Contacts of the helix formed by residues 191 - 200 (chain D) in PDB entry 1XFV
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 GLU 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D LYS* 2.7 35.8 + - - +
188D LEU* 3.8 16.2 - - + -
189D ASP* 2.4 27.8 + - - +
190D PRO* 1.3 82.0 - - - +
192D PHE* 1.3 69.9 + - - +
193D LEU* 2.6 6.9 + - + +
194D ASN* 2.9 12.7 + - - +
195D LEU* 3.0 9.7 + - - -
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Residues in contact with PHE 192 (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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190D PRO 5.5 1.3 - - - -
191D GLU* 1.3 74.0 + - - +
193D LEU* 1.3 59.3 + - - +
195D LEU* 3.8 26.0 - - + -
196D ILE* 2.6 62.9 + - + +
227D ILE* 5.2 11.4 - - + -
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Residues in contact with LEU 193 (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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184D LYS* 2.9 38.8 - - + +
191D GLU* 2.6 5.4 + - + +
192D PHE* 1.3 77.6 - - - +
194D ASN* 1.3 60.4 + - - +
196D ILE* 4.2 1.7 - - - +
197D LYS* 3.1 20.9 + - - +
267D TYR* 5.0 11.1 - - + -
270D LYS* 5.1 12.1 - - - +
278D LYS* 4.7 16.8 - - + +
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Residues in contact with ASN 194 (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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184D LYS* 4.1 11.0 - - + +
185D ASP* 3.0 43.5 + - - +
190D PRO* 5.5 1.0 - - + +
191D GLU 2.9 8.6 + - - +
193D LEU* 1.3 74.4 - - - +
195D LEU* 1.3 73.3 + - - +
197D LYS* 2.8 14.8 + - - +
198D SER* 2.7 30.5 + - - -
230D ILE* 4.8 5.2 - - - +
237D PHE* 5.4 2.9 + - - +
241D PHE* 4.9 6.1 - - - +
264D MET* 5.6 1.6 - - - +
267D TYR* 3.7 32.8 + - - +
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Residues in contact with LEU 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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190D PRO* 5.0 13.1 - - + +
191D GLU 3.0 16.9 + - - +
192D PHE* 3.8 29.2 - - + +
194D ASN* 1.3 81.7 + - - +
196D ILE* 1.3 65.5 + - + +
198D SER* 3.1 10.1 + - - -
199D LEU* 3.2 14.9 + - + +
226D ASP* 3.6 30.1 - - - +
227D ILE* 3.9 24.2 - - + -
230D ILE* 3.7 31.2 - - + -
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Residues in contact with ILE 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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192D PHE* 2.6 64.7 + - + +
193D LEU* 4.2 1.1 - - - +
195D LEU* 1.3 68.8 - - + +
197D LYS* 1.3 61.2 + - - +
198D SER 3.0 6.4 + - - -
199D LEU* 3.1 38.4 + - + +
200D SER* 3.6 3.6 + - - -
204D ASP* 4.4 8.6 - - - +
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Residues in contact with LYS 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 LEU 3.1 20.8 + - - +
194D ASN* 2.8 14.1 + - - +
196D ILE* 1.3 77.4 - - - +
198D SER* 1.3 62.4 + - - +
200D SER* 3.6 14.6 - - - +
263D ASP* 2.9 46.4 - - + +
264D MET* 2.9 32.2 - - + +
267D TYR* 2.9 46.5 - - + -
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Residues in contact with SER 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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194D ASN* 2.7 19.2 + - - -
195D LEU* 3.2 13.0 - - - -
196D ILE 3.0 0.2 - - - -
197D LYS* 1.3 80.0 - - - +
199D LEU* 1.2 64.7 + - - +
200D SER 2.7 8.9 + - - -
201D ASP* 3.0 18.4 + - - +
214D PHE* 4.9 4.8 - - - -
225D ILE* 4.7 5.3 - - - +
230D ILE* 4.5 8.3 - - - +
237D PHE* 3.3 34.8 - - - -
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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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195D LEU* 3.4 16.8 - - + +
196D ILE* 3.1 33.2 + - + +
198D SER* 1.2 73.0 - - - +
200D SER* 1.3 51.1 - - - +
201D ASP* 2.2 28.8 + - - +
202D ASP 3.9 2.8 + - - -
203D SER* 4.3 9.3 + - - +
204D ASP* 4.0 7.0 - - - +
225D ILE* 2.7 35.6 - - - +
226D ASP* 3.0 33.2 - - - +
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Residues in contact with SER 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 ILE 3.6 2.1 + - - -
197D LYS* 3.6 17.2 - - - +
198D SER 2.7 8.0 + - - -
199D LEU* 1.3 70.5 - - - +
201D ASP* 1.3 71.0 + - - +
202D ASP* 4.2 1.5 - - - +
204D ASP* 3.2 36.1 + - - +
205D SER* 4.7 7.4 + - - -
207D ASP 5.2 4.3 + - - +
210D PHE* 4.9 1.7 - - - -
262D PRO* 5.9 2.3 - - - +
263D ASP* 4.6 18.9 - - - +
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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