Contacts of the helix formed by residues 357 - 371 (chain B) in PDB entry 4BL8
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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351B ALA* 4.8 0.2 - - - -
356B GLN* 1.3 77.5 - - - +
358B VAL* 1.3 65.4 + - - +
359B ASP* 3.8 8.0 + - - +
360B ALA* 3.4 22.9 + - - +
361B ALA* 2.9 25.2 + - - +
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Residues in contact with VAL 358 (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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190B LYS* 4.2 11.9 - - + +
193B LEU* 4.0 10.1 - - + +
194B THR* 3.6 27.1 - - - +
197B VAL* 3.4 37.9 - - + -
351B ALA* 4.0 15.5 - - + +
356B GLN 3.9 0.6 + - - -
357B THR* 1.3 72.2 - - - +
359B ASP* 1.3 68.9 + - - +
361B ALA* 4.0 0.4 - - - +
362B LEU* 3.2 43.3 + - + +
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Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 3.4 43.6 + - - +
357B THR* 3.2 7.9 + - - +
358B VAL* 1.3 85.8 - - - +
360B ALA* 1.3 57.2 + - + +
363B ALA* 3.4 21.9 + - - +
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Residues in contact with ALA 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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356B GLN* 2.9 21.1 + - + +
357B THR* 3.2 17.7 + - - +
359B ASP* 1.3 77.2 - - + +
361B ALA* 1.3 61.2 + - - +
362B LEU 3.3 1.6 - - - -
363B ALA* 3.7 8.5 - - + +
364B ALA* 3.1 21.5 + - - +
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Residues in contact with ALA 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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347B ALA* 3.4 40.0 - - + +
350B ASN* 4.8 0.2 - - + -
351B ALA* 4.0 13.7 - - + +
356B GLN* 3.1 23.5 - - + +
357B THR 2.9 17.8 + - - +
358B VAL 4.0 2.2 - - - +
360B ALA* 1.3 78.9 - - - +
362B LEU* 1.3 58.3 + - + +
364B ALA* 3.4 4.7 - - - +
365B ALA 3.2 18.4 + - - -
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Residues in contact with LEU 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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159B TRP* 6.6 0.4 - - + -
162B ILE* 5.4 8.1 - - + -
184B VAL* 3.3 37.1 - - + +
185B ASP* 3.8 6.5 - - - +
189B ALA* 3.9 12.6 - - + +
190B LYS* 3.8 39.9 - - + +
193B LEU* 3.7 33.4 - - + -
344B VAL* 5.8 6.5 - - + -
347B ALA* 4.2 12.8 - - + -
348B VAL* 6.2 0.2 - - + -
358B VAL* 3.2 12.1 + - + +
359B ASP 4.7 1.6 - - - +
361B ALA* 1.3 76.9 - - - +
363B ALA* 1.3 64.1 + - - +
364B ALA 3.0 1.8 - - - -
365B ALA* 3.3 3.4 + - + +
366B GLN* 3.1 19.8 + - - +
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Residues in contact with ALA 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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185B ASP* 3.4 23.9 + - - +
190B LYS* 6.1 0.2 - - - +
359B ASP 3.4 19.3 + - - +
360B ALA* 4.0 8.3 - - - +
361B ALA 3.4 0.4 - - - -
362B LEU* 1.3 78.8 - - - +
364B ALA* 1.3 61.0 + - - +
366B GLN* 3.5 12.8 - - - +
367B THR* 3.5 12.5 + - - -
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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
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356B GLN* 4.1 9.0 - - - +
360B ALA 3.1 18.3 + - - +
361B ALA* 3.4 8.1 - - - +
362B LEU 3.0 0.4 - - - -
363B ALA* 1.3 75.1 - - - +
365B ALA* 1.3 64.7 + - - +
366B GLN 3.0 2.1 + - - -
367B THR* 3.3 4.1 + - - -
368B ASN* 3.1 39.0 + - - +
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Residues in contact with ALA 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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184B VAL* 3.5 18.0 - - + +
343B ALA* 3.4 37.3 - - + +
344B VAL* 4.4 4.5 - - + +
347B ALA* 4.0 7.4 - - + -
361B ALA 3.2 11.3 + - - +
362B LEU* 3.3 5.8 + - + +
364B ALA* 1.3 78.4 - - - +
366B GLN* 1.3 58.1 + - - +
368B ASN* 3.9 3.1 - - - +
369B ALA* 3.0 34.0 + - - +
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Residues in contact with GLN 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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180B LYS 4.9 4.9 + - - -
182B VAL* 3.3 42.2 + - - +
184B VAL* 3.4 16.3 + - - +
185B ASP* 3.4 32.0 + - + +
362B LEU 3.1 12.0 + - - +
363B ALA 3.5 12.3 - - - +
364B ALA 3.0 0.4 - - - -
365B ALA* 1.3 79.3 - - - +
367B THR* 1.3 63.8 + - - +
369B ALA* 4.2 1.7 - - - +
370B ALA* 3.7 19.4 + - - +
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Residues in contact with THR 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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363B ALA 3.5 11.9 + - - -
364B ALA* 3.3 7.3 + - - -
366B GLN* 1.3 79.6 - - - +
368B ASN* 1.3 68.1 + - - +
370B ALA* 3.7 4.4 + - + +
371B ALA* 3.4 23.2 + - - +
374B LEU* 5.5 0.4 - - - +
401B TRP* 6.3 0.2 - - + -
439B TYR* 4.2 23.2 - - + -
443B ARG* 4.5 15.7 - - - +
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Residues in contact with ASN 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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339B ALA* 4.9 6.4 - - - +
343B ALA* 4.3 14.9 + - + +
364B ALA* 3.1 31.1 + - - +
365B ALA* 4.3 3.6 - - - +
367B THR* 1.3 84.3 - - - +
369B ALA* 1.3 62.9 + - - +
370B ALA 3.3 0.2 - - - -
371B ALA* 4.0 7.8 + - - +
374B LEU* 4.4 27.1 - - + +
375B HIS* 5.4 3.1 + - - +
378B TYR* 5.8 7.9 + - + -
410B TYR* 3.7 21.1 + - - -
439B TYR* 6.2 0.2 - - - -
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Residues in contact with ALA 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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170B PHE* 4.9 8.7 - - + -
179B ILE* 5.6 0.5 - - - +
182B VAL* 4.1 26.5 - - + -
184B VAL* 5.4 1.1 - - + -
336B GLN* 5.1 5.0 - - - +
339B ALA* 4.1 15.3 - - - +
340B PHE* 4.2 23.5 + - + +
343B ALA* 4.0 13.4 - - + +
365B ALA 3.0 20.2 + - - +
366B GLN 4.2 0.7 - - - +
368B ASN* 1.3 77.4 - - - +
370B ALA* 1.3 62.2 + - - +
371B ALA 3.6 0.2 + - - -
375B HIS* 5.7 1.2 - - - +
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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
----------------------------------------------------------
179B ILE* 4.5 20.2 - - - +
180B LYS* 5.0 10.5 + - + +
182B VAL* 4.4 15.0 - - + +
336B GLN* 5.8 1.0 - - - +
366B GLN* 3.7 17.5 + - - +
367B THR* 3.7 6.4 + - - +
368B ASN 3.3 0.2 - - - -
369B ALA* 1.3 82.2 - - - +
371B ALA* 1.3 60.6 + - + +
372B PRO* 2.9 22.5 - - - +
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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
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367B THR 3.4 13.8 + - - +
368B ASN 4.0 4.0 + - - +
369B ALA 3.5 2.6 - - - -
370B ALA* 1.3 76.8 - - + +
372B PRO* 1.3 70.4 - - - +
373B GLY 3.3 2.0 - - - -
374B LEU* 3.2 20.3 + - + +
375B HIS* 3.2 12.3 + - - +
438B LEU 3.3 14.4 - - - +
439B TYR* 3.4 30.5 - - + +
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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