Contacts of the helix formed by residues 313 - 329 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310E VAL* 4.4 18.8 - - + -
311E ALA* 3.2 10.8 - - - +
312E GLY* 1.3 82.2 - - - +
314E GLU* 1.3 54.5 + - - +
315E GLU 3.3 2.9 - - - -
316E ALA* 3.1 15.7 + - + +
317E LYS* 2.7 38.4 + - + +
352E THR 4.5 7.9 - - - -
353E GLY 5.5 1.1 - - - -
357E LEU* 4.7 6.7 - - + -
475E ILE* 3.7 31.9 - - - -
476E GLY 5.6 1.6 - - - -
801E ADP 4.7 2.0 - - - -
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Residues in contact with GLU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D THR* 3.6 32.1 + - + +
312E GLY 3.5 5.0 + - - +
313E CYS* 1.3 76.8 - - - +
315E GLU* 1.3 64.8 + - - +
316E ALA 3.5 0.5 + - - -
317E LYS* 3.8 15.7 + - - +
318E LEU* 3.8 12.1 + - - +
321E MET* 6.0 0.2 - - - +
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Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LEU* 3.3 29.0 - - + +
557D GLU* 3.2 13.4 - - - +
558D LYS* 3.7 9.9 - - + -
559D LYS* 3.4 48.9 - - - +
560D THR* 3.9 24.2 + - + +
313E CYS 3.3 0.4 - - - -
314E GLU* 1.3 81.9 - - - +
316E ALA* 1.3 58.4 + - - +
318E LEU* 4.2 19.5 + - - +
319E GLU* 4.2 6.8 - - - +
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Residues in contact with ALA 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LEU* 3.7 23.6 - - + -
558D LYS* 4.8 6.7 - - - +
313E CYS* 3.1 20.5 + - + +
315E GLU* 1.3 78.5 - - - +
317E LYS* 1.3 61.8 + - - +
318E LEU 3.2 1.7 + - - -
319E GLU* 3.5 5.8 + - - +
320E ILE* 3.4 25.7 - - - +
357E LEU* 4.9 4.0 - - + -
473E ILE* 4.0 13.0 - - + +
474E PHE 4.9 0.2 - - - +
475E ILE* 4.7 9.9 - - + -
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Residues in contact with LYS 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E PHE* 2.6 50.7 + - + +
310E VAL* 2.9 27.9 + - + +
311E ALA* 5.4 0.2 - - - -
313E CYS* 2.7 28.8 + - + +
314E GLU* 4.2 8.3 - - - +
315E GLU 3.6 0.4 - - - -
316E ALA* 1.3 72.3 - - - +
318E LEU* 1.3 58.1 + - - +
320E ILE* 4.2 0.8 - - - +
321E MET* 2.9 46.7 + - + +
357E LEU* 3.8 26.5 - - + -
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ARG* 4.4 31.6 - - - +
314E GLU 3.8 12.8 + - - +
315E GLU* 4.2 17.0 - - - +
316E ALA 3.2 1.0 - - - -
317E LYS* 1.3 80.4 - - - +
319E GLU* 1.3 63.9 + - + +
320E ILE 3.5 0.2 + - - -
321E MET* 4.1 17.3 - - + +
322E GLU* 3.3 22.5 + - + +
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Residues in contact with GLU 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ARG* 3.8 21.1 + - - -
551D ARG* 3.5 30.4 + - - +
556D LEU* 3.7 26.2 - - + +
315E GLU 4.2 5.4 - - - +
316E ALA 3.5 6.0 + - - +
317E LYS 3.3 0.2 - - - -
318E LEU* 1.3 81.5 - - + +
320E ILE* 1.3 59.6 + - - +
322E GLU* 3.8 7.2 - - - +
323E PHE* 3.6 13.5 - - - -
471E ARG* 2.4 51.0 + - - +
473E ILE* 3.8 20.4 - - + +
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Residues in contact with ILE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E PHE* 4.5 7.9 - - + -
316E ALA 3.4 18.6 - - - +
317E LYS 3.4 4.3 + - - +
318E LEU 3.3 0.2 - - - -
319E GLU* 1.3 80.5 - - - +
321E MET* 1.3 64.0 + - - +
322E GLU 3.1 1.6 - - - -
323E PHE* 3.2 27.6 + - + +
324E VAL* 3.7 2.8 + - - +
344E ALA* 5.6 1.3 - - + -
346E LEU* 3.8 25.6 - - + -
357E LEU* 3.7 30.3 - - + +
361E THR* 3.3 36.4 - - + +
450E LEU* 5.0 10.5 - - + -
473E ILE* 3.7 15.7 - - + -
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Residues in contact with MET 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E PHE* 3.6 41.7 - - + -
317E LYS* 2.9 40.2 + - + +
318E LEU* 3.8 19.0 + - + +
320E ILE* 1.3 74.0 - - - +
322E GLU* 1.3 53.1 + - - +
323E PHE 3.2 0.2 - - - -
324E VAL* 3.1 7.9 + - + +
325E ASN* 2.6 37.7 + - + +
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Residues in contact with GLU 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D LEU* 4.5 15.9 - - + +
534D ARG* 2.3 52.9 + - + +
318E LEU* 3.3 18.4 - - + +
319E GLU* 3.8 6.3 - - - +
320E ILE 3.1 0.6 - - - -
321E MET* 1.3 76.0 - - - +
323E PHE* 1.3 61.1 + - + +
325E ASN* 3.9 8.1 - - - +
326E PHE* 3.0 27.2 + - - +
333E TYR* 4.3 12.7 + - + +
341E PRO* 5.5 6.2 - - + +
471E ARG* 2.6 39.5 + - - +
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Residues in contact with PHE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E GLU 3.6 18.8 - - - -
320E ILE* 3.2 26.3 + - + +
322E GLU* 1.3 81.0 - - + +
324E VAL* 1.3 60.7 + - - +
326E PHE* 3.6 5.5 + - - +
327E LEU* 3.4 28.8 + - - +
340E ILE* 4.2 9.6 - - + +
341E PRO* 3.3 48.9 - - + -
343E GLY 4.4 2.7 - - - -
344E ALA* 3.9 31.6 - - + -
361E THR* 4.6 10.5 - - + -
403E ILE* 5.7 1.3 - - + -
448E VAL* 3.6 40.4 - - + -
450E LEU* 5.4 1.1 - - + -
471E ARG* 4.2 11.0 - - + -
473E ILE* 5.4 0.2 - - + -
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E PHE* 4.4 7.2 - - + -
320E ILE 4.3 3.8 - - - +
321E MET* 3.1 11.0 + - + +
323E PHE* 1.3 74.8 - - - +
325E ASN* 1.3 60.9 + - - +
326E PHE 3.1 1.3 - - - -
327E LEU* 3.1 5.3 + - - +
328E LYS* 2.9 42.6 + - + +
361E THR* 3.4 44.0 - - + +
364E GLU* 3.7 29.2 - - + +
365E ALA* 4.4 10.5 - - + +
403E ILE* 5.2 1.1 - - + -
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Residues in contact with ASN 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D ALA 5.7 0.4 + - - -
534D ARG* 6.3 0.8 - - - +
321E MET 2.6 21.2 + - - +
322E GLU* 4.0 3.8 - - - +
324E VAL* 1.3 74.0 - - - +
326E PHE* 1.3 59.9 + - - +
328E LYS* 4.6 4.1 - - - +
329E ASN* 3.2 32.6 + - - +
332E GLN* 3.6 23.4 + - - +
333E TYR* 2.8 29.8 + - - +
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Residues in contact with PHE 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D LEU* 5.3 2.7 - - + -
322E GLU 3.0 17.6 + - - +
323E PHE 3.7 6.1 - - - +
324E VAL 3.1 0.2 - - - -
325E ASN* 1.3 78.9 - - - +
327E LEU* 1.3 68.2 + - + +
330E PRO* 3.3 35.7 - - + +
333E TYR* 3.7 39.0 - + + -
334E GLN* 4.1 22.4 - - + -
338E ALA 4.3 4.0 - - - -
339E LYS* 3.9 11.9 - - - -
340E ILE* 3.6 60.1 - - + -
341E PRO* 6.0 0.4 - - + -
446E ASN* 4.6 10.1 - - - -
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Residues in contact with LEU 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E PHE 3.4 15.2 + - - +
324E VAL 3.1 6.9 + - - +
326E PHE* 1.3 80.4 - - + +
328E LYS* 1.3 63.5 + - - +
330E PRO* 4.3 8.1 - - - +
340E ILE* 4.4 16.2 - - + -
365E ALA* 4.3 26.0 - - + -
367E VAL* 4.4 5.6 - - + -
401E PRO* 4.2 23.8 - - + +
403E ILE* 4.7 14.6 - - + -
446E ASN* 4.0 28.3 - - + +
448E VAL* 5.1 4.3 - - + -
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Residues in contact with LYS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E VAL* 2.9 28.2 + - + +
325E ASN* 4.5 4.0 - - - +
327E LEU* 1.3 81.7 - - - +
329E ASN* 1.3 74.2 + - - +
330E PRO* 3.4 8.2 - - - +
364E GLU* 3.3 30.0 + - - -
365E ALA* 3.8 17.7 + - + +
366E ASN* 4.1 14.1 - - - +
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Residues in contact with ASN 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E ASN* 3.2 29.3 + - - +
326E PHE 3.5 2.5 - - - -
328E LYS* 1.3 88.7 - - - +
330E PRO* 1.3 64.7 - - - +
331E LYS* 3.3 3.0 + - + +
332E GLN* 3.7 25.0 + - + +
333E TYR* 3.4 13.3 - - - -
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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
------------------------------------------------------------
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