Contacts of the helix formed by residues 198 - 210 (chain D) in PDB entry 3IML
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 ASP 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D GLU 3.8 3.4 + - - +
197D ILE* 1.3 80.3 - - - +
199D LEU* 1.3 65.5 + - - +
200D PRO* 3.5 16.8 - - + +
201D ALA* 3.3 31.6 + - - +
202D LEU* 3.0 20.5 + - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D HIS* 4.7 9.1 - - + +
197D ILE 3.9 1.4 + - - -
198D ASP* 1.3 70.3 - - - +
200D PRO* 1.3 74.2 - - + +
202D LEU* 3.1 11.3 + - + +
203D ARG* 2.9 48.8 + - - +
229D ASN* 4.1 20.0 - - + +
232D GLY* 3.4 48.0 - - - +
233D ARG* 3.8 9.6 - - + +
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Residues in contact with PRO 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ASP* 3.5 17.0 - - + +
199D LEU* 1.3 95.9 - - + +
201D ALA* 1.3 59.8 - - - +
203D ARG* 3.4 14.4 + - + +
204D GLU* 3.2 31.7 + - - +
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TRP* 4.8 0.7 - - - -
197D ILE* 4.1 13.7 - - + -
198D ASP* 3.3 27.6 + - - +
200D PRO* 1.3 77.1 - - - +
202D LEU* 1.3 65.2 + - - +
204D GLU* 4.1 9.8 - - - +
205D ALA* 3.2 24.3 + - - +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TRP* 3.6 33.2 - - + -
191D THR* 4.2 4.9 - - + -
193D HIS* 3.6 42.0 - - + +
197D ILE* 4.3 7.3 - - + +
198D ASP 3.0 14.0 + - - +
199D LEU* 3.1 14.8 + - + +
201D ALA* 1.3 76.4 - - - +
203D ARG* 1.3 63.2 + - + +
205D ALA* 3.4 1.7 + - - +
206D VAL* 2.9 40.3 + - + +
228D VAL* 3.6 25.8 - - + -
229D ASN* 4.0 16.4 - - + +
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Residues in contact with ARG 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 2.9 53.5 + - + +
200D PRO* 3.8 11.4 - - + +
202D LEU* 1.3 78.9 - - + +
204D GLU* 1.3 66.5 + - + +
206D VAL* 3.8 0.9 - - - +
207D ILE* 2.9 36.7 + - + +
228D VAL* 2.9 41.0 + - + +
229D ASN* 3.1 20.4 + - + -
230D PRO* 4.5 7.2 + - - +
232D GLY* 4.1 4.9 - - - +
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Residues in contact with GLU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D PRO* 3.2 20.8 + - - +
201D ALA* 4.1 7.9 - - - +
202D LEU 3.4 0.2 - - - -
203D ARG* 1.3 79.1 - - + +
205D ALA* 1.3 57.0 + - - +
207D ILE* 3.4 9.3 + - + +
208D GLU* 2.9 32.9 + - - +
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 4.0 14.1 - - + -
163D TRP* 3.9 23.3 - - + -
201D ALA 3.2 16.7 + - - +
202D LEU 3.9 0.4 - - - +
204D GLU* 1.3 78.1 - - - +
206D VAL* 1.3 58.5 + - - +
208D GLU* 4.6 4.0 - - - +
209D GLU* 2.8 42.3 + - + +
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 4.9 2.5 - - + -
163D TRP* 4.1 13.7 - - + -
164D LEU* 5.0 2.5 - - + -
189D LEU* 3.4 39.7 - - + -
191D THR* 4.3 11.0 - - + -
202D LEU* 2.9 37.2 + - + +
205D ALA* 1.3 72.9 - - - +
207D ILE* 1.3 62.2 + - - +
210D VAL* 3.0 40.0 + - + +
211D ILE* 3.0 10.0 + - + +
228D VAL* 3.8 20.2 - - + -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ARG* 2.9 29.8 + - + +
204D GLU* 3.7 8.5 - - + +
206D VAL* 1.3 78.6 - - - +
208D GLU* 1.3 59.9 + - + +
211D ILE* 3.5 8.0 - - + +
212D LYS* 3.0 54.7 + - + +
226D PHE* 4.0 39.3 - - + +
228D VAL* 3.9 18.2 - - + -
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Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLU 2.9 18.1 + - - +
205D ALA* 4.1 4.1 - - - +
207D ILE* 1.3 81.4 - - + +
209D GLU* 1.3 72.2 + - + +
212D LYS* 4.2 12.4 - - + +
213D PRO* 3.4 20.0 - - - +
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Residues in contact with GLU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 3.0 36.3 + - - +
155D LEU* 3.5 15.6 - - + +
160D ARG* 3.0 42.9 + - - -
161D LEU* 4.4 16.8 - - + -
205D ALA* 2.8 29.2 + - + +
208D GLU* 1.3 93.9 - - + +
210D VAL* 1.3 60.4 + - - +
213D PRO* 3.5 5.6 - - - +
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Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 3.4 23.1 - - + +
151D ARG* 3.7 11.1 - - + +
152D GLN* 4.2 18.2 - - + -
155D LEU* 3.7 20.4 - - + -
161D LEU* 4.4 9.9 - - + -
164D LEU* 5.2 0.9 - - + -
189D LEU* 3.3 29.4 - - + -
206D VAL* 3.0 29.4 + - + +
209D GLU* 1.3 75.8 - - - +
211D ILE* 1.3 59.9 + - - +
213D PRO* 3.9 1.8 - - - +
214D THR* 2.7 28.2 + - - -
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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