Contacts of the helix formed by residues 383 - 399 (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 GLY 383 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D LEU* 3.4 28.1 - - - +
379D GLU* 4.1 3.5 - - - -
382E VAL* 1.3 74.3 - - - +
384E VAL* 1.3 61.8 + - - +
385E GLY 3.3 1.8 - - - -
386E PRO* 3.8 12.4 - - - +
387E ALA* 3.3 20.8 + - - +
390E ARG* 4.9 0.2 + - - -
426E GLU* 2.9 20.3 + - - -
429E ASN* 5.8 2.2 - - - -
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Residues in contact with VAL 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D GLU* 5.5 1.1 - - + -
380D MET* 3.9 28.7 - - + -
291E VAL* 3.8 14.4 - - + -
292E GLY* 4.2 9.2 - - - +
377E PHE 4.5 0.4 - - - -
379E GLU* 3.8 22.9 - - + -
381E PHE* 3.7 30.5 - - + +
382E VAL* 3.2 1.3 - - - +
383E GLY* 1.3 76.0 - - - +
385E GLY* 1.3 59.9 + - - +
387E ALA* 3.1 6.7 + - + +
388E ARG* 2.9 51.3 + - - +
426E GLU* 3.8 0.8 + - - -
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Residues in contact with GLY 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E PHE* 3.5 22.1 + - - +
378E LEU* 5.7 0.2 - - - -
379E GLU 5.4 1.2 + - - +
381E PHE 5.6 0.2 + - - -
384E VAL* 1.3 76.4 - - - +
386E PRO* 1.3 67.3 - - - +
388E ARG* 3.2 5.2 + - - +
389E VAL* 3.1 25.8 + - - +
426E GLU* 3.6 6.3 + - - -
430E THR* 3.3 21.1 - - - +
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Residues in contact with PRO 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D SER* 3.6 32.1 - - - +
383E GLY* 3.8 12.8 - - - +
385E GLY* 1.3 87.6 - - - +
387E ALA* 1.3 59.9 + - - +
389E VAL* 4.5 1.3 - - + -
390E ARG* 3.2 35.4 + - - +
426E GLU* 3.7 10.5 - - - +
429E ASN* 3.3 34.5 - - + +
430E THR* 3.4 11.7 - - - +
433E GLN* 3.5 13.8 - - + +
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Residues in contact with ALA 387 (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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379D GLU* 3.9 23.6 - - + +
292E GLY* 3.3 20.5 - - - +
383E GLY 3.3 18.4 + - - +
384E VAL* 3.1 11.2 + - - +
386E PRO* 1.3 78.6 - - - +
388E ARG* 1.3 59.0 + - - +
390E ARG* 3.6 20.4 + - - +
391E ASP* 3.7 14.4 + - - +
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Residues in contact with ARG 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E SER 5.0 2.0 + - - -
291E VAL* 3.9 23.6 - - - +
292E GLY 3.4 16.4 - - - +
293E GLU 3.1 27.0 + - - +
294E THR* 3.5 14.7 + - - +
295E THR* 4.9 9.7 - - - +
376E GLU* 2.8 30.4 + - - +
377E PHE* 4.3 18.9 - - + +
379E GLU* 3.6 28.4 + - - +
384E VAL* 2.9 29.5 + - - +
385E GLY* 3.2 4.7 + - - +
387E ALA* 1.3 76.6 - - - +
389E VAL* 1.3 60.7 + - - +
390E ARG 3.3 0.9 - - - -
391E ASP* 3.7 4.7 - - - +
392E LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E PHE* 4.3 18.6 - - + -
385E GLY 3.1 15.9 + - - +
386E PRO* 4.6 0.7 - - + -
387E ALA 3.6 0.2 - - - -
388E ARG* 1.3 76.8 - - - +
390E ARG* 1.3 61.3 + - - +
392E LEU* 3.2 6.0 + - + +
393E PHE* 3.1 53.3 + - + -
430E THR* 3.9 26.9 - - + +
433E GLN* 3.7 33.0 - - + +
434E LEU* 3.8 12.3 - - + +
437E GLU* 4.3 1.3 - - + -
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Residues in contact with ARG 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D THR* 5.1 10.5 - - - +
375D SER 3.4 22.6 + - - -
376D GLU* 3.4 39.1 + - - +
378D LEU 5.0 2.0 + - - -
379D GLU* 4.4 11.7 + - - -
388D ARG* 4.4 2.6 - - - +
383E GLY 4.9 1.6 + - - -
386E PRO* 3.2 24.5 + - - +
387E ALA* 3.6 27.1 - - - +
388E ARG 3.3 0.4 - - - -
389E VAL* 1.3 76.7 - - - +
391E ASP* 1.3 59.6 + - - +
393E PHE* 4.3 0.3 - - - +
394E ALA* 3.3 22.6 + - - +
433E GLN* 3.3 35.6 + - - +
437E GLU* 4.1 13.8 - - - +
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Residues in contact with ASP 391 (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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292E GLY 4.3 1.5 - - - +
293E GLU* 3.3 19.2 - - - +
294E THR* 3.2 37.6 + - - +
387E ALA 3.7 16.9 + - - +
388E ARG 3.5 1.7 + - - +
389E VAL 3.2 0.8 - - - -
390E ARG* 1.3 77.5 - - - +
392E LEU* 1.3 65.3 + - - +
394E ALA* 3.8 8.6 - - - +
395E LEU* 3.1 22.0 + - - +
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Residues in contact with LEU 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E THR* 3.5 17.9 + - + +
296E ALA* 3.8 20.4 - - + -
370E ILE* 4.1 4.4 - - + +
372E VAL* 3.8 25.6 - - + -
377E PHE* 3.9 16.4 - - + -
388E ARG 3.0 18.1 + - - +
389E VAL* 3.2 6.5 + - - +
391E ASP* 1.3 77.2 - - - +
393E PHE* 1.3 65.3 + - + +
395E LEU* 3.1 6.6 + - + +
396E ALA* 2.8 25.1 + - - +
404E LEU* 3.9 36.1 - - + -
406E ILE* 4.2 9.4 - - + -
434E LEU* 5.8 0.4 - - + -
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Residues in contact with PHE 393 (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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389E VAL* 3.1 32.9 + - + +
390E ARG 4.7 1.1 - - - +
392E LEU* 1.3 82.9 - - + +
394E ALA* 1.3 64.5 + - - +
395E LEU 3.3 0.2 - - - -
396E ALA* 3.7 8.0 - - + +
397E ARG* 3.2 42.2 + - - +
404E LEU* 4.1 14.4 - - + -
406E ILE* 4.9 2.7 - - + -
434E LEU* 3.6 26.2 - - + -
437E GLU* 3.5 42.6 - - + +
438E MET* 3.7 28.3 - - + -
447E VAL* 6.1 2.5 - - + -
449E ILE* 3.9 25.8 - - + -
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Residues in contact with ALA 394 (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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390E ARG 3.3 20.6 + - - +
391E ASP* 3.8 12.6 - - - +
392E LEU 3.2 0.6 - - - -
393E PHE* 1.3 76.7 - - - +
395E LEU* 1.3 57.4 + - - +
397E ARG* 3.5 5.8 + - - +
398E LYS* 3.1 27.0 + - - +
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Residues in contact with LEU 395 (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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294E THR* 4.3 15.5 - - + -
296E ALA* 3.4 25.8 - - + +
298E VAL* 3.7 27.1 - - + -
370E ILE* 3.7 19.3 - - + +
391E ASP* 3.1 15.4 + - - +
392E LEU* 3.1 8.7 + - + +
394E ALA* 1.3 75.1 - - - +
396E ALA* 1.3 60.2 + - - +
397E ARG 3.1 3.3 + - - -
398E LYS* 4.6 15.0 - - + +
399E ASN* 3.5 24.0 + - - +
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Residues in contact with ALA 396 (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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370E ILE* 3.9 13.5 - - + -
392E LEU 2.8 15.5 + - - +
393E PHE* 3.7 17.0 - - + +
394E ALA 3.3 0.6 - - - -
395E LEU* 1.3 76.6 - - - +
397E ARG* 1.3 58.1 + - + +
399E ASN 2.9 16.3 - - - +
400E ALA 4.2 0.2 - - - +
402E CYS* 3.2 17.4 - - - -
404E LEU* 4.3 20.6 - - + -
447E VAL* 3.4 18.9 - - + +
449E ILE* 5.7 0.4 - - + -
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Residues in contact with ARG 397 (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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297D LYS* 5.6 0.4 - - - +
393E PHE* 3.2 32.2 + - - +
394E ALA* 4.2 4.7 - - - +
395E LEU 3.1 0.4 - - - -
396E ALA* 1.3 81.9 - - + +
398E LYS* 1.3 64.8 + - - +
399E ASN 3.2 3.4 - - - -
400E ALA* 3.7 18.0 - - - +
437E GLU* 3.0 44.2 + - - -
442E ASN* 2.8 48.3 + - - +
443E THR* 4.2 4.9 - - - +
444E THR* 3.4 39.5 - - + +
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Residues in contact with LYS 398 (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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394E ALA 3.1 17.2 + - - +
395E LEU* 3.8 16.6 + - + +
397E ARG* 1.3 76.8 - - - +
399E ASN* 1.3 65.9 + - - +
400E ALA* 3.7 2.9 + - - +
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Residues in contact with ASN 399 (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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298E VAL* 4.1 17.5 - - - +
300E LYS* 5.5 3.0 - - - +
368E PRO* 3.9 35.8 - - + +
370E ILE* 4.9 2.4 - - + +
395E LEU* 3.5 25.5 + - - +
396E ALA 2.9 19.6 - - - +
397E ARG 3.9 1.1 - - - -
398E LYS* 1.3 81.0 + - - +
400E ALA* 1.3 62.4 + - - +
401E PRO* 3.8 2.9 - - - -
402E CYS* 3.3 12.4 - - + -
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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