Contacts of the helix formed by residues 407 - 424 (chain B) in PDB entry 3H44
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 GLN 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 4.5 7.9 - - - +
333B TYR* 3.0 18.7 + - - +
404B GLU* 3.3 12.8 - - - +
405B GLY 3.1 18.8 - - - +
406B PRO* 1.3 68.1 - - - +
408B GLU* 1.3 65.4 + - - +
409B TRP* 3.2 36.7 - - + +
410B VAL* 3.2 20.3 + - + +
411B PHE 3.3 9.2 + - - -
459B PHE* 3.8 2.5 - - - -
524B LEU* 4.3 30.9 - - + +
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.5 12.6 + - - +
130A PHE* 3.9 8.7 - - - -
159A GLU* 4.9 1.0 - - - +
160A GLY* 3.3 24.2 + - - -
163A ASP* 4.4 7.1 + - + +
164A ARG* 2.9 35.6 + - - +
406B PRO 3.5 5.5 + - - -
407B GLN* 1.3 68.7 - - - +
409B TRP* 1.3 56.7 + - - +
410B VAL 3.1 0.3 + - - -
411B PHE* 3.2 3.3 + - + -
412B GLN* 2.7 35.6 + - + +
459B PHE* 3.5 45.8 - - + +
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Residues in contact with TRP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.7 52.8 - - + +
121A TYR* 3.3 15.7 + - + -
163A ASP* 4.5 0.8 + - - -
407B GLN* 3.4 36.9 - - + +
408B GLU* 1.3 78.2 - - - +
410B VAL* 1.3 77.3 + - + +
412B GLN* 3.5 1.4 - - - +
413B GLU* 2.7 49.9 + - - +
524B LEU* 5.0 6.8 - - + +
525B PRO* 3.4 30.3 - - + -
526B THR* 3.7 14.1 - - - -
527B LYS* 3.7 38.3 - - + -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TYR* 3.8 20.0 - - + -
336B HIS* 4.2 7.9 - - + +
337B LEU* 4.1 24.7 - - + -
407B GLN* 3.2 20.1 + - + +
408B GLU 3.1 0.4 - - - -
409B TRP* 1.3 115.6 - - + +
411B PHE* 1.3 68.4 + - - +
413B GLU* 3.0 8.8 + - - +
414B LEU* 2.9 33.4 + - + +
524B LEU* 5.6 1.3 - - + -
525B PRO* 5.4 4.0 - - + -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 3.3 26.7 - - - -
333B TYR* 4.3 18.4 - + + -
407B GLN 3.3 3.2 + - - +
408B GLU* 3.2 7.3 + - + +
410B VAL* 1.3 79.8 - - - +
412B GLN* 1.3 60.8 + - + +
414B LEU* 3.1 9.1 + - + +
415B LYS* 2.7 54.1 + - + -
456B LEU* 4.1 17.7 - - + -
457B GLU 3.9 19.3 - - - -
458B GLU 3.7 17.0 - - - -
459B PHE* 3.5 57.4 - + + -
464B ILE* 5.4 1.6 - - + -
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.9 31.4 - - + -
123A LYS* 4.7 1.6 - - - +
126A GLU* 3.6 27.0 + - + +
129A GLN* 5.8 0.4 - - - +
164A ARG* 3.8 12.3 + - - +
408B GLU* 2.7 21.4 + - + +
409B TRP 3.5 4.0 - - - +
411B PHE* 1.3 75.6 - - - +
413B GLU* 1.3 66.6 + - - +
415B LYS* 3.3 33.4 + - - +
416B ASP* 2.8 59.0 + - - +
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B HIS* 5.4 8.3 + - - -
409B TRP* 2.7 28.9 + - + +
410B VAL* 3.0 11.3 + - - +
412B GLN* 1.3 71.9 - - - +
414B LEU* 1.3 61.3 + - + +
416B ASP* 3.4 7.6 + - + +
417B LEU* 3.0 34.9 + - + +
526B THR 4.9 1.4 - - - +
527B LYS* 2.8 34.5 + - - +
528B ASN* 2.7 49.1 + - - +
531B ILE* 4.0 13.4 - - + +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B HIS* 4.1 21.8 - - + +
333B TYR* 4.7 12.1 - - + -
336B HIS* 3.4 55.9 - - + +
410B VAL* 2.9 23.9 + - + +
411B PHE* 3.4 11.7 - - + +
413B GLU* 1.3 78.6 - - + +
415B LYS* 1.3 65.9 + - - +
417B LEU* 3.4 13.5 + - + +
418B ASN* 3.0 32.4 + - - +
456B LEU* 4.6 11.0 - - + -
613B LEU* 5.8 1.3 - - + -
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Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN* 5.8 4.0 - - - +
133A GLU* 5.2 4.4 + - - -
884A LYS* 4.9 8.8 - - - +
411B PHE* 2.7 34.4 + - + +
412B GLN* 3.6 29.8 + - - +
414B LEU* 1.3 73.6 - - - +
416B ASP* 1.3 52.0 + - - +
418B ASN* 3.2 4.4 + - - +
419B ALA* 2.8 35.1 + - + +
455B LEU* 5.2 4.1 - - + +
456B LEU* 3.4 29.8 + - + +
457B GLU* 3.3 43.3 + - - +
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Residues in contact with ASP 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 3.9 25.3 + - - +
412B GLN* 2.8 55.0 + - - +
413B GLU* 3.6 7.8 + - + +
415B LYS* 1.3 73.9 - - - +
417B LEU* 1.3 61.0 + - + +
419B ALA* 3.2 9.5 - - - +
420B VAL* 2.9 30.5 + - - +
531B ILE* 6.1 4.5 - - + -
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLU* 3.0 21.5 + - + +
414B LEU* 3.7 13.5 - - + +
416B ASP* 1.3 75.8 - - + +
418B ASN* 1.3 57.7 + - - +
420B VAL* 3.1 10.6 + - + +
421B ALA* 2.8 35.6 + - - +
528B ASN* 4.4 8.1 - - - +
531B ILE* 3.6 49.8 - - + -
532B PRO* 4.4 11.9 - - + -
613B LEU* 3.6 30.5 - - + +
614B ALA* 4.4 5.8 - - - -
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Residues in contact with ASN 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B HIS* 4.8 14.7 - - - -
414B LEU* 3.0 14.8 + - - +
415B LYS* 3.4 9.6 - - - +
417B LEU* 1.3 74.6 - - - +
419B ALA* 1.3 64.8 + - - +
421B ALA* 3.7 8.1 - - - +
422B PHE* 2.9 28.5 + - - +
453B GLU 5.2 2.0 + - - -
454B TYR* 2.8 33.1 + - + +
455B LEU* 4.7 5.4 - - - -
456B LEU* 3.8 23.2 - - - +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B LYS* 2.8 15.3 + - + +
416B ASP* 3.2 16.6 - - - +
417B LEU 3.2 0.2 - - - -
418B ASN* 1.3 76.5 - - - +
420B VAL* 1.3 58.0 + - + +
422B PHE* 3.5 5.7 + - - +
423B ARG* 3.0 26.7 + - - +
455B LEU* 3.8 20.6 - - + +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ASP 2.9 20.2 - - - +
417B LEU* 3.1 14.8 + - + +
419B ALA* 1.3 73.7 - - + +
421B ALA* 1.3 68.5 + - - +
422B PHE 3.0 1.6 - - - -
423B ARG* 3.0 7.3 + - - +
424B PHE* 3.0 34.7 + - + -
531B ILE* 5.6 3.1 - - + -
532B PRO* 4.6 7.0 - - + +
535B PHE* 3.6 39.3 - - + -
634B TYR* 3.6 11.9 + - + +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LEU 2.8 20.3 + - - +
418B ASN* 3.3 9.4 + - - +
420B VAL* 1.3 72.2 - - - +
422B PHE* 1.3 57.1 + - - +
424B PHE 3.4 1.9 + - - -
425B LYS* 3.0 29.1 + - - +
454B TYR* 4.0 16.0 - - + -
634B TYR* 3.5 14.8 + - + +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876A ASP 6.0 0.7 - - - -
55B THR* 5.4 1.6 - - + -
56B LYS* 4.0 6.1 - - - -
57B SER* 3.4 46.5 - - - -
58B PRO* 4.8 4.5 - - + -
418B ASN 2.9 17.6 + - - +
419B ALA* 3.5 6.1 - - - +
421B ALA* 1.3 75.5 - - - +
423B ARG* 1.3 68.6 + - - +
424B PHE 3.3 0.2 + - - -
425B LYS* 3.6 27.5 + - - +
450B LEU* 3.3 24.9 - - + -
451B THR* 3.4 29.2 - - + -
454B TYR* 3.4 35.8 - + + -
455B LEU* 3.9 17.5 - - + -
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER* 2.7 23.1 + - - -
58B PRO* 3.3 38.3 - - + +
59B GLU* 3.4 42.8 + - - +
419B ALA 3.0 15.1 + - - +
420B VAL* 3.0 11.2 + - - +
422B PHE* 1.3 75.1 - - - +
424B PHE* 1.3 89.2 + - + +
425B LYS 3.7 1.6 + - - +
535B PHE* 6.0 0.6 - - - +
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Residues in contact with PHE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.3 25.6 - - + -
420B VAL* 3.0 31.9 + - + +
421B ALA 3.6 3.1 - - - -
423B ARG* 1.3 112.9 - - + +
425B LYS* 1.3 60.7 + - - +
535B PHE* 3.3 46.4 - + + -
537B ILE* 5.4 1.6 - - + -
569B LEU* 3.6 16.4 - - + +
570B PRO* 3.4 23.6 - - + -
571B LYS* 2.8 25.8 + - - +
634B TYR* 4.0 22.0 - + + +
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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
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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