Contacts of the helix formed by residues 193 - 201 (chain D) in PDB entry 2W8I
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 THR 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A TYR* 4.4 1.8 + - - +
76D LEU* 4.5 8.7 - - + -
80D LEU* 4.0 28.9 - - + -
191D PRO* 5.0 0.9 - - + -
192D LEU* 1.3 79.3 - - - +
194D VAL* 1.3 66.7 + - - +
195D MET* 3.5 1.2 - - - +
196D ASP* 2.7 33.9 + - - +
197D ALA* 2.8 21.7 + - - +
238D ASN* 2.9 31.4 + - - +
239D HIS 3.0 10.3 - - - +
240D LEU* 4.2 5.4 - - + -
241D LEU* 3.7 2.7 - - - -
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D THR* 1.3 70.1 - - - +
195D MET* 1.3 58.4 + - - +
197D ALA* 3.1 3.3 + - - +
198D ILE* 2.9 43.3 + - + +
213D VAL* 5.6 0.9 - - + -
215D LEU* 4.7 0.9 - - + -
224D ILE* 3.8 29.6 - - + -
226D LEU* 4.2 19.3 - - + -
229D LEU* 4.7 4.3 - - + -
238D ASN* 2.9 9.7 + - - +
239D HIS* 2.8 34.0 + - + +
241D LEU* 3.8 21.4 - - + +
247D LEU* 4.1 19.7 - - + -
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Residues in contact with MET 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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174A TYR* 3.6 37.2 - - + -
176A THR* 5.2 0.4 - - - +
246A ILE* 4.0 15.9 - - + -
193D THR* 3.5 1.3 - - - +
194D VAL* 1.3 79.8 - - - +
196D ASP* 1.3 63.7 + - - +
198D ILE* 3.2 14.2 + - + +
199D ASN* 3.0 36.2 + - - +
226D LEU* 4.7 2.9 - - + -
229D LEU* 3.8 32.5 - - + -
230D MET* 3.6 33.4 - - + -
238D ASN* 3.1 23.3 + - - +
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Residues in contact with ASP 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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172A LYS* 3.8 8.3 + - - +
174A TYR* 2.6 35.3 + - - -
184A LYS* 3.6 21.2 + - - +
191D PRO* 3.5 12.5 - - - +
192D LEU* 3.5 17.0 - - + -
193D THR* 2.7 40.0 + - - +
195D MET* 1.3 76.4 - - - +
197D ALA* 1.3 53.1 + - - +
199D ASN* 3.3 1.7 + - - +
200D ALA* 2.7 37.8 + - - +
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Residues in contact with ALA 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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175D VAL* 4.1 12.8 - - + +
185D GLN* 2.9 40.6 + - - +
192D LEU* 3.7 5.8 - - + +
193D THR 2.8 14.4 + - - +
194D VAL 3.5 7.6 - - - +
196D ASP* 1.3 73.4 - - - +
198D ILE* 1.3 57.9 + - - +
201D ALA* 3.1 11.3 + - - +
241D LEU* 3.6 21.5 - - + -
247D LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 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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176A THR* 4.9 6.3 - - + -
175D VAL* 5.3 1.3 - - + -
179D VAL* 4.5 3.8 - - + -
194D VAL* 2.9 32.0 + - + +
195D MET* 3.2 15.0 + - + +
197D ALA* 1.3 75.2 - - - +
199D ASN* 1.3 71.0 + - - +
201D ALA* 3.0 15.3 + - - +
202D GLY 3.3 0.3 + - - -
203D GLY* 3.1 29.1 + - - -
204D LEU* 4.2 20.2 - - + -
213D VAL* 5.4 1.1 - - + -
226D LEU* 3.8 25.6 - - + -
230D MET* 5.0 1.3 - - - -
247D LEU* 4.4 10.5 - - + -
249D ILE* 4.0 25.1 - - + -
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Residues in contact with ASN 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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174A TYR* 3.7 21.9 - - - +
175A VAL 3.6 15.8 + - - +
176A THR* 4.0 17.2 + - - +
182A SER 4.1 0.7 - - - +
183A GLY* 3.2 37.8 + - - +
184A LYS* 3.5 23.5 + - + +
195D MET* 3.0 24.2 + - - +
196D ASP 3.7 3.4 - - - +
198D ILE* 1.3 72.2 - - - +
200D ALA* 1.3 59.6 + - - +
202D GLY* 2.7 25.6 + - - -
203D GLY* 4.4 4.9 - - - +
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Residues in contact with ALA 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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184A LYS* 4.9 12.0 - - - +
181D ASN* 5.2 3.5 - - - +
185D GLN* 3.0 32.7 + - - +
192D LEU* 5.2 2.5 - - + -
196D ASP 2.7 21.1 + - - +
199D ASN* 1.3 73.3 - - - +
201D ALA* 1.3 58.7 + - - +
202D GLY* 3.3 0.9 + - - -
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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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175D VAL* 4.0 9.4 - - + -
179D VAL* 3.9 18.4 - - + -
180D ALA* 3.2 4.3 + - - +
181D ASN* 2.6 52.2 + - - +
185D GLN* 3.5 11.0 - - - +
197D ALA 3.1 18.0 + - - +
198D ILE* 3.0 10.6 + - - +
200D ALA* 1.3 75.0 - - - +
202D GLY* 1.3 55.9 + - - +
203D GLY 3.5 1.3 - - - -
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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