Contacts of the helix formed by residues 194 - 206 (chain D) in PDB entry 1P7L
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 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D HIS* 6.3 0.4 - - - -
192D GLU 4.3 0.4 + - - -
193D ILE* 1.3 80.0 - - - +
195D GLN* 1.3 60.6 + - - +
196D LYS* 3.5 10.8 + - - +
197D SER* 2.4 47.3 + - - -
198D LEU* 2.9 32.5 + - - +
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Residues in contact with GLN 195 (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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189D HIS* 4.4 11.0 + - + +
193D ILE 4.2 0.2 + - - -
194D ASP* 1.3 72.8 - - - +
196D LYS* 1.3 54.3 + - - +
198D LEU* 3.0 9.9 + - - +
199D GLN* 2.6 72.4 + - - +
224D ILE 3.8 2.2 + - - -
225D ASN* 3.5 38.0 + - - +
228D GLY* 3.1 35.4 - - - +
229D ARG 4.2 0.5 + - - -
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Residues in contact with LYS 196 (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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194D ASP* 3.5 8.9 + - - +
195D GLN* 1.3 78.0 - - - +
197D SER* 1.3 65.8 + - - +
199D GLN* 3.0 19.3 + - + +
200D GLU* 2.7 39.1 + - + +
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Residues in contact with SER 197 (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 ILE* 3.8 13.7 - - - -
194D ASP* 2.4 45.5 + - - -
196D LYS* 1.3 71.3 - - - +
198D LEU* 1.3 52.9 + - - +
200D GLU* 3.1 7.5 + - - +
201D ALA* 2.7 38.7 + - - +
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Residues in contact with LEU 198 (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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159D TRP* 3.4 29.8 - - + -
187D THR* 4.7 4.3 - - + -
189D HIS* 3.3 39.5 - - + +
193D ILE* 3.3 16.0 - - + +
194D ASP 2.9 17.7 + - - +
195D GLN* 3.1 15.9 - - - +
197D SER* 1.3 71.5 - - - +
199D GLN* 1.3 58.0 + - + +
201D ALA* 2.9 3.6 + - - +
202D VAL* 2.7 44.7 + - + +
224D ILE* 3.8 21.1 - - + -
225D ASN* 3.6 20.2 - - - +
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Residues in contact with GLN 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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195D GLN* 2.6 47.1 + - - +
196D LYS* 3.4 29.1 + - + +
198D LEU* 1.3 76.1 - - + +
200D GLU* 1.3 64.8 + - - +
202D VAL* 3.1 10.0 + - - +
203D MET* 3.2 11.8 + - - +
224D ILE* 3.2 52.2 + - + +
225D ASN 5.1 0.2 + - - -
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Residues in contact with GLU 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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196D LYS* 2.7 33.6 + - + +
197D SER* 3.5 6.3 - - - +
199D GLN* 1.3 74.3 - - - +
201D ALA* 1.3 62.4 + - - +
203D MET* 3.5 8.2 + - - +
204D GLU* 3.5 37.5 + - + +
208D LYS* 6.0 0.2 + - - -
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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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157D LEU* 4.5 11.4 - - + -
159D TRP* 3.8 24.0 - - + -
193D ILE* 5.3 0.2 - - + -
197D SER 2.7 21.0 + - - +
198D LEU 3.4 3.6 - - - +
200D GLU* 1.3 73.1 - - - +
202D VAL* 1.3 64.4 + - - +
204D GLU* 3.4 4.9 + - - +
205D GLU* 3.0 30.1 + - - +
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Residues in contact with VAL 202 (chain D).
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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157D LEU* 5.2 1.1 - - + -
159D TRP* 4.8 7.0 - - + -
160D LEU* 5.3 1.3 - - + -
185D LEU* 3.9 27.8 - - + -
187D THR* 4.2 17.9 - - + -
198D LEU* 2.7 40.7 + - + +
199D GLN 3.1 4.9 + - - +
201D ALA* 1.3 73.2 - - - +
203D MET* 1.3 57.5 + - - +
206D ILE* 2.8 43.0 + - + -
207D ILE* 2.9 16.0 + - + -
224D ILE* 3.8 21.8 - - + -
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Residues in contact with MET 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 GLN 3.2 9.9 + - - +
200D GLU* 3.6 15.5 - - - +
201D ALA 3.2 0.2 - - - -
202D VAL* 1.3 78.9 - - - +
204D GLU* 1.3 62.0 + - - +
207D ILE* 4.2 9.9 - - + -
208D LYS* 2.6 66.8 + - + +
222D PHE* 3.2 61.7 - - + -
224D ILE* 4.3 15.7 - - - -
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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 GLU* 3.5 30.6 + - + +
201D ALA* 3.4 7.3 + - - +
203D MET* 1.3 77.4 - - - +
205D GLU* 1.3 69.6 + - - +
208D LYS* 3.1 36.4 + - - +
209D PRO* 2.9 23.0 - - - +
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Residues in contact with GLU 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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147D ARG* 2.6 49.8 + - - +
151D VAL* 3.7 11.4 - - + -
156D THR* 3.5 32.7 - - + +
157D LEU* 3.8 21.1 - - + +
201D ALA 3.0 14.8 + - - +
204D GLU* 1.3 92.6 - - - +
206D ILE* 1.3 53.2 + - + +
209D PRO* 3.1 6.4 - - - +
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Residues in contact with ILE 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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144D LEU* 3.5 32.4 - - + +
147D ARG* 3.6 11.9 - - + -
148D GLN* 3.6 32.5 - - + +
151D VAL* 4.2 15.3 - - + -
157D LEU* 4.6 1.6 - - + -
160D LEU* 4.3 7.9 - - + -
185D LEU* 4.6 11.0 - - + -
187D THR* 5.6 0.2 - - + -
202D VAL* 2.8 44.6 + - + +
205D GLU* 1.3 80.4 - - + +
207D ILE* 1.3 62.0 + - + +
209D PRO* 3.6 2.7 - - - +
210D ILE* 3.4 24.1 - - - +
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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