Contacts of the strand formed by residues 202 - 207 (chain D) in PDB entry 3H3B
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 ALA 202 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 4.2 4.2 + - - +
182D ILE* 3.6 30.1 - - + -
194D TYR* 3.4 16.9 - - + -
198D PHE* 3.0 10.9 + - + +
199D LYS 3.7 12.3 - - - +
200D ASN 5.2 0.2 - - - -
201D LYS* 1.3 80.2 + - + +
203D ALA* 1.3 61.9 + - - +
204D PHE* 4.3 9.9 - - + -
215D MET* 4.3 2.5 - - + -
216D GLN 3.4 6.1 - - - +
217D LEU* 4.2 12.3 - - + -
218D ASN* 5.0 1.8 - - - -
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Residues in contact with ALA 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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89A ASN* 3.7 20.0 - - - +
90A TYR* 5.9 0.2 - - - +
157A LEU* 4.9 5.8 - - + -
159A LEU* 3.7 32.2 - - + +
194D TYR* 3.3 5.8 - - - -
202D ALA* 1.3 77.8 - - - +
204D PHE* 1.3 65.2 + - - +
205D THR* 4.1 0.5 + - - +
214D PHE 3.9 0.3 - - - +
215D MET* 3.4 4.0 - - - -
216D GLN* 2.9 36.6 + - + +
218D ASN* 5.3 1.1 - - - +
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Residues in contact with PHE 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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90A TYR* 4.0 4.9 + - - -
161A LEU* 3.8 7.4 - - - +
170D TRP* 3.4 34.1 - + + +
182D ILE* 3.8 14.4 - - + -
183D GLY* 3.5 38.6 - - - -
184D HIS* 3.6 16.4 - - - -
185D ILE* 3.8 22.3 - - + +
192D SER* 3.7 21.3 + - - +
193D THR 3.8 2.0 - - - -
194D TYR* 2.8 41.7 + + - -
202D ALA* 4.3 1.3 - - + -
203D ALA* 1.3 79.0 - - - +
205D THR* 1.3 68.4 + - - +
214D PHE 3.5 4.3 - - - +
215D MET* 3.8 19.1 - - + -
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Residues in contact with THR 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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90A TYR* 3.9 9.4 - - - +
159A LEU* 4.3 25.5 - - + +
160A THR 4.1 16.8 + - - +
161A LEU* 3.8 24.9 - - + -
153D LYS* 5.0 6.1 + - - -
185D ILE* 4.2 1.7 - - - +
203D ALA 4.1 0.8 + - - +
204D PHE* 1.3 79.9 - - - +
206D VAL* 1.3 64.9 + - - +
213D ALA* 4.2 0.3 - - - +
214D PHE* 2.7 59.0 + - - +
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Residues in contact with VAL 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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161A LEU* 3.6 17.7 - - + +
162A ILE 5.6 0.3 + - - -
163D PHE* 4.1 15.7 - - + -
185D ILE* 3.9 31.4 - - + +
186D SER 4.3 2.2 - - - +
187D SER* 3.6 28.5 - - - +
190D ALA* 4.4 13.0 - - + -
205D THR* 1.3 80.9 - - - +
207D ASP* 1.3 60.0 + - - +
208D THR* 3.9 6.2 + - - +
212D THR 3.4 5.6 - - - +
213D ALA* 3.8 21.3 - - + -
214D PHE* 4.6 2.5 - - - -
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Residues in contact with ASP 207 (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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163D PHE* 4.0 2.9 - - - -
206D VAL* 1.3 70.5 - - - +
208D THR* 1.3 59.3 + - - +
209D SER* 2.9 24.2 + - - -
210D SER* 2.9 25.2 + - - +
211D SER* 3.0 23.0 + - - -
212D THR 2.8 19.5 + - - +
214D PHE* 4.1 16.9 - - + -
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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