Contacts of the helix formed by residues 407 - 419 (chain A) in PDB entry 4I6J
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 ASP 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 4.4 7.8 + - - +
69A ARG* 4.9 0.2 - - - +
121A GLU* 3.8 7.4 - - - +
148A HIS* 4.3 2.3 + - - -
274A ARG* 3.4 38.2 - - + +
311A ARG* 5.3 1.0 + - - -
315A TYR* 2.2 34.7 + - - +
400A ASP* 5.3 2.7 - - - -
405A ASP 3.4 3.6 + - - +
406A ALA* 1.3 73.6 - - - +
408A PHE* 1.3 65.7 + - - +
409A SER 3.5 1.9 + - - -
410A VAL* 3.1 29.8 + - - +
411A ASN* 3.1 22.8 + - - +
428B TRP* 6.1 0.2 - - - -
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Residues in contact with PHE 408 (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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121A GLU* 3.6 21.2 + - + +
122A PRO* 3.7 35.7 - - + -
123A PHE* 5.8 5.8 - - + -
318A ALA* 4.2 2.7 - - + -
321A ASN 4.4 1.1 - - - -
322A PRO 4.4 7.6 - - - -
324A PHE* 3.8 35.2 - + + -
325A ASP* 3.5 37.6 - - + +
396A VAL* 6.1 0.2 - - - +
400A ASP* 5.5 2.1 + - - -
407A ASP* 1.3 75.0 - - - +
409A SER* 1.3 73.6 + - - +
411A ASN* 4.5 0.6 - - - +
412A ALA* 3.2 27.9 + - - +
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Residues in contact with SER 409 (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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121A GLU* 2.8 23.1 + - - +
314A PHE* 3.5 14.7 - - - +
315A TYR* 3.3 26.7 - - - -
318A ALA* 3.5 27.9 - - - +
324A PHE* 3.4 8.4 - - - -
408A PHE* 1.3 81.6 - - - +
410A VAL* 1.3 58.3 + - - +
413A GLY* 3.0 25.8 + - - -
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Residues in contact with VAL 410 (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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311A ARG* 4.0 23.3 - - + +
314A PHE* 3.9 12.7 - - + -
315A TYR* 3.8 24.2 - - + -
405A ASP 4.8 2.7 - - - +
406A ALA* 5.7 1.1 - - - -
407A ASP* 3.1 23.4 + - - +
409A SER* 1.3 76.2 - - - +
411A ASN* 1.3 58.2 + - - +
413A GLY* 3.8 0.2 - - - -
414A SER* 2.9 33.1 + - - +
428B TRP* 3.5 49.4 - - + +
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Residues in contact with ASN 411 (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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396A VAL* 3.2 34.9 - - + +
399A PHE* 3.6 17.3 - - - +
400A ASP* 4.1 5.5 + - - +
403A LEU* 5.1 1.4 - - - +
406A ALA* 3.8 24.2 - - + +
407A ASP 3.1 20.2 + - - +
408A PHE* 4.5 0.4 - - - +
410A VAL* 1.3 77.5 - - - +
412A ALA* 1.3 65.2 + - - +
414A SER* 3.5 3.6 + - - -
415A TRP* 3.1 57.4 + - - +
428B TRP* 5.7 3.2 + - - -
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Residues in contact with ALA 412 (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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324A PHE* 3.6 30.3 - - + +
325A ASP* 3.8 19.3 - - + -
392A TRP* 4.2 2.0 - - + -
396A VAL* 4.0 13.3 - - + +
408A PHE 3.2 19.1 + - - +
411A ASN* 1.3 76.1 + - - +
413A GLY* 1.3 64.9 - - - +
415A TRP* 3.2 3.1 + - - +
416A MET* 2.9 29.4 + - + +
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Residues in contact with GLY 413 (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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314A PHE* 3.4 34.4 - - - -
324A PHE* 3.6 9.7 - - - -
409A SER 3.0 14.0 + - - -
410A VAL 3.8 0.4 - - - -
411A ASN 3.2 0.2 - - - -
412A ALA* 1.3 77.9 - - - +
414A SER* 1.3 62.7 + - - +
416A MET* 3.2 2.8 + - - -
417A TRP* 3.0 21.5 + - - +
423A PHE* 3.6 4.0 - - - -
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Residues in contact with SER 414 (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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314A PHE* 3.8 13.5 - - - -
410A VAL 2.9 19.7 + - - -
411A ASN* 3.5 4.4 + - - -
413A GLY* 1.3 73.0 - - - +
415A TRP* 1.3 61.5 + - - +
417A TRP* 3.5 3.8 - - - +
418A LEU* 2.8 38.0 + - - +
426B PRO* 4.6 6.2 - - - +
428B TRP* 3.3 42.4 + - - +
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Residues in contact with TRP 415 (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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348A TRP* 3.9 13.5 - + - -
380A ALA* 3.5 44.6 - - + -
383A LEU* 4.0 8.1 - - + -
384A THR* 4.4 8.7 - - + -
392A TRP* 3.9 30.4 - - + +
395A GLY* 3.5 33.8 + - - -
396A VAL* 3.7 21.1 - - + -
399A PHE* 3.3 36.1 - + - -
411A ASN* 3.1 47.5 + - - +
412A ALA 3.2 4.9 + - - +
414A SER* 1.3 80.2 - - - +
416A MET* 1.3 51.3 + - - +
418A LEU* 4.0 2.4 - - + +
419A SER* 2.6 40.3 + - - -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A PHE* 3.3 54.1 - - + +
330A ASN* 3.7 21.5 - - - -
332A ILE* 4.2 7.4 - - + -
333A CYS* 4.3 6.1 - - - -
392A TRP* 3.5 29.4 - - + -
412A ALA 2.9 18.4 + - - +
413A GLY* 3.8 4.0 - - - +
415A TRP* 1.3 75.3 - - - +
417A TRP* 1.3 60.2 + - - +
419A SER* 3.7 4.5 - - - -
420A CYS 3.3 1.7 + - - -
421A SER* 2.8 34.5 + - - -
422A ALA* 3.3 29.3 + - + -
423A PHE* 4.2 3.4 - - + -
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Residues in contact with TRP 417 (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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168A TYR* 4.2 14.8 - - + -
310A TRP* 3.6 31.2 - + - -
313A PHE* 4.2 12.3 - + - -
314A PHE* 4.5 2.2 - + + -
413A GLY 3.0 13.0 + - - +
414A SER* 3.5 8.5 - - - +
416A MET* 1.3 76.7 - - - +
418A LEU* 1.3 62.0 + - + +
420A CYS* 2.9 25.3 + - - -
422A ALA 4.2 2.9 - - - +
423A PHE* 3.6 40.3 - + + -
425A GLN* 3.2 47.4 + - + +
424B MET* 3.4 17.7 + - + -
425B MET* 3.6 21.6 - - - -
426B PRO* 3.3 31.3 - - + +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A ARG 5.0 0.2 - - - +
377A HIS* 3.5 61.5 - - + +
380A ALA* 4.0 23.6 - - + -
381A CYS* 4.6 6.0 - - + +
384A THR* 4.6 3.1 + - - +
385A ARG* 2.6 41.4 + - - +
414A SER* 2.8 25.9 + - - +
415A TRP* 4.0 3.4 - - + +
417A TRP* 1.3 74.2 - - + +
419A SER* 1.3 49.5 + - - +
420A CYS 3.1 5.3 + - - -
431A TYR* 4.4 12.6 - - + +
425B MET* 4.8 6.1 - - - -
426B PRO* 4.2 15.9 - - + -
428B TRP 5.3 0.2 - - - +
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Residues in contact with SER 419 (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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336A ILE* 4.5 0.2 - - - +
338A TRP* 4.1 13.5 - - - -
384A THR* 3.6 36.5 + - - -
385A ARG* 3.7 10.6 - - - +
392A TRP* 3.6 7.4 - - - +
415A TRP 2.6 26.0 + - - -
416A MET* 3.5 2.6 + - - -
418A LEU* 1.3 75.3 - - - +
420A CYS* 1.3 69.9 + - - +
421A SER* 3.0 24.4 + - - -
502A MET* 4.5 4.3 - - - +
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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
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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