Contacts of the helix formed by residues 384 - 399 (chain B) in PDB entry 6NYY
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 VAL 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL 3.4 20.6 - - - +
292B GLY* 3.6 23.8 - - - +
377B PHE 4.4 0.4 - - - -
379B GLU* 3.7 25.6 - - + -
381B PHE* 3.5 27.6 + - + +
383B GLY* 1.3 80.8 - - - +
385B GLY* 1.3 57.0 + - - +
386B PRO 3.4 0.4 - - - -
387B ALA* 2.9 5.4 + - - +
388B ARG* 2.8 53.7 + - + +
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Residues in contact with GLY 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 3.3 24.6 + - - +
378B LEU* 4.9 2.5 - - - -
379B GLU 5.0 1.8 - - - +
381B PHE 4.9 0.4 + - - -
384B VAL* 1.3 78.7 - - - +
386B PRO* 1.3 64.7 - - - +
387B ALA 3.2 3.6 + - - -
388B ARG* 3.7 3.2 + - - +
389B VAL* 3.4 23.9 - - - +
426B GLU* 3.8 6.9 + - - -
430B THR* 3.5 16.5 - - - +
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Residues in contact with PRO 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLY* 4.3 8.7 - - - +
384B VAL 4.0 4.9 - - - +
385B GLY* 1.3 86.7 - - - +
387B ALA* 1.3 54.8 + - - +
390B ARG* 3.1 28.7 + - - +
426B GLU* 3.3 16.8 - - - +
429B ASN* 3.5 46.0 - - + +
430B THR* 3.5 3.4 - - - +
433B GLN* 3.6 21.8 - - + +
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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
----------------------------------------------------------
292B GLY* 5.4 7.6 - - - -
383B GLY 3.3 22.0 + - - +
384B VAL* 2.9 8.0 + - - +
386B PRO* 1.3 78.4 - - - +
388B ARG* 1.3 64.2 + - - +
389B VAL 3.3 2.0 - - - -
390B ARG* 3.4 32.6 - - - +
391B ASP* 3.5 13.0 + - - +
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 4.1 15.2 - - - +
292B GLY 4.2 8.1 - - - +
293B GLU* 2.9 31.5 + - - +
294B THR* 3.9 9.0 + - - +
295B THR* 4.6 4.3 - - - +
376B GLU 2.6 40.3 + - - -
377B PHE* 3.9 31.1 + - + +
378B LEU 4.6 1.0 + - - -
379B GLU* 2.8 38.4 + - - +
384B VAL* 2.8 33.6 + - + +
385B GLY 3.7 3.1 + - - +
387B ALA* 1.3 72.3 - - - +
389B VAL* 1.3 53.6 + - - +
391B ASP* 2.9 10.5 + - - +
392B LEU* 2.8 34.6 + - - +
390C ARG* 4.3 10.1 - - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 4.2 28.9 - - + -
385B GLY 3.4 18.8 + - - +
387B ALA 3.3 0.8 - - - -
388B ARG* 1.3 74.0 - - - +
390B ARG* 1.3 63.0 + - - +
392B LEU* 4.4 7.2 - - + +
393B PHE* 3.2 48.3 + - + +
430B THR* 4.3 11.4 - - + +
433B GLN* 3.8 19.5 - - + +
434B LEU* 4.0 27.1 - - + -
437B GLU* 5.2 0.5 - - - +
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PRO* 3.1 29.1 + - - +
387B ALA* 3.4 22.4 - - - +
388B ARG 3.2 0.4 - - - -
389B VAL* 1.3 75.5 - - - +
391B ASP* 1.3 55.5 + - - +
393B PHE* 3.3 3.9 + - - +
394B ALA* 2.7 38.8 + - - +
397B ARG* 5.4 0.3 + - - -
433B GLN* 3.2 32.5 + - - +
437B GLU* 5.9 3.4 - - - +
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY* 2.9 23.8 - - - +
294B THR* 3.8 23.4 + - + +
387B ALA 3.5 11.3 + - - +
388B ARG* 2.9 8.5 + - - +
390B ARG* 1.3 80.4 - - - +
392B LEU* 1.3 64.2 + - - +
394B ALA* 4.3 7.2 - - - +
395B LEU* 3.2 22.2 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR* 3.5 7.5 + - - +
296B ALA* 3.8 17.3 - - + -
370B ILE* 4.2 7.0 - - + +
371B THR 5.4 0.2 - - - +
372B VAL* 3.8 31.6 - - + -
377B PHE* 3.7 28.9 - - + -
388B ARG 2.8 17.9 + - - +
389B VAL* 4.1 8.7 - - + +
391B ASP* 1.3 74.8 - - - +
393B PHE* 1.3 65.9 + - + +
395B LEU* 3.2 7.9 + - + +
396B ALA* 3.2 23.0 + - - +
404B LEU* 3.8 30.5 - - + -
406B ILE* 4.6 10.1 - - + -
434B LEU* 6.5 0.2 - - + -
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B VAL* 3.2 26.1 + - + +
390B ARG* 3.5 1.8 - - - +
392B LEU* 1.3 83.6 - - + +
394B ALA* 1.3 61.2 + - - +
396B ALA* 3.8 9.4 + - + +
397B ARG* 3.3 24.2 + - - +
404B LEU* 3.6 30.7 - - + -
406B ILE* 5.1 1.3 - - + -
434B LEU* 3.6 44.0 - - + -
437B GLU* 3.5 37.2 - - + -
438B MET* 4.2 8.1 - - + -
441B PHE* 4.0 23.6 - + + -
449B ILE* 3.7 20.9 - - + -
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ARG* 2.7 23.5 + - + +
391B ASP* 4.3 8.3 - - - +
393B PHE* 1.3 72.7 - - - +
395B LEU* 1.3 63.8 + - - +
396B ALA 3.2 0.4 - - - -
397B ARG* 3.4 25.9 + - - +
398B LYS* 3.5 23.4 + - - +
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR* 5.0 7.9 - - + -
296B ALA* 4.0 27.8 - - + +
298B VAL* 3.7 33.0 - - + -
370B ILE* 3.9 18.4 - - + +
391B ASP 3.2 19.2 + - - +
392B LEU* 3.4 7.2 - - + +
394B ALA* 1.3 78.9 - - - +
396B ALA* 1.3 60.9 + - - +
397B ARG 3.3 0.5 + - - -
398B LYS* 3.4 12.2 + - + -
399B ASN* 3.4 25.1 + - - +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 3.7 17.7 - - + +
392B LEU 3.2 8.7 + - - +
393B PHE* 4.0 10.8 - - + +
394B ALA 3.2 0.8 - - - -
395B LEU* 1.3 75.5 - - - +
397B ARG* 1.3 57.3 + - - +
399B ASN* 2.9 18.5 - - - +
400B ALA* 3.4 12.1 - - - +
402B CYS* 3.5 18.9 - - - -
404B LEU* 3.8 15.9 - - + -
441B PHE* 5.6 0.4 - - + -
447B VAL* 4.1 15.7 - - + +
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ARG 5.4 0.2 + - - -
393B PHE 3.3 27.9 + - - +
394B ALA* 3.4 17.9 + - - +
395B LEU 3.2 1.2 - - - -
396B ALA* 1.3 77.6 - - - +
398B LYS* 1.3 64.8 + - + +
399B ASN 3.2 1.6 - - - -
400B ALA* 3.3 22.6 - - - +
437B GLU* 2.3 33.9 + - - -
440B GLY 4.2 11.1 + - - -
441B PHE* 4.3 11.1 - - + -
443B THR* 5.0 9.1 + - - -
444B THR* 5.5 10.4 - - - +
447B VAL* 5.4 9.2 - - + -
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Residues in contact with LYS 398 (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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394B ALA* 3.5 17.4 + - - +
395B LEU* 3.4 16.8 + - + +
397B ARG* 1.3 77.4 - - + +
399B ASN* 1.3 68.3 + - - +
400B ALA 3.7 1.2 + - - -
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Residues in contact with ASN 399 (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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298B VAL* 3.5 35.2 - - + +
368B PRO* 3.7 27.8 - - + +
370B ILE* 5.0 3.8 - - + +
395B LEU* 3.4 16.7 + - - +
396B ALA* 2.9 12.9 - - - +
398B LYS* 1.3 83.3 + - - +
400B ALA* 1.3 62.1 + - - +
401B PRO* 3.8 1.8 - - - -
402B CYS* 3.3 17.4 - - + +
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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