Contacts of the strand formed by residues 349 - 357 (chain D) in PDB entry 1WUU
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 GLY 349 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D SER* 3.9 0.7 - - - -
227D VAL* 3.2 17.0 - - - -
229D HIS 4.7 0.4 - - - -
322D CYS* 3.6 15.8 - - - -
325D LEU* 3.2 23.0 - - - +
344D THR 5.2 2.4 - - - +
347D GLY* 4.2 9.2 + - - -
348D PHE* 1.3 77.1 - - - +
350D GLY* 1.3 66.7 + - - -
351D CYS 3.7 1.4 + - - +
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Residues in contact with GLY 350 (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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136D GLY 4.3 5.1 + - - -
137D GLY* 3.4 22.9 - - - -
138D GLY* 5.2 1.1 - - - -
224D ASN* 3.8 12.1 - - - -
225D SER* 2.6 35.0 + - - -
227D VAL 2.6 18.7 + - - -
228D ARG* 4.9 0.2 - - - +
325D LEU* 3.6 3.5 - - - +
349D GLY* 1.3 74.0 - - - +
351D CYS* 1.4 56.8 + - - -
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Residues in contact with CYS 351 (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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137D GLY 3.0 15.3 + - - +
139D LEU* 3.5 20.9 - - + -
222D ILE* 3.4 29.8 - - + -
223D THR 2.9 7.4 - - - -
224D ASN* 3.6 30.7 - - - -
325D LEU* 3.6 7.7 - - - +
344D THR* 3.1 36.5 + - + +
349D GLY 3.7 0.8 + - - +
350D GLY* 1.4 68.6 - - - -
352D THR* 1.3 64.4 + - - +
379D TYR* 4.8 1.3 - - - -
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Residues in contact with THR 352 (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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222D ILE* 3.3 10.4 - - - +
223D THR* 2.6 48.5 + - - +
325D LEU* 3.5 40.8 - - + +
328D LEU* 4.4 15.6 + - + +
329D VAL* 4.4 5.8 - - + -
341D SER* 4.7 1.5 + - - -
342D ARG 2.8 22.7 - - - +
343D MSE 4.0 4.0 - - - +
344D THR* 3.8 3.7 - - - +
351D CYS* 1.3 74.2 - - - +
353D VAL* 1.3 61.1 + - - +
354D THR* 4.1 8.7 + - - -
368D ILE* 6.1 0.7 - - - +
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Residues in contact with VAL 353 (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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38D VAL* 3.6 22.2 - - + -
39D ASN 3.7 20.4 - - - +
40D LEU* 3.8 17.9 - - + +
220D VAL* 3.6 27.6 - - + -
221D LEU 3.4 1.6 - - - +
222D ILE* 4.5 1.1 - - + -
307D MSE 4.6 6.5 - - - +
341D SER* 3.5 4.4 - - - -
342D ARG* 2.7 49.0 + - + +
344D THR* 3.8 9.2 - - - -
352D THR* 1.3 75.5 - - - +
354D THR* 1.3 66.4 - - - +
355D LEU* 4.2 1.9 + - + +
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Residues in contact with THR 354 (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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220D VAL* 3.3 4.7 - - - -
221D LEU* 2.4 71.6 + - + +
223D THR* 4.9 2.9 + - - -
332D ALA* 4.5 9.9 - - + +
338D VAL* 4.0 22.9 - - + -
340D GLY 3.2 11.7 - - - +
341D SER* 2.4 24.5 + - - +
352D THR* 4.1 9.2 + - - -
353D VAL* 1.3 77.4 - - - +
355D LEU* 1.4 59.2 + - - +
356D LEU* 3.4 7.5 - - + +
364D ALA* 6.1 0.2 - - + -
368D ILE* 5.0 2.6 - - + +
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Residues in contact with LEU 355 (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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40D LEU* 5.9 3.4 - - + -
213D LEU* 6.1 2.7 - - + -
218D LEU* 3.5 28.9 - - + -
219D ALA 3.3 14.8 - - - +
220D VAL* 3.9 15.9 - - + -
295D LEU* 5.0 3.6 - - + -
300D TYR* 4.3 25.1 - - + +
303D PHE* 3.3 37.5 - - + -
307D MSE 3.8 20.7 - - + +
338D VAL* 3.6 0.5 - - - -
339D TYR* 2.6 36.7 + - + +
340D GLY 3.6 7.3 + - - +
353D VAL* 4.2 1.4 + - + +
354D THR* 1.4 69.7 - - - +
356D LEU* 1.3 56.9 + - - +
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Residues in contact with LEU 356 (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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218D LEU* 3.0 4.7 - - - +
219D ALA* 2.7 67.5 + - + +
220D VAL 4.1 0.9 - - - +
221D LEU* 4.1 10.3 - - + +
337D GLY 3.4 9.6 - - - +
338D VAL* 3.7 14.1 - - + -
339D TYR* 3.1 14.1 - - - -
354D THR* 3.4 20.2 - - + +
355D LEU* 1.3 79.0 - - - +
357D GLU* 1.3 69.3 + - - +
358D ALA 4.6 0.4 - - - +
360D ALA* 3.5 11.2 - - + +
361D ALA* 3.5 35.0 - - + +
364D ALA* 4.4 9.4 - - + -
380D LEU* 5.4 1.6 - - + -
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Residues in contact with GLU 357 (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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375B THR* 3.0 33.1 + - - +
217D LYS 3.3 9.4 - - - +
336D PRO 5.2 0.2 - - - +
337D GLY* 3.3 18.4 + - - +
339D TYR* 2.9 33.2 + - + +
356D LEU* 1.3 78.7 - - - +
358D ALA* 1.3 71.9 + - - +
359D SER* 3.3 13.6 + - - +
360D ALA* 2.5 30.3 + - + +
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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