Contacts of the helix formed by residues 313 - 329 (chain D) 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 CYS 313 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C LYS* 6.1 3.1 - - - +
310D VAL* 4.1 17.3 - - - -
311D ALA 3.2 10.9 - - - -
312D GLY* 1.3 78.2 - - - +
314D GLU* 1.3 65.4 + - - +
315D GLU* 3.4 6.7 - - - +
316D ALA* 4.1 18.6 - - + +
317D LYS* 3.3 22.7 + - - +
352D THR 4.7 2.2 - - - -
353D GLY 5.2 0.7 - - - -
357D LEU* 4.8 4.9 - - - -
475D ILE* 3.9 27.6 - - + -
476D GLY 5.9 0.4 - - - +
801D ANP 4.3 5.8 - - - -
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C LYS* 5.6 7.4 - - + -
560C THR* 5.2 3.5 + - - +
311D ALA* 5.1 2.8 - - - +
312D GLY 4.5 4.2 + - - -
313D CYS* 1.3 74.1 - - - +
315D GLU* 1.3 73.1 + - - +
316D ALA 3.2 0.4 - - - -
317D LYS* 3.7 16.5 - - + +
318D LEU* 2.9 33.4 + - - +
485D SER* 5.1 0.5 + - - -
768D GLU* 2.8 45.7 - - - +
769D ASP 4.0 17.7 - - - +
770D THR* 3.3 29.2 - - + +
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C LEU* 3.4 36.7 - - + +
557C GLU 3.3 23.3 - - - +
558C LYS* 3.4 23.1 + - + +
559C LYS* 2.5 45.6 + - + +
560C THR* 4.0 6.2 + - - +
312D GLY 5.1 1.2 - - - +
313D CYS* 3.4 5.4 - - + +
314D GLU* 1.3 94.5 + - - +
316D ALA* 1.3 57.6 + - - +
318D LEU* 4.3 5.4 - - - +
319D GLU* 4.0 13.9 + - - +
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C LEU* 4.3 5.3 - - + +
313D CYS* 3.8 16.1 + - + +
314D GLU 3.2 0.2 - - - -
315D GLU* 1.3 78.1 - - - +
317D LYS* 1.3 62.0 + - - +
318D LEU 3.4 0.4 - - - -
319D GLU* 3.8 3.8 + - - +
320D ILE* 3.4 28.2 + - - +
357D LEU* 4.0 9.2 - - + -
473D ILE* 3.7 17.5 - - + +
474D PHE 5.0 1.1 - - - +
475D ILE* 3.7 30.5 - - + -
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PHE* 2.8 44.2 + - + +
308D LYS* 4.7 2.0 - - - +
310D VAL* 3.3 26.9 + - + +
311D ALA* 5.1 0.4 - - - -
313D CYS 3.3 20.3 + - - +
314D GLU* 3.7 19.5 - - + +
316D ALA* 1.3 78.8 - - - +
318D LEU* 1.3 52.9 + - - +
320D ILE* 2.9 5.2 + - - +
321D MET* 2.6 51.3 + - + +
357D LEU* 3.7 27.5 - - + +
770D THR* 5.6 7.7 - - - +
772D LEU* 6.1 1.7 - - - +
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C ARG* 3.8 30.1 - - - +
559C LYS* 6.1 5.2 - - + -
314D GLU* 2.9 18.0 + - + +
315D GLU* 4.7 5.6 - - - +
316D ALA 3.4 0.2 - - - -
317D LYS* 1.3 77.2 - - - +
319D GLU* 1.3 61.5 + - + +
321D MET* 4.3 6.1 - - - -
322D GLU* 3.2 30.5 + - - +
772D LEU* 4.2 13.0 - - + -
773D PRO* 3.7 33.0 - - + -
776D LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C ARG* 5.2 6.1 + - - +
551C ARG* 2.6 54.0 + - - +
556C LEU* 3.4 15.2 - - + +
315D GLU 4.0 11.7 + - - +
316D ALA* 3.8 5.2 + - - +
317D LYS 3.2 0.8 - - - -
318D LEU* 1.3 80.1 - - + +
320D ILE* 1.3 62.2 + - - +
322D GLU* 4.2 9.3 - - - +
323D PHE* 4.2 15.2 - - - -
471D ARG* 3.3 38.3 + - - +
473D ILE* 4.0 13.6 - - + +
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Residues in contact with ILE 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D PHE* 4.8 5.2 - - + -
316D ALA 3.4 16.2 - - - +
317D LYS* 2.9 7.4 + - - +
319D GLU* 1.3 81.8 - - - +
321D MET* 1.3 63.1 + - - +
322D GLU 3.2 0.9 - - - -
323D PHE* 3.2 32.2 + - + +
324D VAL* 3.7 8.5 + - - +
346D LEU* 3.7 30.1 - - + -
357D LEU* 3.7 29.2 - - + +
361D THR* 3.3 31.6 - - + +
450D LEU* 4.8 11.0 - - + -
473D ILE* 3.7 12.1 - - + -
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Residues in contact with MET 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D PHE* 3.7 37.2 - - + -
317D LYS* 2.6 40.2 + - - +
318D LEU* 4.0 7.2 - - - +
320D ILE* 1.3 73.3 - - - +
322D GLU* 1.3 56.2 + - - +
324D VAL* 3.3 4.1 + - - +
325D ASN* 2.8 30.3 + - - +
772D LEU* 3.8 36.3 - - + -
776D LEU* 3.9 14.4 - - + +
779D TRP* 3.6 46.1 - - + -
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C LEU* 4.1 16.2 - - + +
534C ARG* 2.6 41.7 + - + -
318D LEU 3.2 19.3 + - - +
319D GLU* 4.3 7.4 - - - +
320D ILE 3.2 0.6 - - - -
321D MET* 1.3 75.2 - - - +
323D PHE* 1.3 64.6 + - + +
325D ASN* 4.0 1.8 - - - -
326D PHE* 3.3 20.8 + - - +
333D TYR* 3.9 25.8 - - + +
341D PRO* 5.7 2.0 - - + +
471D ARG* 2.6 42.4 + - - +
776D LEU* 4.6 10.3 - - + -
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Residues in contact with PHE 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D GLU 4.2 16.2 - - - -
320D ILE* 3.2 19.0 + - + +
321D MET 3.2 0.8 - - - -
322D GLU* 1.3 82.3 - - + +
324D VAL* 1.3 66.9 + - + +
326D PHE* 3.5 6.6 + - - +
327D LEU* 3.3 27.9 + - - +
340D ILE* 5.3 2.7 - - + +
341D PRO* 3.6 39.5 - - + -
343D GLY* 4.0 12.6 - - - -
344D ALA* 3.6 32.3 - - + -
361D THR* 5.5 2.9 - - + -
403D ILE* 5.6 3.4 - - + -
448D VAL* 3.8 30.5 - - + -
450D LEU* 3.7 16.4 - - + -
471D ARG* 4.0 18.4 - - + -
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D PHE* 4.4 10.5 - - + -
320D ILE 3.7 6.5 + - - +
321D MET* 3.3 7.9 + - - +
323D PHE* 1.3 75.4 - - + +
325D ASN* 1.3 60.8 + - - +
327D LEU* 3.1 7.9 + - + +
328D LYS* 3.0 34.5 + - + +
361D THR* 3.9 27.6 - - + +
364D GLU* 4.2 4.7 - - + -
365D ALA* 3.8 43.5 - - + +
403D ILE* 5.0 1.8 - - + -
779D TRP* 3.8 23.1 - - + -
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D MET 2.8 18.3 + - - +
322D GLU 4.3 0.9 - - - +
324D VAL* 1.3 73.0 - - - +
326D PHE* 1.3 60.9 + - - +
328D LYS* 3.9 2.3 - - - +
329D ASN* 2.9 48.3 + - - +
332D GLN* 4.1 3.5 + - - +
333D TYR* 3.4 26.8 + - + +
775D GLY 2.8 28.3 + - - -
776D LEU* 3.4 18.3 - - + +
778D ASP* 3.7 4.0 - - - +
779D TRP* 3.9 16.8 - - + -
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Residues in contact with PHE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C LEU* 5.4 2.2 - - + -
322D GLU 3.3 15.1 + - - +
323D PHE* 3.6 10.3 - - - +
324D VAL 3.2 0.4 - - - -
325D ASN* 1.3 78.4 - - - +
327D LEU* 1.3 67.8 + - + +
328D LYS 3.2 1.2 + - - -
330D PRO* 3.3 34.5 - - + +
333D TYR* 3.4 35.8 - + + -
334D GLN* 3.9 26.2 - - + -
338D ALA* 3.8 20.2 - - + -
339D LYS* 4.2 2.0 - - - -
340D ILE* 3.6 57.7 - - + -
341D PRO* 5.4 3.8 - - + -
446D ASN* 5.3 4.9 - - + -
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D PHE 3.3 14.8 + - - +
324D VAL* 3.1 9.4 + - - +
326D PHE* 1.3 82.9 - - + +
328D LYS* 1.3 60.8 + - + +
330D PRO* 4.8 5.6 - - - +
340D ILE* 4.2 21.8 - - + -
365D ALA* 5.0 4.9 - - + -
366D ASN* 6.0 2.8 - - - +
367D VAL* 3.8 39.1 - - + +
401D PRO* 3.8 28.3 - - + +
403D ILE* 3.9 19.1 - - + -
446D ASN* 5.0 5.2 - - + +
448D VAL* 4.8 6.5 - - + -
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Residues in contact with LYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D VAL* 3.0 24.3 + - + +
325D ASN* 4.3 3.8 - - - +
327D LEU* 1.3 82.5 - - + +
329D ASN* 1.3 71.8 + - - +
330D PRO* 3.4 8.8 - - - +
364D GLU* 3.3 34.9 + - - +
365D ALA* 4.7 0.7 - - - +
366D ASN* 3.9 25.5 - - + +
778D ASP* 5.4 7.4 + - + +
779D TRP* 3.9 29.3 - - + +
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Residues in contact with ASN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ASN* 2.9 31.4 + - - +
326D PHE 3.5 3.4 - - - +
328D LYS* 1.3 83.8 - - - +
330D PRO* 1.3 63.3 - - - +
331D LYS* 3.3 3.5 + - - +
332D GLN* 3.8 24.9 + - + +
333D TYR* 4.0 12.5 + - - -
778D ASP* 2.6 32.5 + - - -
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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