Contacts of the helix formed by residues 361 - 377 (chain B) in PDB entry 5D0B
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 ASP 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B PRO* 3.8 23.7 - - + +
333B ARG* 4.2 13.2 - - - +
359B GLU* 2.8 13.4 + - - +
360B LYS* 1.3 77.0 - - - +
362B GLU* 1.3 54.6 + - - +
363B GLU* 3.1 13.3 + - - +
364B ALA* 2.6 33.3 + - + +
365B LYS* 2.8 36.3 + - - +
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Residues in contact with GLU 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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360B LYS 3.6 6.7 + - - +
361B ASP* 1.3 73.6 - - - +
363B GLU* 1.3 62.0 + - + +
365B LYS* 3.3 14.1 - - + +
366B LEU* 3.2 29.8 + - + +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 3.4 31.8 - - + -
361B ASP* 3.1 10.1 + - - +
362B GLU* 1.3 76.9 - - + +
364B ALA* 1.3 65.3 + - - +
366B LEU* 3.4 17.2 + - + +
367B GLU* 3.3 25.6 + - - +
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 4.1 9.3 - - - -
330B PRO* 3.8 21.3 - - + +
333B ARG* 4.9 0.2 - - + -
334B GLY* 4.3 9.6 - - - +
359B GLU* 3.5 27.8 - - + +
361B ASP* 2.6 23.5 + - + +
363B GLU* 1.3 69.8 - - - +
365B LYS* 1.3 66.2 + - - +
367B GLU* 3.2 4.0 + - - +
368B ILE* 3.2 27.6 + - + +
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Residues in contact with LYS 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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356B LEU* 3.7 26.4 - - + +
359B GLU* 4.3 25.5 + - + +
360B LYS 6.1 0.7 - - - -
361B ASP 2.8 18.1 + - - +
362B GLU* 3.3 15.0 - - + +
364B ALA* 1.3 76.3 - - - +
366B LEU* 1.3 62.9 + - + +
368B ILE* 3.2 8.8 + - - +
369B GLU* 3.0 50.4 + - - +
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Residues in contact with LEU 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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42A SER* 3.5 46.4 - - - +
43A LEU* 3.9 16.7 - - + +
362B GLU* 3.2 16.5 + - + +
363B GLU* 3.6 17.9 - - + +
364B ALA 3.3 0.4 - - - -
365B LYS* 1.3 78.5 - - + +
367B GLU* 1.3 57.9 + - + +
369B GLU* 3.3 22.9 + - - +
370B LYS* 3.1 36.4 + - - +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 3.5 29.2 - - + +
230B ARG* 2.9 40.1 + - - -
334B GLY* 3.4 21.4 - - - +
335B THR* 5.3 0.5 - - - -
338B TRP* 4.0 16.1 - - - +
363B GLU 3.3 14.1 + - - +
364B ALA 3.2 9.4 + - - +
366B LEU* 1.3 75.4 - - + +
368B ILE* 1.3 64.2 + - - +
370B LYS* 2.8 34.9 + - - +
371B GLY* 3.1 17.5 + - - -
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Residues in contact with ILE 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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324B MET* 5.0 3.4 - - + +
333B ARG* 5.7 2.5 - - + +
334B GLY* 5.1 2.2 - - - -
337B ALA* 3.8 21.1 - - + -
352B LEU* 3.3 36.6 - - + +
355B ALA* 3.7 24.2 - - + +
356B LEU* 3.8 16.2 - - + +
359B GLU* 3.5 33.4 - - + -
364B ALA* 3.2 12.9 + - + +
365B LYS* 3.2 7.4 + - - +
367B GLU* 1.3 76.2 - - - +
369B GLU* 1.3 58.4 + - - +
371B GLY* 3.0 2.9 + - - -
372B ILE* 2.8 30.7 + - + +
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Residues in contact with GLU 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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39A LEU* 3.2 37.2 - - + +
42A SER* 4.5 1.3 + - - -
43A LEU* 4.3 4.7 - - + +
356B LEU* 3.7 19.3 - - + +
365B LYS* 3.0 40.9 + - - +
366B LEU* 3.4 30.9 - - - +
368B ILE* 1.3 78.4 - - - +
370B LYS* 1.3 61.2 + - - +
372B ILE* 3.4 9.2 + - + +
373B GLU* 3.1 24.6 + - - +
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Residues in contact with LYS 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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43A LEU* 4.1 24.7 - - + -
45A TYR* 4.5 13.2 - - + +
205A ASN* 4.8 2.6 + - - +
227B ASP* 3.2 36.2 + - - +
230B ARG* 4.3 0.6 - - - +
338B TRP* 3.8 14.1 - - + +
366B LEU* 3.1 19.5 + - - +
367B GLU* 2.8 44.2 + - - +
368B ILE 3.2 0.2 - - - -
369B GLU* 1.3 75.4 - - - +
371B GLY* 1.3 61.8 + - - +
373B GLU* 3.3 8.0 + - - +
374B LEU* 3.1 29.0 + - + +
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Residues in contact with GLY 371 (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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337B ALA 4.0 19.5 - - - -
338B TRP* 4.1 7.6 - - - -
341B GLY* 3.4 17.3 - - - -
352B LEU* 3.9 9.7 - - - +
367B GLU 3.1 8.9 + - - -
368B ILE 3.0 6.7 + - - -
370B LYS* 1.3 75.4 - - - +
372B ILE* 1.3 64.4 + - - +
374B LEU* 3.4 3.8 + - - -
375B LEU* 3.3 16.5 + - - +
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Residues in contact with ILE 372 (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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349B ALA* 5.3 1.1 - - + +
352B LEU* 3.8 27.4 - - + +
353B GLU* 3.8 30.1 - - + +
356B LEU* 3.6 31.0 - - + -
368B ILE* 2.8 26.4 + - + +
369B GLU* 3.7 9.9 - - - +
371B GLY* 1.3 77.3 - - - +
373B GLU* 1.3 63.1 + - - +
375B LEU* 3.2 14.3 + - - +
376B LYS* 3.4 35.2 + - + +
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Residues in contact with GLU 373 (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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36A ARG* 3.2 39.2 + - - -
39A LEU* 4.5 6.2 - - - +
205A ASN* 3.2 22.2 - - + +
206A PRO 4.5 0.7 - - - +
208A GLN* 3.1 33.2 + - - +
503A B12 3.8 18.3 - - - +
369B GLU 3.1 14.6 + - - +
370B LYS* 3.5 11.9 - - - +
372B ILE* 1.3 78.8 - - - +
374B LEU* 1.3 61.6 + - - +
376B LYS* 3.6 23.6 + - - +
377B ALA* 3.6 8.8 + - - +
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Residues in contact with LEU 374 (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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204A VAL 4.9 4.0 - - - +
205A ASN* 3.3 26.0 - - - +
338B TRP* 3.7 32.8 - - + +
341B GLY 3.6 15.0 - - - +
342B LYS* 4.0 43.1 - - + +
344B GLY* 6.0 0.2 - - - -
370B LYS 3.1 16.5 + - - +
371B GLY* 3.6 6.5 - - - +
372B ILE 3.2 0.4 - - - -
373B GLU* 1.3 76.0 - - - +
375B LEU* 1.3 59.4 + - - +
377B ALA* 3.1 26.4 + - + +
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Residues in contact with LEU 375 (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 ILE* 4.1 4.3 - - + +
341B GLY* 3.6 19.1 - - - +
344B GLY* 3.6 14.8 - - - +
345B ASP 3.3 48.0 - - - +
346B PRO* 4.0 13.6 - - + +
348B TYR 4.2 1.1 - - - -
349B ALA* 3.8 28.5 - - + +
352B LEU* 3.6 26.5 - - + -
371B GLY 3.3 3.6 + - - +
372B ILE* 3.2 10.1 + - - +
374B LEU* 1.3 76.4 - - - +
376B LYS* 1.3 65.2 + - + +
377B ALA 3.6 6.2 - - - +
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Residues in contact with LYS 376 (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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503A B12 4.4 23.7 - - + +
353B GLU* 5.3 3.3 + - - -
372B ILE* 3.6 33.3 - - + +
373B GLU* 3.7 19.3 + - - +
374B LEU 3.2 0.2 - - - -
375B LEU* 1.3 78.8 - - + +
377B ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 377 (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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205A ASN* 4.1 6.5 - - - +
206A PRO* 3.7 37.0 - - + -
373B GLU 3.6 7.7 + - - +
374B LEU* 3.1 18.4 + - + +
375B LEU 3.6 5.9 - - - +
376B LYS* 1.3 84.9 - - - +
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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