Contacts of the helix formed by residues 379 - 393 (chain B) in PDB entry 6YB9
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 SER 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU 6.1 1.1 - - - -
370A SER* 5.8 4.6 - - - -
372A LEU 5.4 3.8 - - - -
350B CYS* 3.6 6.2 - - - -
377B VAL* 3.5 4.7 - - - +
378B LEU* 1.3 76.4 - - - +
380B PRO* 1.3 65.3 - - - +
381B GLU* 3.6 13.2 + - - +
382B GLY* 3.1 23.9 + - - -
383B SER* 3.0 22.3 + - - -
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Residues in contact with PRO 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS* 4.0 32.1 - - + +
283B LYS* 4.1 18.6 - - + -
284B ILE* 3.7 27.2 - - + +
350B CYS* 3.7 10.3 - - - -
378B LEU 3.6 7.6 - - - +
379B SER* 1.3 84.8 - - - +
381B GLU* 1.3 76.8 + - - +
383B SER* 2.9 17.8 + - - +
384B ALA* 3.4 7.1 + - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LYS* 4.0 25.7 - - - +
287B ALA* 4.0 23.1 - - + +
291B PHE* 5.4 0.9 - - - -
379B SER* 3.6 11.5 + - - +
380B PRO* 1.3 82.2 - - - +
382B GLY* 1.3 57.7 + - - +
384B ALA* 3.2 6.1 + - - +
385B GLN* 3.0 28.0 + - - +
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Residues in contact with GLY 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU 4.0 17.3 - - - -
373A GLY* 3.7 4.7 - - - -
377B VAL* 3.7 8.2 - - - +
379B SER* 3.1 24.0 + - - -
381B GLU* 1.3 76.7 - - - +
383B SER* 1.3 54.3 + - - +
385B GLN* 3.3 9.2 + - - +
386B PHE* 2.9 29.8 + - - +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 3.8 19.8 - - - +
326B VAL* 4.1 7.9 - - - +
348B ILE* 4.0 15.0 - - - +
350B CYS* 3.8 19.0 - - - -
377B VAL* 3.9 15.9 - - - -
379B SER 3.0 13.5 + - - -
380B PRO* 2.9 19.6 + - - +
382B GLY* 1.3 72.1 - - - +
384B ALA* 1.3 59.3 + - - +
386B PHE* 3.4 4.9 + - - +
387B ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 6.4 0.2 - - - -
284B ILE* 3.8 10.5 - - + +
287B ALA* 3.6 28.0 - - + +
288B CYS* 3.8 27.0 - - - +
291B PHE* 4.5 3.0 - - + -
293B ILE* 5.2 1.0 - - - +
326B VAL* 6.3 0.2 - - - -
380B PRO 3.4 3.6 + - - +
381B GLU 3.2 9.8 + - - +
382B GLY 3.2 0.2 - - - -
383B SER* 1.3 79.0 + - - +
385B GLN* 1.3 58.9 + - - +
387B ALA* 3.1 6.9 + - - +
388B ALA* 2.8 29.1 + - - +
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Residues in contact with GLN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER 5.2 3.2 + - - -
371A GLY* 3.4 38.1 + - - -
372A LEU* 3.6 4.7 + - - +
373A GLY* 3.7 11.7 - - - +
291B PHE* 3.9 21.5 - - + -
381B GLU 3.0 13.4 + - - +
382B GLY* 3.3 10.3 + - - +
384B ALA* 1.3 75.1 - - - +
386B PHE* 1.3 56.8 + - - +
388B ALA* 3.2 2.8 + - - +
389B GLN* 2.9 56.1 + - - +
402B LEU* 4.1 14.7 - - + +
405B SER* 5.8 1.4 + - - -
406B ILE* 6.1 4.0 - - - +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PRO* 3.9 22.9 - - + -
347A VAL 3.5 22.4 - - - -
348A ILE* 4.4 4.5 - - + -
373A GLY* 3.3 26.2 - - - +
375A SER* 3.1 26.7 - - - -
386A PHE* 3.3 37.2 - + - -
390A ILE* 4.4 2.5 - - + -
348B ILE* 3.6 22.4 - - + -
375B SER* 4.2 0.7 - - - -
377B VAL* 4.5 5.2 - - + -
382B GLY 2.9 13.1 + - - +
383B SER 3.7 5.2 - - - +
384B ALA 3.2 0.2 - - - -
385B GLN* 1.3 73.3 - - - +
387B ALA* 1.3 65.0 + - - +
389B GLN* 3.1 20.3 + - - +
390B ILE* 3.0 31.4 + - + +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.8 31.0 - - + -
288B CYS* 5.2 0.4 - - - -
293B ILE* 4.7 0.9 - - + -
324B VAL* 4.3 15.7 - - + -
326B VAL* 5.3 1.1 - - + -
348B ILE* 4.4 2.7 - - + +
383B SER 2.9 14.1 + - - +
384B ALA* 3.1 11.2 + - - +
386B PHE* 1.3 76.9 - - - +
388B ALA* 1.3 61.2 + - - +
390B ILE* 3.3 14.1 + - - +
391B PHE* 3.1 30.0 + - + -
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 3.7 33.9 - - + -
293B ILE* 3.7 15.0 - - + +
384B ALA 2.8 12.6 + - - +
385B GLN 3.3 9.4 - - - +
386B PHE 3.2 0.2 - - - -
387B ALA* 1.3 73.6 - - - +
389B GLN* 1.3 53.0 - - - +
391B PHE 3.0 1.6 + - - -
392B GLY* 2.7 32.7 + - - -
398B VAL* 3.2 16.5 - - + +
402B LEU* 3.8 8.3 - - + -
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER* 4.5 8.6 + - - +
343A THR 4.3 12.7 + - - -
344A ALA 3.2 20.9 - - - +
345A TYR* 4.1 8.5 + - - +
346A PRO* 3.7 30.3 - - + +
347A VAL 4.4 2.1 + - - -
373A GLY* 4.3 11.8 - - - +
374A CYS 4.9 0.2 + - - -
385B GLN* 2.9 42.9 + - - +
386B PHE* 3.1 30.3 + - - +
388B ALA* 1.3 74.6 - - - +
390B ILE* 1.3 63.1 + - - +
392B GLY* 3.3 9.0 + - - -
393B LEU* 3.5 7.6 + - - +
402B LEU* 3.6 17.3 - - + +
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Residues in contact with ILE 390 (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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346A PRO* 4.2 9.2 - - + -
386A PHE* 4.5 6.7 - - + -
390A ILE* 3.7 41.2 - - + +
393A LEU* 3.5 32.0 - - + +
324B VAL* 4.0 19.7 - - + -
346B PRO* 4.5 4.0 - - + -
348B ILE* 4.6 3.8 - - + -
386B PHE* 3.0 44.1 + - + +
387B ALA* 3.5 9.0 - - - +
389B GLN* 1.3 76.3 - - - +
391B PHE* 1.3 62.2 + - + +
393B LEU* 3.4 20.6 + - - +
394B SER* 4.6 2.4 + - - -
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Residues in contact with PHE 391 (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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393A LEU* 3.9 22.0 - - + -
264B SER* 6.0 0.4 - - - -
265B GLN 4.6 1.8 - - - -
266B CYS* 3.6 35.4 - - + -
267B ARG 3.3 36.1 - - - -
268B VAL* 4.3 7.6 - - + -
293B ILE* 4.1 9.9 - - + -
322B PRO* 3.6 25.4 - - + -
324B VAL* 3.6 27.4 - - + -
387B ALA 3.1 20.2 + - - -
388B ALA 3.0 7.1 + - - +
390B ILE* 1.3 71.1 - - - +
392B GLY* 1.3 59.8 + - - +
393B LEU 3.1 2.7 - - - -
394B SER* 3.0 12.2 + - - +
395B ASN* 2.9 28.5 + - - +
398B VAL* 4.5 6.5 - - + -
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Residues in contact with GLY 392 (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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344A ALA 5.7 0.2 - - - -
345A TYR* 5.2 0.8 - - - -
178B LYS* 5.6 2.3 - - - +
388B ALA 2.7 19.1 + - - -
389B GLN 3.3 5.6 + - - -
390B ILE 3.2 0.8 - - - -
391B PHE* 1.3 71.6 - - - +
393B LEU* 1.3 62.8 + - - +
394B SER 3.2 0.9 + - - -
395B ASN 3.6 16.1 + - - +
396B HIS* 5.2 0.2 - - - -
398B VAL* 4.1 0.9 - - - +
399B TRP* 3.6 43.5 - - - +
402B LEU* 4.7 2.0 - - - -
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Residues in contact with LEU 393 (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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322A PRO* 4.1 27.3 - - + +
323A THR 3.7 24.2 - - - +
324A VAL* 4.1 3.1 - - + -
345A TYR* 3.6 32.8 - - + -
346A PRO* 3.9 13.7 - - + -
390A ILE* 3.3 34.3 - - + +
391A PHE* 4.0 18.2 - - + -
394A SER* 5.6 1.8 - - - +
389B GLN 3.5 7.0 + - - +
390B ILE 3.5 11.2 - - - +
391B PHE 3.1 1.0 - - - -
392B GLY* 1.3 78.2 - - - +
394B SER* 1.3 59.1 + - - +
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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
------------------------------------------------------------
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