Contacts of the strand formed by residues 247 - 251 (chain D) 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 247 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLU* 3.4 21.0 + - + +
141D SER* 4.0 9.2 - - - +
143D GLY* 3.1 24.0 + - - -
154D LEU* 3.8 37.2 - - + -
226D ALA 3.8 0.2 - - - +
227D VAL* 3.5 2.9 - - - -
228D TYR* 2.8 39.6 + - + +
246D GLY* 1.3 74.2 - - - -
248D LEU* 1.3 60.9 + - - +
249D VAL* 3.6 1.8 + - + -
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 5.2 3.4 - - - +
16A MET* 3.4 56.2 - - + +
17A LEU* 4.4 9.9 - - + +
20A GLN* 2.4 45.3 - - + +
81A LEU* 6.3 0.7 - - + -
143D GLY* 3.4 3.3 - - - -
144D GLY 2.9 22.2 + - - -
226D ALA 3.7 10.5 - - - +
227D VAL* 4.2 9.6 - - + +
247D THR* 1.3 74.6 + - - +
249D VAL* 1.3 72.9 + - - +
250D THR* 3.7 12.1 - - - +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D GLY* 3.8 11.4 - - - -
144D GLY 3.5 2.0 - - - -
146D VAL* 5.3 0.4 - - + -
152D LEU* 3.8 29.4 - - + -
154D LEU* 4.1 14.6 - - + -
217D MET* 4.1 14.6 - - + -
220D LEU* 5.3 1.6 - - + -
224D ASP 4.2 5.4 - - - +
225D THR* 3.2 3.6 - - - +
226D ALA 2.8 42.7 + - - +
228D TYR* 3.8 22.9 - - + -
247D THR 3.6 1.1 + - - +
248D LEU* 1.3 78.9 - - - +
250D THR* 1.3 64.1 + - - +
251D VAL* 4.5 13.7 - - + -
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Residues in contact with THR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU 4.9 0.9 - - - +
16A MET* 3.5 35.6 + - - +
19A ALA* 3.4 27.4 - - + +
20A GLN* 4.6 0.2 + - - -
149A MET* 5.4 1.1 - - + -
144D GLY 2.8 12.9 + - - +
145D LEU* 3.4 15.2 - - + +
146D VAL* 3.1 27.0 + - - +
225D THR* 3.7 9.6 - - + +
248D LEU* 3.7 13.5 - - - +
249D VAL* 1.3 74.2 - - - +
251D VAL* 1.3 69.8 + - - +
252D SER* 4.1 5.4 - - - +
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Residues in contact with VAL 251 (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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146D VAL* 3.3 18.2 - - + +
147D GLN 4.1 2.5 - - - +
148D PRO* 3.7 31.0 - - + -
220D LEU* 4.1 12.8 - - + -
221D ARG* 3.2 37.9 - - - +
222D ALA* 3.7 15.4 - - - +
224D ASP* 4.5 8.5 - - + -
225D THR* 3.0 20.2 + - - +
249D VAL* 4.5 8.1 - - + -
250D THR* 1.3 78.5 - - - +
252D SER* 1.3 63.0 + - - +
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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