Contacts of the helix formed by residues 419 - 438 (chain E) in PDB entry 3HN3
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 ASN 419 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E PRO* 4.3 3.8 + - - +
179E THR* 4.2 5.5 - - - +
416E GLN 2.6 28.8 + - - +
417E PHE* 3.6 3.0 + - - +
418E PHE* 1.3 73.2 - - - +
420E ASN* 1.3 59.9 + - - +
421E VAL* 3.2 17.5 + - + +
422E SER* 2.7 42.4 + - - -
423E LEU* 2.9 29.7 + - - +
462E TYR* 4.3 1.8 - - - -
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Residues in contact with ASN 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E ASN* 1.3 74.7 - - - +
421E VAL* 1.3 61.3 + - + +
423E LEU* 3.6 18.2 - - - +
424E HIS* 3.0 30.7 + - - +
427E MET* 5.7 1.9 - - - +
461E TYR* 5.7 2.1 + - - -
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Residues in contact with VAL 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E THR* 3.9 21.1 - - + -
419E ASN* 3.2 11.3 + - + +
420E ASN* 1.3 79.5 - - + +
422E SER* 1.3 65.3 + - - +
424E HIS* 3.4 5.2 + - - +
425E HIS* 3.1 22.0 + - + +
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Residues in contact with SER 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E PRO 2.9 25.8 + - - -
179E THR* 3.5 12.2 - - - +
181E LEU* 5.5 1.5 - - - +
412E LEU* 6.3 0.7 - - - -
417E PHE 3.3 22.4 + - - -
419E ASN* 2.7 26.5 + - - -
421E VAL* 1.3 73.3 - - - +
423E LEU* 1.3 56.2 + - - +
425E HIS* 3.3 8.4 + - - +
426E HIS* 2.9 29.8 + - - +
462E TYR* 3.6 9.5 + - - -
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E ASN 2.9 18.2 + - - +
420E ASN* 3.6 18.4 - - - +
422E SER* 1.3 74.3 - - - +
424E HIS* 1.3 65.3 + - - +
426E HIS* 3.2 3.3 + - - +
427E MET* 3.0 41.5 + - + +
461E TYR* 3.8 32.1 - - + +
462E TYR* 3.4 44.8 - - + +
465E MET* 4.0 15.3 - - + -
466E VAL* 3.6 19.3 - - + -
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Residues in contact with HIS 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E ASN* 3.0 18.7 + - - +
421E VAL* 3.8 6.1 - - - +
422E SER 3.4 0.2 - - - -
423E LEU* 1.3 75.2 - - - +
425E HIS* 1.3 63.1 + - - +
427E MET* 3.2 24.4 + - + +
428E GLN* 3.1 66.3 + - + +
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Residues in contact with HIS 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E GLU* 2.5 38.4 + - + -
144E GLY* 5.7 2.7 - - - -
179E THR* 3.4 22.1 + - - +
181E LEU* 3.8 36.0 - - + +
421E VAL* 3.1 14.1 + - + +
422E SER* 3.6 8.8 + - - +
423E LEU 3.2 0.2 - - - -
424E HIS* 1.3 77.2 + - - +
426E HIS* 1.3 57.4 + - - +
428E GLN* 3.2 19.4 + - + +
429E VAL* 3.0 49.7 + - + +
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Residues in contact with HIS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E LEU* 3.4 23.5 - - + +
407E CYS* 3.5 10.8 - - - -
409E GLY* 3.9 17.5 - - - -
412E LEU* 4.2 6.1 - - + -
422E SER 2.9 9.5 + - - +
423E LEU 3.2 4.9 + - - +
425E HIS* 1.3 76.8 + - - +
427E MET* 1.3 58.3 + - - +
429E VAL* 3.3 1.3 + - + +
430E MET* 2.9 30.6 + - + +
448E VAL* 2.8 30.0 + - + -
449E ALA* 4.6 2.9 - - + -
462E TYR* 2.6 43.8 + + + +
463E LEU* 5.6 0.7 - - + -
466E VAL* 3.7 25.7 - - + +
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Residues in contact with MET 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E ASN* 5.3 2.5 - - - +
423E LEU* 3.0 30.9 + - + +
424E HIS* 3.2 45.3 - - + +
426E HIS* 1.3 77.2 - - - +
428E GLN* 1.3 57.5 + - + +
430E MET* 3.4 4.1 + - - +
431E GLU* 3.0 29.2 + - - +
465E MET* 4.8 9.4 - - - +
466E VAL* 4.4 14.8 - - + -
469E HIS* 3.4 44.7 - - + +
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Residues in contact with GLN 428 (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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424E HIS* 3.1 50.7 + - + +
425E HIS* 3.2 19.5 + - + +
427E MET* 1.3 75.3 - - + +
429E VAL* 1.3 64.6 + - + +
431E GLU* 3.1 22.9 + - - +
432E GLU* 3.0 29.1 + - - +
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Residues in contact with VAL 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E GLU* 5.1 3.1 - - - +
144E GLY* 6.0 2.7 - - - -
147E LEU* 4.2 14.1 - - + -
181E LEU* 4.3 12.1 - - + -
407E CYS* 4.4 4.3 - - + -
408E PRO* 3.9 30.1 - - + -
425E HIS* 3.0 45.2 + - + +
426E HIS 3.3 7.4 + - - +
428E GLN* 1.3 76.0 - - + +
430E MET* 1.3 56.8 + - - +
432E GLU* 3.1 17.7 + - - +
433E VAL* 2.9 35.5 + - + +
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Residues in contact with MET 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E ASP 5.7 0.4 - - - +
407E CYS* 3.5 33.7 - - - +
426E HIS* 2.9 19.5 + - + +
427E MET* 3.6 7.4 - - - +
429E VAL* 1.3 74.8 - - - +
431E GLU* 1.3 62.5 + - - +
433E VAL* 3.6 11.3 - - + +
434E VAL* 3.0 38.3 + - + +
446E TRP* 4.3 12.3 - - + -
447E SER 4.6 2.0 - - - +
448E VAL* 4.1 11.9 - - + -
466E VAL* 3.6 28.3 - - + -
469E HIS* 5.0 2.9 - - + -
470E THR* 3.5 34.1 - - + +
473E LEU* 4.2 7.0 - - + -
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Residues in contact with GLU 431 (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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24E GLN* 4.4 16.2 + - - +
427E MET* 3.0 13.6 + - - +
428E GLN* 3.1 23.9 + - - +
430E MET* 1.3 76.8 - - - +
432E GLU* 1.3 56.7 - - + +
434E VAL* 3.9 1.0 - - - +
435E ARG* 2.9 31.7 + - - +
469E HIS* 2.7 39.9 + - - +
473E LEU* 3.6 21.4 - - + +
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Residues in contact with GLU 432 (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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142E HIS* 2.7 36.0 + - - -
143E GLU 4.4 5.5 - - - +
147E LEU* 3.5 27.8 - - + +
148E PRO* 4.2 5.7 - - - +
428E GLN* 3.0 19.4 + - + +
429E VAL* 3.4 17.0 - - - +
431E GLU* 1.3 73.2 - - + +
433E VAL* 1.3 65.8 + - - +
435E ARG* 3.4 29.6 + - - +
436E ARG* 3.0 26.2 + - - +
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Residues in contact with VAL 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LEU* 4.1 14.3 - - + +
387E PRO* 4.0 21.1 - - + -
405E ASP* 4.5 16.6 - - - +
407E CYS* 3.9 26.7 - - + +
429E VAL* 2.9 23.7 + - + +
430E MET* 3.6 15.0 - - + +
432E GLU* 1.3 76.3 - - - +
434E VAL* 1.3 63.1 + - - +
436E ARG* 3.3 2.8 + - - +
437E ASP* 3.1 26.5 + - - +
446E TRP* 3.9 23.3 - - + -
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Residues in contact with VAL 434 (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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430E MET* 3.0 35.0 + - + +
431E GLU 3.9 2.2 - - - +
433E VAL* 1.3 73.7 - - - +
435E ARG* 1.3 61.1 + - - +
438E LYS* 2.8 45.6 + - + +
446E TRP* 3.9 30.3 - - + +
470E THR* 4.4 7.2 - - + -
473E LEU* 4.1 28.5 - - + +
474E ASP* 4.0 23.3 - - + -
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Residues in contact with ARG 435 (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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24E GLN* 3.0 33.5 + - - +
25E GLY 3.0 21.3 + - - -
26E GLY* 3.9 6.1 + - - -
27E MET* 3.6 51.4 - - + +
148E PRO 4.8 2.8 + - - -
230E ASP* 5.2 4.0 - - - +
431E GLU 2.9 19.8 + - - +
432E GLU* 3.6 32.0 + - - +
433E VAL 3.3 0.2 - - - -
434E VAL* 1.3 78.4 - - - +
436E ARG* 1.3 62.3 + - - +
438E LYS* 3.6 27.8 - - - +
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Residues in contact with ARG 436 (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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27E MET* 4.6 18.4 - - + +
146E TYR 3.9 6.1 + - - -
147E LEU* 4.3 4.8 - - + +
148E PRO* 3.6 33.0 - - + +
216E ARG* 3.5 18.4 - - - +
387E PRO* 3.5 17.5 - - - +
388E TYR 2.7 32.0 + - - +
390E GLU* 3.6 35.9 + - + +
393E MET* 4.2 8.1 - - - +
405E ASP* 5.0 0.4 + - - -
432E GLU 3.0 17.8 + - - +
433E VAL* 3.7 4.5 - - - +
435E ARG* 1.3 81.0 - - - +
437E ASP* 1.3 93.6 + - - +
438E LYS* 3.6 0.6 - - - +
439E ASN* 5.1 2.1 + - - +
440E HIS* 4.5 5.9 + - - -
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Residues in contact with ASP 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E PRO* 4.6 1.7 - - - +
390E GLU* 5.1 0.7 - - - +
393E MET* 4.2 4.1 - - - +
405E ASP* 2.5 34.1 - - - +
433E VAL* 3.1 16.3 + - - +
436E ARG* 1.3 123.1 + - - +
438E LYS* 1.3 64.0 + - - +
439E ASN 3.0 5.1 + - - -
440E HIS* 3.1 40.2 + - + +
443E VAL* 4.4 2.6 - - + +
446E TRP* 4.0 10.5 - - + -
477E ARG* 4.1 3.8 + - - -
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Residues in contact with LYS 438 (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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28E LEU* 6.0 0.9 - - - -
230E ASP* 2.8 34.7 + - - -
231E ILE 3.2 15.6 + - - +
232E THR* 2.8 32.8 + - + +
233E VAL 4.4 6.8 - - - +
434E VAL* 2.8 31.3 + - + +
435E ARG* 3.6 25.4 - - - +
436E ARG 5.2 0.4 - - - -
437E ASP* 1.3 76.2 - - - +
439E ASN* 1.3 74.2 + - - +
440E HIS 3.4 0.7 - - - -
446E TRP* 4.0 4.2 - - - -
474E ASP* 5.5 3.1 - - - -
477E ARG* 2.9 32.9 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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