Contacts of the helix formed by residues 355 - 365 (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 THR 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LYS* 1.3 77.9 - - - +
356B LEU* 1.3 59.8 + - - +
357B LEU 3.3 1.8 - - - -
358B ALA* 3.1 6.3 + - - +
359B LYS* 3.0 31.2 + - - +
405B PHE* 4.4 5.8 - - + -
407B ASP* 3.3 23.2 + - - +
801B ANP 2.8 14.3 + - - +
802B MG 2.1 32.3 - - - -
440C GLY* 4.0 24.2 - - - -
441C PHE* 4.3 15.8 - - + -
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Residues in contact with LEU 356 (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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305B VAL* 3.7 34.8 - - + -
309B ASP* 3.5 28.0 - - + +
310B VAL* 4.7 6.5 - - + -
353B GLY* 3.4 7.4 + - - +
355B THR* 1.3 74.8 - - - +
357B LEU* 1.3 57.3 + - - +
359B LYS* 3.1 17.0 + - + +
360B ALA* 2.9 26.5 + - - +
801B ANP 3.1 73.3 + - + +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 4.4 15.5 - - + -
310B VAL* 3.7 38.5 - - + +
313B CYS* 5.1 4.3 - - + -
316B ALA* 4.0 17.7 - - + +
317B LYS* 4.6 13.2 - - + -
320B ILE* 3.7 31.0 - - + +
346B LEU* 5.0 2.5 - - + -
353B GLY 3.0 16.9 + - - +
356B LEU* 1.3 76.7 - - - +
358B ALA* 1.3 57.3 + - - +
360B ALA* 3.9 1.1 - - - +
361B THR* 2.8 25.8 + - - -
475B ILE* 3.8 24.9 - - + -
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.9 2.6 - - + +
354B LYS 4.4 2.3 + - - +
355B THR* 3.1 12.4 + - - +
357B LEU* 1.3 77.4 - - - +
359B LYS* 1.3 63.1 + - - +
360B ALA 3.3 0.4 - - - -
361B THR* 3.5 8.4 + - - -
362B ALA* 3.4 13.9 + - - +
369B PHE* 3.8 8.4 - - + -
405B PHE* 3.6 48.7 - - + -
450B LEU* 4.7 8.5 - - + -
441C PHE* 3.7 10.7 - - + -
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Residues in contact with LYS 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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303B ILE* 4.9 13.1 - - + +
305B VAL* 3.9 25.3 - - + +
355B THR* 3.0 21.0 + - - +
356B LEU* 3.1 24.8 + - + +
358B ALA* 1.3 78.9 - - - +
360B ALA* 1.3 57.1 + - - +
362B ALA* 3.0 18.7 + - - +
363B GLY 3.3 8.3 + - - -
801B ANP 4.3 16.9 + - - -
439C ASP* 4.5 9.9 + - - -
440C GLY* 3.3 36.5 + - - -
441C PHE* 3.6 26.2 - - + +
443C THR* 5.8 1.2 - - - -
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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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305B VAL* 3.6 14.5 - - + +
306B LYS 3.4 25.1 - - - +
307B PHE* 3.6 20.8 - - + -
310B VAL* 4.0 9.2 - - + -
356B LEU 2.9 13.8 + - - +
357B LEU 3.8 2.9 + - - +
358B ALA 3.3 0.2 - - - -
359B LYS* 1.3 74.6 - - - +
361B THR* 1.3 60.2 + - - +
364B GLU* 3.0 34.3 + - - +
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Residues in contact with THR 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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307B PHE* 4.3 9.7 - - + -
320B ILE* 3.3 29.2 - - + +
324B VAL* 4.2 13.7 - - + -
357B LEU 2.8 17.0 + - - -
358B ALA* 3.7 11.9 - - - -
359B LYS 3.2 0.6 - - - -
360B ALA* 1.3 78.0 - - - +
362B ALA* 1.3 61.7 + - - +
364B GLU 4.8 0.2 - - - +
365B ALA* 3.2 24.5 + - - +
367B VAL* 5.4 0.3 - - - +
403B ILE* 3.7 41.3 - - + +
450B LEU* 4.5 1.1 - - + +
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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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299B LEU* 4.4 9.9 - - + -
301B ASP 5.6 2.2 - - - +
303B ILE* 4.6 8.3 - - + -
358B ALA 3.4 6.0 + - - +
359B LYS* 3.0 12.1 + - - +
361B THR* 1.3 80.8 - - - +
363B GLY* 1.3 58.4 + - - +
365B ALA 3.4 13.2 - - - +
367B VAL 4.5 5.5 - - - +
369B PHE* 3.5 45.8 - - + +
403B ILE* 5.7 0.4 - - - -
441C PHE* 4.9 0.2 - - + -
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Residues in contact with GLY 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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301B ASP 5.8 1.8 - - - -
303B ILE* 4.9 11.2 - - - +
305B VAL 4.2 8.3 - - - -
306B LYS* 3.5 26.3 + - - -
359B LYS 3.3 8.9 + - - -
360B ALA 3.6 1.5 + - - -
362B ALA* 1.3 79.1 - - - +
364B GLU* 1.3 65.3 + - - +
365B ALA 3.9 2.9 - - - +
366B ASN* 5.0 3.1 - - - +
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Residues in contact with GLU 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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306B LYS* 3.3 34.3 - - - +
307B PHE* 3.4 53.5 + - + +
308B LYS 5.1 0.3 + - - -
360B ALA 3.0 17.8 + - - +
363B GLY* 1.3 75.5 - - - +
365B ALA* 1.3 64.4 + - - +
366B ASN* 3.5 10.2 + - - +
779B TRP* 5.3 13.3 - - + +
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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
----------------------------------------------------------
324B VAL* 3.7 37.2 - - + +
328B LYS* 5.6 0.9 - - - +
361B THR* 3.2 17.8 + - + +
362B ALA 3.4 19.1 - - - +
363B GLY 3.9 2.6 - - - +
364B GLU* 1.3 79.9 - - - +
366B ASN* 1.3 61.4 + - - +
367B VAL* 3.2 26.9 + - + +
403B ILE* 5.1 0.2 - - + -
779B TRP* 5.7 1.3 - - - +
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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