Contacts of the helix formed by residues 419 - 438 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PRO* 3.8 8.5 + - - +
179A THR* 3.8 9.5 - - - +
416A GLN 2.8 26.3 + - - +
417A PHE 3.5 3.0 + - - -
418A PHE* 1.3 74.0 - - - +
420A ASN* 1.3 58.4 + - - +
421A VAL* 3.0 16.3 - - + +
422A SER* 2.4 65.8 + - - -
423A LEU* 2.8 13.5 + - - +
462A TYR* 4.5 1.0 - - - -
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASN* 1.3 71.5 - - - +
421A VAL* 1.3 58.8 + - + +
423A LEU* 3.6 18.7 + - - +
424A HIS* 3.1 26.9 + - - +
427A MET* 5.5 1.2 - - - +
461A TYR* 6.1 1.6 - - - -
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 4.1 20.6 - - + -
419A ASN* 3.0 11.9 - - + +
420A ASN* 1.3 78.6 - - + +
422A SER* 1.3 63.4 + - - +
424A HIS* 3.5 5.8 + - - +
425A HIS* 3.2 22.4 + - + +
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO 3.1 13.9 + - - -
179A THR* 3.8 10.8 - - - +
181A LEU* 5.4 3.4 - - - +
412A LEU* 5.6 1.2 - - - +
417A PHE 2.9 28.9 + - - -
419A ASN* 2.4 39.7 + - - -
421A VAL* 1.3 71.7 - - - +
423A LEU* 1.3 57.3 + - - +
425A HIS* 3.4 7.3 + - - +
426A HIS* 2.9 30.8 + - - +
462A TYR* 3.7 11.4 + - - -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASN 2.8 10.9 + - - +
420A ASN* 3.6 23.1 - - - +
422A SER* 1.3 76.1 - - - +
424A HIS* 1.3 59.6 + - - +
426A HIS* 3.4 0.9 + - - +
427A MET* 2.9 53.0 + - + +
461A TYR* 4.1 26.7 - - + -
462A TYR* 3.6 33.1 - - + +
465A MET* 4.2 10.1 - - + -
466A VAL* 3.4 31.4 - - + +
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Residues in contact with HIS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ASN 3.1 16.9 + - - +
421A VAL* 3.9 6.5 - - - +
422A SER 3.4 0.2 - - - -
423A LEU* 1.3 71.9 - - - +
425A HIS* 1.3 67.4 + - - +
427A MET* 3.3 24.8 + - + +
428A GLN* 3.0 52.2 + - + +
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Residues in contact with HIS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 3.5 40.6 + - + +
144A GLY* 4.8 6.9 - - - -
179A THR* 3.6 20.9 + - - +
180A THR* 4.5 2.0 - - - -
181A LEU* 3.8 36.5 - - + +
421A VAL* 3.2 12.9 + - + +
422A SER 3.8 5.8 + - - +
424A HIS* 1.3 79.7 + - - +
426A HIS* 1.3 56.1 + - - +
428A GLN* 3.1 13.2 + - + +
429A VAL* 2.8 57.9 + - + +
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 3.4 27.8 - - + +
407A CYS* 3.5 13.5 - - - -
409A GLY* 4.0 10.5 - - - -
412A LEU* 4.1 8.1 - - + -
422A SER 2.9 17.9 + - - +
423A LEU 3.7 4.5 - - - +
424A HIS 3.2 0.2 - - - -
425A HIS* 1.3 72.2 - - - +
427A MET* 1.3 60.5 + - - +
429A VAL* 3.2 1.3 + - - +
430A MET* 2.9 29.5 + - + +
448A VAL* 2.7 31.8 + - + -
449A ALA* 4.7 2.5 - - + -
462A TYR* 2.6 36.6 + + + +
463A LEU* 5.6 0.4 - - + -
466A VAL* 3.7 24.6 - - + +
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Residues in contact with MET 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ASN* 6.2 1.1 - - - +
423A LEU* 2.9 47.9 + - + +
424A HIS* 3.3 29.4 - - + +
426A HIS* 1.3 77.1 - - - +
428A GLN* 1.3 57.2 + - + +
430A MET* 3.4 5.0 + - - +
431A GLU* 3.0 31.3 + - - +
465A MET* 4.7 12.6 - - - +
466A VAL* 4.5 8.1 - - - -
469A HIS* 3.4 44.0 - - + +
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Residues in contact with GLN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 5.0 1.0 - - - -
23A LEU* 3.2 48.1 - - + +
424A HIS* 3.0 42.4 + - + +
425A HIS* 3.4 14.4 - - + +
427A MET* 1.3 72.6 - - + +
429A VAL* 1.3 68.1 + - + +
431A GLU* 3.1 19.8 + - - +
432A GLU* 3.0 28.8 + - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU 5.6 1.6 - - - +
144A GLY* 5.9 2.5 - - - -
147A LEU* 4.2 12.1 - - + -
181A LEU* 4.2 11.7 - - + -
407A CYS* 4.3 8.3 - - + -
408A PRO* 3.9 29.4 - - + -
425A HIS* 2.8 53.3 + - + +
426A HIS 3.6 5.6 - - - +
428A GLN* 1.3 75.7 - - + +
430A MET* 1.3 62.0 + - - +
432A GLU* 3.1 18.0 + - - +
433A VAL* 2.9 25.5 + - - +
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Residues in contact with MET 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ASP 5.5 0.7 - - - +
407A CYS* 3.6 31.4 - - - -
426A HIS* 2.9 21.5 + - + +
427A MET* 3.7 7.0 - - - +
429A VAL* 1.3 74.3 - - - +
431A GLU* 1.3 57.5 + - - +
433A VAL* 3.1 8.5 + - + +
434A VAL* 2.8 42.5 + - + +
446A TRP* 4.1 22.7 - - + -
447A SER 4.5 2.7 - - - +
448A VAL* 4.2 11.4 - - + -
466A VAL* 3.9 18.2 - - + -
469A HIS* 5.1 4.0 - - + -
470A THR* 3.7 43.1 - - + +
473A LEU* 4.5 1.6 - - + -
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.0 30.0 + - - +
23A LEU* 4.9 4.9 + - - +
427A MET* 3.0 12.4 + - - +
428A GLN* 3.1 24.5 + - - +
430A MET* 1.3 77.2 - - - +
432A GLU* 1.3 57.9 + - - +
434A VAL* 3.6 1.2 + - - +
435A ARG* 2.9 24.4 + - - +
469A HIS* 2.9 38.9 + - - +
473A LEU* 3.3 28.3 - - + +
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.5 21.5 - - - +
23A LEU* 6.5 0.4 - - + -
142A HIS* 2.7 36.8 + - - -
143A GLU 4.4 5.7 - - - +
147A LEU* 3.6 30.3 - - + +
148A PRO* 4.2 6.4 - - - +
428A GLN* 3.0 18.4 + - - +
429A VAL* 3.4 16.4 - - - +
431A GLU* 1.3 72.7 - - - +
433A VAL* 1.3 66.0 + - - +
435A ARG* 3.4 15.4 + - - +
436A ARG* 3.0 26.0 + - - +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.0 24.2 - - + -
387A PRO* 4.1 13.7 - - + -
405A ASP* 4.5 17.5 - - - +
407A CYS* 4.0 26.0 - - + +
429A VAL* 2.9 20.2 + - + +
430A MET* 3.5 15.7 - - + +
432A GLU* 1.3 76.5 - - - +
434A VAL* 1.3 62.8 + - - +
436A ARG* 3.2 3.4 + - - +
437A ASP* 3.0 26.4 + - - +
446A TRP* 3.9 23.1 - - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A MET* 2.8 29.4 + - + +
431A GLU 4.0 4.0 - - - +
433A VAL* 1.3 72.7 - - - +
435A ARG* 1.3 58.9 + - - +
438A LYS* 2.8 47.4 + - + +
446A TRP* 3.9 27.4 - - + +
470A THR* 4.3 19.5 - - + -
473A LEU* 4.2 25.6 - - + +
474A ASP* 4.1 21.3 - - + -
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Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.1 32.6 + - - +
24A GLN* 2.9 20.8 + - - +
25A GLY 2.9 30.2 + - - -
26A GLY* 3.7 7.7 + - - -
27A MET* 3.3 52.4 + - + +
148A PRO 4.8 2.4 + - - -
230A ASP* 5.1 2.7 - - - +
431A GLU 2.9 18.6 + - - +
432A GLU* 3.7 22.0 + - - +
434A VAL* 1.3 77.4 - - - +
436A ARG* 1.3 62.4 + - - +
438A LYS* 3.6 30.4 - - - +
439A ASN* 5.6 0.2 + - - -
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Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 4.6 17.5 - - + +
146A TYR 3.7 7.3 + - - -
147A LEU* 4.3 6.6 - - + +
148A PRO* 3.5 33.4 - - + +
216A ARG* 3.4 19.0 - - - +
387A PRO* 3.7 16.9 - - - +
388A TYR 2.7 32.5 + - - +
390A GLU* 3.7 33.2 + - + +
393A MET* 4.1 8.9 - - - +
432A GLU 3.0 18.5 + - - +
433A VAL* 3.8 3.3 - - - +
434A VAL 3.2 0.2 - - - -
435A ARG* 1.3 80.3 - - - +
437A ASP* 1.3 96.7 + - - +
438A LYS* 3.7 0.6 - - - +
439A ASN* 5.2 0.9 + - - +
440A HIS* 4.5 6.1 + - - -
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Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A PRO* 4.7 1.7 - - - +
390A GLU* 5.1 1.4 - - - +
393A MET* 4.0 6.0 - - - +
405A ASP* 2.5 33.5 - - - +
433A VAL* 3.0 15.9 + - - +
436A ARG* 1.3 123.5 + - - +
438A LYS* 1.3 65.8 + - - +
439A ASN 3.0 4.9 + - - -
440A HIS* 3.1 38.0 + - + +
443A VAL* 4.3 3.3 - - + +
446A TRP* 4.0 8.4 - - + -
477A ARG* 4.2 3.8 + - - -
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 6.2 0.7 - - - -
230A ASP* 2.9 29.7 + - - -
231A ILE 3.4 17.3 - - - -
232A THR* 2.9 32.2 + - + +
233A VAL 4.4 6.9 - - - +
434A VAL* 2.8 32.0 + - + +
435A ARG* 3.6 26.5 - - - +
436A ARG 3.7 0.2 - - - -
437A ASP* 1.3 76.3 - - - +
439A ASN* 1.3 73.4 + - - +
440A HIS 3.4 0.4 - - - -
446A TRP* 4.0 4.4 - - - -
474A ASP* 5.3 2.9 - - - +
477A ARG* 3.0 33.2 + - - +
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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