Contacts of the strand formed by residues 191 - 199 (chain D) in PDB entry 4OBZ
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 TYR 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D THR* 4.1 14.3 + - - -
187D ASP 3.3 21.3 - - - -
188D SER* 3.3 46.8 + - - +
189D LYS 3.7 0.8 - - - -
190D TYR* 1.4 79.6 - - - +
192D LYS* 1.3 62.0 + - - +
193D GLY 3.4 24.6 + - - -
194D SER* 5.0 0.2 - - - -
195D LEU* 3.5 29.1 - - + +
330D TYR* 3.6 39.0 - + + -
343D ALA* 3.6 15.9 - - + -
344D GLU 3.4 8.3 - - - +
346D ALA* 3.8 5.0 - - - +
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Residues in contact with LYS 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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191D TYR* 1.3 74.7 - - - +
193D GLY* 1.3 67.8 + - - +
194D SER 3.9 0.7 + - - +
343D ALA* 3.8 4.5 - - - +
344D GLU* 2.7 60.3 + - + +
345D ALA 3.6 17.2 + - - -
346D ALA* 4.3 14.4 - - + +
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Residues in contact with GLY 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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191D TYR* 3.4 20.3 + - - -
192D LYS* 1.3 76.9 - - - +
194D SER* 1.3 58.4 + - - -
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Residues in contact with SER 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D TYR* 5.0 0.9 - - - -
192D LYS 4.7 0.5 - - - +
193D GLY* 1.3 74.0 - - - -
195D LEU* 1.4 69.3 + - - +
196D SER* 3.8 8.1 + - - -
281D LYS* 5.1 5.4 + - - -
342D PHE 3.8 5.5 - - - +
343D ALA* 4.0 8.7 - - - +
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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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186D THR* 4.9 5.6 - - + -
191D TYR* 3.5 33.9 - - + +
194D SER* 1.4 81.1 + - - +
196D SER* 1.3 59.6 + - - +
197D TYR* 3.6 40.8 - - + +
281D LYS* 5.2 0.7 + - - -
330D TYR* 4.5 4.3 - - + +
332D VAL* 3.7 29.2 - - + -
342D PHE* 3.4 14.6 - - - +
343D ALA* 3.4 23.8 - - + +
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Residues in contact with SER 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 SER 3.9 7.1 + - - -
195D LEU* 1.3 74.4 + - - +
197D TYR* 1.3 63.1 + - - +
198D LEU* 4.0 1.7 + - - +
281D LYS* 2.8 39.9 + - - +
283D TYR* 3.4 25.2 + - - -
340D VAL 3.8 1.0 - - - +
341D GLY* 3.4 1.2 - - - -
342D PHE* 3.0 30.5 + - - +
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Residues in contact with TYR 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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164D ILE* 6.1 0.5 - - - +
186D THR* 5.6 1.6 - - - +
195D LEU* 3.6 43.0 - - + +
196D SER* 1.3 75.8 - - - +
198D LEU* 1.3 62.5 + - - +
199D ASN* 4.6 0.8 + - - +
279D GLY* 5.3 4.3 - - - -
332D VAL* 4.7 15.1 - - + +
334D ASP* 5.0 2.9 - - + -
339D ARG* 3.3 61.6 + - + +
340D VAL 3.4 2.9 - - - -
341D GLY* 3.4 26.0 - - - -
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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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196D SER 4.4 1.3 - - - +
197D TYR* 1.3 74.1 - - - +
199D ASN* 1.3 62.4 + - - +
200D VAL 3.7 0.2 + - - -
208D VAL* 3.7 27.4 - - + +
209D HIS* 3.8 9.6 - - + +
278D LEU* 3.7 39.5 - - + +
279D GLY* 3.7 26.7 - - - +
283D TYR* 4.4 6.1 - - - +
339D ARG* 3.2 4.9 - - - +
340D VAL* 2.8 34.7 + - + +
342D PHE* 3.7 31.2 - - + -
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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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197D TYR* 4.3 1.1 - - - +
198D LEU* 1.3 71.8 - - - +
200D VAL* 1.3 64.8 + - - +
201D THR* 3.4 11.4 + - - +
208D VAL* 3.9 10.0 - - - +
209D HIS 4.9 0.7 + - - -
337D ASN 4.9 3.5 - - - +
338D ASN 4.1 5.5 - - - +
339D ARG* 4.2 14.7 - - - +
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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