Contacts of the strand formed by residues 212 - 217 (chain B) in PDB entry 3UX9
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 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER* 3.9 8.5 - - - +
156B CYS 3.3 18.6 - - - +
157B ALA* 4.7 4.6 - - + +
163B PHE* 3.4 7.5 - - - -
206B ARG* 3.6 1.9 - - - -
207B ASP 3.0 30.5 + - - -
210B LYS* 2.9 22.9 + - - +
211B ASN* 1.3 78.5 + - - +
213B LEU* 1.3 67.6 + - - +
214B TYR* 3.6 37.8 + - + +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU 3.6 0.2 - - - +
155B SER* 3.3 4.2 - - - -
156B CYS* 2.8 36.6 + - + +
163B PHE* 4.0 11.2 - - + -
168B MET* 3.7 28.9 - - + -
169B SER 3.9 5.8 - - - +
170B TRP* 3.3 32.6 - - + +
185B ILE* 3.5 28.5 - - + -
204B ILE* 3.8 9.4 - - + -
205B SER 3.4 17.9 - - - +
206B ARG* 4.5 4.0 - - + +
212B THR* 1.3 76.7 - - - +
214B TYR* 1.3 60.1 + - - +
230B CYS* 3.8 18.6 - - + -
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG* 3.5 43.4 + - + +
154B LEU 3.0 9.4 - - - +
155B SER* 3.5 20.4 - - - -
170B TRP* 2.9 16.4 + - - -
204B ILE* 3.6 4.2 - - - +
205B SER* 3.1 50.0 + - - +
206B ARG 4.0 4.5 - - - -
207B ASP* 4.0 31.3 + - + +
210B LYS* 5.0 3.6 - - - +
212B THR* 3.6 34.6 + - + +
213B LEU* 1.3 75.3 - - - +
215B LEU* 1.3 62.7 + - - +
216B GLN 5.1 0.2 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 3.7 0.5 - - - +
153B ARG* 3.5 3.4 - - - -
154B LEU* 2.9 35.6 + - + +
170B TRP* 3.4 42.6 - - + +
182B VAL* 4.5 2.7 - - + -
183B SER* 4.4 8.1 - - - -
202B PHE* 3.9 29.6 - - + -
203B THR 3.5 16.4 - - - +
204B ILE* 4.1 9.4 - - + +
214B TYR* 1.3 79.9 - - - +
216B GLN* 1.3 59.9 + - - +
217B MET* 3.5 23.1 + - + +
228B TYR* 4.2 20.6 - - + -
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 5.6 1.4 - - - -
152B LEU 3.4 12.4 + - - +
153B ARG* 3.3 31.6 - - - +
201B ARG 3.7 1.7 - - - +
202B PHE* 3.0 7.8 - - - +
203B THR* 2.9 48.4 + - + +
205B SER* 5.5 2.0 + - - +
214B TYR* 5.1 0.6 - - - +
215B LEU* 1.3 69.8 - - - +
217B MET* 1.3 58.5 + - - +
218B ASN* 3.5 30.5 + - - +
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 3.1 4.3 - - - -
152B LEU* 2.7 49.8 + - - +
154B LEU* 3.8 33.9 - - - -
202B PHE* 3.7 25.1 - - + -
215B LEU* 4.1 9.6 - - + +
216B GLN* 1.3 73.9 - - - +
218B ASN* 1.3 67.0 + - - +
220B LEU* 3.6 29.3 - - + +
228B TYR* 3.2 44.6 - - + +
249B VAL* 4.1 12.3 - - + -
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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