Contacts of the helix formed by residues 358 - 372 (chain B) in PDB entry 6D1U
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 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B ALA* 4.7 1.1 - - - -
357B GLN* 1.3 75.2 - - - +
359B VAL* 1.3 58.9 + - - +
360B ASP* 3.6 8.2 + - - +
361B GLU* 2.9 45.1 + - - +
362B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 359 (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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191B LYS* 3.8 17.3 - - + +
194B LEU* 4.2 10.1 - - + -
195B THR* 3.6 34.1 - - + +
198B VAL* 4.0 31.0 - - + -
352B ALA* 4.3 8.2 - - + +
358B THR* 1.3 73.3 - - - +
360B ASP* 1.3 65.9 + - - +
362B ALA* 3.3 1.4 + - - +
363B LEU* 3.0 45.9 + - + +
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Residues in contact with ASP 360 (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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191B LYS* 3.3 44.0 - - - +
358B THR* 3.3 8.1 + - - +
359B VAL* 1.3 80.8 - - - +
361B GLU* 1.3 57.5 + - + +
363B LEU* 4.4 0.5 - - - +
364B LYS* 3.0 31.1 + - - +
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Residues in contact with GLU 361 (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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356B ARG 4.8 0.5 - - - +
357B GLN* 3.4 25.8 - - + +
358B THR* 2.9 43.2 + - - +
360B ASP* 1.3 76.9 - - + +
362B ALA* 1.3 66.7 + - - +
364B LYS* 3.8 6.5 - - - +
365B ASP* 3.2 28.1 + - - +
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Residues in contact with ALA 362 (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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194B LEU* 5.1 0.2 - - + -
348B ALA* 3.6 38.8 - - + +
352B ALA* 4.2 10.5 - - + +
357B GLN* 3.5 23.1 - - + +
358B THR 2.9 18.1 + - - +
359B VAL 3.7 3.6 - - - +
361B GLU* 1.3 77.7 - - - +
363B LEU* 1.3 58.9 + - + +
365B ASP* 3.4 3.8 + - - +
366B ALA 3.0 21.7 + - - -
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Residues in contact with LEU 363 (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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163B ILE* 5.9 7.4 - - + -
185B VAL* 3.3 33.6 - - + +
186B ASP* 3.4 17.0 - - + +
190B ALA* 3.9 7.9 - - + +
191B LYS* 3.8 39.0 - - + +
194B LEU* 3.9 21.8 - - + -
345B VAL* 5.9 4.7 - - + -
348B ALA* 4.0 13.9 - - + -
349B VAL* 6.1 0.2 - - + -
359B VAL* 3.0 27.0 + - + +
360B ASP 4.4 1.3 - - - +
362B ALA* 1.3 73.6 - - - +
364B LYS* 1.3 60.0 + - - +
366B ALA* 3.5 2.6 - - + +
367B GLN 2.9 24.3 + - - -
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Residues in contact with LYS 364 (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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186B ASP* 4.1 16.4 - - - +
360B ASP 3.0 20.1 + - - +
361B GLU* 3.8 7.9 - - - +
363B LEU* 1.3 76.6 - - - +
365B ASP* 1.3 70.7 + - - +
367B GLN* 3.4 6.0 + - + +
368B THR* 3.1 29.9 + - - +
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Residues in contact with ASP 365 (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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357B GLN* 2.9 26.8 + - - +
361B GLU 3.2 10.3 + - - +
362B ALA 3.6 8.7 - - - +
364B LYS* 1.3 84.8 + - - +
366B ALA* 1.3 53.8 + - - +
368B THR* 3.2 8.7 + - - -
369B ASN* 2.7 49.3 + - - +
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Residues in contact with ALA 366 (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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185B VAL* 3.3 22.2 - - + -
344B ALA* 3.4 33.8 - - + +
345B VAL* 4.5 2.9 - - - +
348B ALA* 3.9 9.4 - - + -
362B ALA 3.0 14.8 + - - +
363B LEU* 3.3 7.2 + - + +
365B ASP* 1.3 75.3 - - - +
367B GLN* 1.3 55.9 - - - +
369B ASN* 4.5 1.3 - - - +
370B ALA* 2.8 34.7 + - - +
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Residues in contact with GLN 367 (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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181B LYS 4.2 16.2 + - - -
183B VAL* 2.9 33.4 - - - +
185B VAL* 3.4 7.7 + - + +
186B ASP* 3.3 29.3 - - + +
363B LEU 2.9 13.6 + - - +
364B LYS* 3.4 10.5 - - + +
366B ALA* 1.3 76.0 - - - +
368B THR* 1.3 65.6 + - - +
370B ALA* 3.4 4.0 + - - +
371B ALA* 3.2 27.9 + - - +
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Residues in contact with THR 368 (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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364B LYS* 3.1 19.3 + - - +
365B ASP* 3.2 11.9 + - - -
367B GLN* 1.3 81.4 - - - +
369B ASN* 1.3 69.1 + - - +
371B ALA* 3.4 3.7 + - - +
372B ALA* 3.1 24.6 + - + +
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Residues in contact with ASN 369 (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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340B ALA* 4.2 12.2 - - - +
343B TYR* 4.7 17.1 - - + -
344B ALA* 3.7 22.5 + - + +
347B THR* 5.3 8.1 - - - +
365B ASP* 2.7 34.8 + - - +
366B ALA* 4.5 2.0 - - - +
368B THR* 1.3 80.3 - - - +
370B ALA* 1.3 61.6 + - - +
371B ALA 3.5 0.2 + - - -
372B ALA* 3.5 18.3 + - - +
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Residues in contact with ALA 370 (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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171B PHE* 4.5 13.1 - - + -
180B ILE 4.8 0.5 - - - +
183B VAL* 3.9 29.2 - - + -
185B VAL* 5.7 1.3 - - + -
337B GLN* 4.9 6.4 - - - +
340B ALA* 4.1 21.4 - - - +
341B PHE* 3.9 24.5 - - + -
344B ALA* 3.8 3.5 - - + +
345B VAL* 6.2 0.2 - - + -
366B ALA 2.8 20.8 + - - +
367B GLN 4.0 1.1 - - - +
369B ASN* 1.3 75.2 - - - +
371B ALA* 1.3 59.3 + - - +
372B ALA 4.7 1.4 - - - +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 4.2 21.2 - - - +
181B LYS* 4.6 10.1 - - + +
183B VAL* 4.4 8.1 - - + -
367B GLN* 3.2 25.0 + - - +
368B THR* 3.8 3.1 - - - +
370B ALA* 1.3 74.7 - - - +
372B ALA* 1.3 67.0 + - - +
373B GLU* 3.7 4.3 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLN* 6.1 0.7 - - - +
340B ALA* 5.7 3.6 - - - +
368B THR* 3.1 17.6 + - + +
369B ASN* 3.6 14.7 - - - +
370B ALA 3.5 4.5 - - - +
371B ALA* 1.3 81.1 - - - +
373B GLU* 1.3 61.7 + - - +
2116B ALA 5.5 2.6 - - - +
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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