Contacts of the helix formed by residues 317 - 329 (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 LYS 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B PHE* 3.4 33.6 - - + +
310B VAL* 3.5 19.3 - - - +
311B ALA* 3.4 16.1 - - - +
312B GLY 4.1 1.8 - - - +
313B CYS 2.8 19.3 + - - +
314B GLU* 2.7 48.3 + - - +
316B ALA* 1.3 78.9 - - - +
318B LEU* 1.3 65.7 + - + +
319B GLU 3.2 0.6 + - - -
320B ILE* 3.4 5.9 + - - +
321B MET* 3.2 45.3 + - + +
357B LEU* 4.6 16.1 - - + +
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Residues in contact with LEU 318 (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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314B GLU* 3.4 16.5 + - - +
315B GLU* 4.3 23.5 + - - +
316B ALA 3.5 0.2 - - - -
317B LYS* 1.3 79.8 - - + +
319B GLU* 1.3 59.5 + - + +
321B MET* 3.2 28.9 + - + +
322B GLU* 2.8 26.2 + - - +
771B SER 4.3 11.2 - - - +
772B LEU* 4.0 7.2 - - + -
773B PRO* 3.7 40.4 - - + -
776B LEU* 4.6 7.6 - - + +
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Residues in contact with GLU 319 (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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534A ARG* 6.3 0.2 - - - +
556A LEU* 2.6 39.6 - - - +
315B GLU 3.9 18.2 - - - +
316B ALA 4.0 3.5 + - - +
317B LYS 3.2 1.2 - - - -
318B LEU* 1.3 79.8 - - + +
320B ILE* 1.3 59.1 + - - +
322B GLU* 3.5 16.3 - - - +
323B PHE* 3.4 28.4 + - - -
471B ARG* 3.1 29.6 + - - +
473B ILE* 3.3 32.4 - - + +
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Residues in contact with ILE 320 (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* 5.3 4.9 - - + -
316B ALA 4.2 3.6 + - - +
317B LYS 3.4 7.6 + - - +
318B LEU 3.3 0.4 - - - -
319B GLU* 1.3 73.2 - - - +
321B MET* 1.3 61.4 + - - +
322B GLU 3.1 1.1 - - - -
323B PHE* 3.0 27.8 + - + +
324B VAL* 3.1 16.0 + - + +
346B LEU* 3.8 28.0 - - + -
357B LEU* 3.7 37.5 - - + +
361B THR* 3.3 32.8 - - + +
450B LEU* 4.2 15.3 - - + -
473B ILE* 3.7 17.5 - - + -
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Residues in contact with MET 321 (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* 3.6 40.8 - - + -
317B LYS* 3.2 36.0 + - + +
318B LEU* 3.2 23.7 + - + +
320B ILE* 1.3 77.1 - - - +
322B GLU* 1.3 55.6 + - - +
324B VAL* 3.6 6.7 + - - +
325B ASN* 3.1 19.1 + - - +
772B LEU* 3.7 31.6 - - + -
776B LEU* 3.4 23.1 - - + +
779B TRP* 3.6 26.8 - - + +
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Residues in contact with GLU 322 (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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530A LEU* 4.1 8.0 - - - +
534A ARG* 3.5 31.7 + - - -
318B LEU 2.8 12.0 + - - +
319B GLU* 3.5 19.9 - - - +
320B ILE 3.1 0.2 - - - -
321B MET* 1.3 76.7 - - - +
323B PHE* 1.3 60.2 + - - +
325B ASN* 3.2 8.0 + - - +
326B PHE* 3.0 46.4 + - + -
333B TYR* 3.3 33.8 - - - +
471B ARG* 4.5 19.8 + - - -
776B LEU* 4.1 6.5 - - + +
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Residues in contact with PHE 323 (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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319B GLU 3.4 16.3 + - - -
320B ILE* 3.0 18.4 + - + +
322B GLU* 1.3 77.3 - - + +
324B VAL* 1.3 65.1 + - + +
326B PHE* 3.4 45.5 + + - +
327B LEU* 3.6 13.4 + - - +
341B PRO* 4.5 5.4 - - + -
343B GLY* 3.8 12.3 - - - -
344B ALA* 3.6 44.4 - - + -
403B ILE* 5.4 4.5 - - + -
448B VAL* 4.1 21.1 - - + +
450B LEU* 3.6 25.1 - - + -
471B ARG* 4.1 21.1 - - - -
473B ILE* 4.1 4.9 - - + -
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Residues in contact with VAL 324 (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* 5.2 6.7 - - + -
320B ILE* 3.1 15.5 + - + +
321B MET* 3.9 3.1 - - - +
323B PHE* 1.3 75.8 - - - +
325B ASN* 1.3 58.2 + - - +
327B LEU* 3.3 9.2 + - + +
328B LYS* 3.1 40.2 + - + +
361B THR* 4.2 17.3 - - + -
365B ALA* 3.7 32.3 - - + -
367B VAL* 5.7 1.8 - - + -
403B ILE* 4.8 3.6 - - + -
779B TRP* 3.4 34.8 - - + +
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Residues in contact with ASN 325 (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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321B MET 3.1 15.3 + - - +
322B GLU* 3.2 13.9 + - - +
324B VAL* 1.3 76.0 - - - +
326B PHE* 1.3 59.2 + - - +
328B LYS* 4.6 1.1 - - - +
329B ASN* 2.9 55.0 + - - +
332B GLN* 3.0 21.3 + - - +
333B TYR* 3.0 24.1 + - - +
775B GLY 3.2 16.2 + - - -
776B LEU* 4.3 5.3 - - - +
779B TRP* 3.6 16.1 - - + -
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Residues in contact with PHE 326 (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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530A LEU* 4.2 5.4 - - + -
322B GLU* 3.0 32.5 + - + -
323B PHE* 3.5 41.7 - + - +
324B VAL 3.2 0.4 - - - -
325B ASN* 1.3 80.3 - - - +
327B LEU* 1.3 64.7 + - + +
329B ASN 3.8 4.1 - - - +
330B PRO* 3.8 19.1 - - - +
333B TYR* 3.5 46.9 - + + -
340B ILE* 3.6 28.7 - - + +
341B PRO* 3.6 37.2 - - + -
446B ASN* 5.0 3.1 - - - +
448B VAL* 5.3 5.8 - - + -
471B ARG* 5.9 0.9 - - - -
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Residues in contact with LEU 327 (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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323B PHE 3.6 10.5 + - - +
324B VAL* 3.3 8.8 + - + +
326B PHE* 1.3 82.4 - - + +
328B LYS* 1.3 63.3 + - + +
330B PRO* 4.1 9.2 - - - +
367B VAL* 4.0 31.2 - - + -
401B PRO* 4.4 6.7 - - + +
402B CYS 4.1 13.5 - - - +
403B ILE* 3.8 17.5 - - + -
446B ASN* 3.8 49.3 + - + +
447B VAL 4.4 0.2 - - - +
448B VAL* 3.8 31.6 - - + +
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Residues in contact with LYS 328 (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 VAL* 3.1 30.5 + - + +
325B ASN* 4.6 1.8 - - - +
327B LEU* 1.3 81.0 - - + +
329B ASN* 1.3 75.6 + - - +
330B PRO* 3.7 6.0 - - - +
365B ALA* 5.7 0.2 - - - +
366B ASN* 4.4 18.3 - - - +
367B VAL* 3.5 38.3 - - + +
401B PRO* 6.0 0.2 - - - +
778B ASP* 5.4 5.4 - - + +
779B TRP* 5.1 4.0 - - + -
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Residues in contact with ASN 329 (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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325B ASN* 2.9 39.5 + - - +
326B PHE* 3.8 3.3 - - - +
328B LYS* 1.3 89.0 - - - +
330B PRO* 1.3 58.3 - - - +
331B LYS* 3.2 12.2 + - + +
332B GLN* 4.4 18.1 + - + +
333B TYR* 3.8 15.6 - - - -
778B ASP* 3.6 22.2 + - - -
779B TRP* 5.2 0.4 - - - -
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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
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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