues in contact with GLY 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 ILE 3.2 1.7 + - - -
202A SER* 3.1 16.7 + - - -
203A ALA 3.4 0.6 - - - -
204A LYS* 1.3 79.3 - - - +
206A ILE* 1.3 63.1 + - - +
207A ALA 3.5 10.2 - - - +
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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