Contacts of the strand formed by residues 186 - 194 (chain D) in PDB entry 3OAD
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 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D SER* 3.7 11.4 + - - -
182D ASP 3.4 27.1 - - - -
183D PRO* 3.0 37.8 + - + +
185D HIS* 1.3 77.5 - - - +
187D GLU* 1.3 64.5 + - - +
188D GLY 3.9 19.1 - - - -
189D ASN* 5.3 0.4 - - - -
190D PHE* 3.3 33.1 - + - -
324D TYR* 3.5 33.2 - + + -
337D ALA* 3.9 17.9 - - + -
338D LEU 3.1 12.8 - - - +
340D ARG* 3.3 15.1 + - - +
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Residues in contact with GLU 187 (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 TYR* 1.3 77.2 - - - +
188D GLY* 1.3 67.4 + - - +
189D ASN 3.8 1.4 + - - +
337D ALA* 4.0 3.3 - - - +
338D LEU* 2.6 63.0 + - + +
339D ALA 4.4 2.7 - - - +
340D ARG* 3.3 46.3 + - - +
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Residues in contact with GLY 188 (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 TYR* 3.9 15.5 - - - -
187D GLU* 1.3 77.7 - - - +
189D ASN* 1.3 73.6 + - - +
340D ARG* 5.4 0.4 - - - +
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Residues in contact with ASN 189 (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 TYR* 5.3 0.4 - - - -
187D GLU 3.8 0.8 + - - +
188D GLY* 1.3 83.1 - - - +
190D PHE* 1.3 70.5 + - - +
191D HIS* 3.6 27.6 + - + +
336D PHE 3.7 5.4 - - - +
337D ALA* 4.0 10.1 - - - +
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Residues in contact with PHE 190 (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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181D SER* 3.5 17.5 - - - -
186D TYR* 3.3 47.6 - + - -
189D ASN* 1.3 77.5 - - - +
191D HIS* 1.3 69.0 + - - +
192D TYR* 3.4 38.8 - - + +
324D TYR* 3.7 35.7 - + - -
326D GLU* 3.8 18.4 - - + -
335D GLY* 3.7 21.3 - - - -
336D PHE 3.4 7.6 - - - -
337D ALA* 3.9 4.9 - - + -
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Residues in contact with HIS 191 (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 ASN* 3.7 27.5 + - + +
190D PHE* 1.3 81.2 + - - +
192D TYR* 1.3 63.6 + - - +
193D ILE* 4.3 1.0 - - - +
274D GLY 5.7 2.9 - - - +
275D LYS* 3.9 27.7 - - + +
277D TYR* 3.8 19.7 + - - +
334D ILE 4.0 0.9 - - - +
335D GLY* 3.5 0.2 - - - -
336D PHE 3.1 28.2 + - - +
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Residues in contact with TYR 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 PHE* 3.4 36.1 - - + +
191D HIS* 1.3 77.7 - - - +
193D ILE* 1.3 67.2 + - - +
194D ASN* 4.3 2.5 - - - +
273D GLY* 5.1 4.2 - - - -
274D GLY 5.2 3.1 + - - -
326D GLU* 2.5 32.4 + - + -
328D ASP* 4.6 2.9 - - + -
333D ARG* 3.2 65.1 + - + +
334D ILE* 3.4 3.4 - - - -
335D GLY* 3.4 25.1 - - - -
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Residues in contact with ILE 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 HIS 4.3 0.4 - - - +
192D TYR* 1.3 79.4 - - - +
194D ASN* 1.3 75.7 + - - +
203D ILE* 3.8 30.2 - - + +
204D GLN* 4.5 11.0 - - + +
272D LEU* 3.9 27.1 - - + +
273D GLY* 3.9 16.2 - - - +
277D TYR* 4.2 9.4 - - - +
333D ARG* 3.8 2.9 - - - -
334D ILE 2.8 45.6 + - - +
336D PHE* 3.6 31.6 - - + -
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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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192D TYR* 5.3 1.6 - - - +
193D ILE* 1.3 83.6 - - - +
195D LEU* 1.3 69.8 + - - +
196D ILE* 3.8 0.5 + - - +
203D ILE* 3.5 10.5 - - - +
204D GLN* 4.9 1.9 + - - +
331D ASN 4.4 5.8 + - - -
332D ASN 3.6 7.2 - - - +
333D ARG* 3.5 24.6 - - - +
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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