Contacts of the helix formed by residues 423 - 437 (chain B) in PDB entry 5IXC
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 THR 423 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B LEU* 5.3 4.2 - - - +
421B PRO* 4.8 7.9 - - + -
422B THR* 1.3 84.0 - - - +
424B PHE* 1.3 67.8 + - - +
425B VAL* 3.1 16.8 - - - +
426B ASP* 2.4 49.1 + - - +
427B LEU* 3.5 4.5 + - - +
601B ARG* 6.0 3.6 - - + +
602B SER* 4.6 18.2 - - - +
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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
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423B THR* 1.3 72.3 - - - +
425B VAL* 1.3 59.8 + - - +
427B LEU* 2.9 33.8 + - + -
428B TRP* 2.8 29.1 + - + +
531B PHE* 4.1 45.1 - + + -
532B SER 5.2 7.4 - - - +
534B ASN 6.4 1.6 - - - -
585B LEU* 5.5 0.9 - - + -
643B LEU* 5.6 3.8 - - + -
901B 7FA 4.0 40.4 - - + -
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B THR* 3.1 25.9 + - - +
424B PHE* 1.3 78.6 - - - +
426B ASP* 1.3 63.0 + - - +
428B TRP* 3.3 7.4 + - + +
429B ALA 2.8 23.0 + - - -
522B PHE 5.8 0.2 - - - +
525B ALA* 3.3 47.0 - - + +
526B ILE* 4.0 22.4 - - + +
529B ASN* 4.1 23.3 - - + +
531B PHE* 5.9 0.7 - - - -
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Residues in contact with ASP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.3 14.4 - - + -
415B ARG* 2.3 41.2 + - - +
421B PRO 4.2 6.7 - - - +
422B THR* 5.2 1.3 - - - -
423B THR* 2.4 41.7 + - - +
425B VAL* 1.3 82.5 - - - +
427B LEU* 1.3 63.3 + - - +
429B ALA* 3.3 19.8 - - - +
430B LEU* 3.4 15.4 + - - +
522B PHE* 3.7 11.2 - - + -
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TYR* 4.3 27.8 - - + -
412B LEU* 4.6 16.8 - - + +
423B THR 3.5 3.7 + - - +
424B PHE* 2.9 35.0 + - + +
426B ASP* 1.3 76.3 - - - +
428B TRP* 1.3 65.3 + - - +
430B LEU* 2.9 18.0 + - + -
431B VAL* 3.0 31.3 + - + +
585B LEU* 4.4 27.1 - - + +
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 4.6 1.8 - + - -
424B PHE* 2.8 18.7 + + + +
425B VAL* 3.4 9.6 - - + +
427B LEU* 1.3 72.7 - - - +
429B ALA* 1.3 56.5 + - - +
431B VAL* 3.3 38.6 - - + -
432B LEU* 2.9 67.7 + - + +
435B MET* 4.7 5.2 - - - -
525B ALA* 3.6 33.6 + - + +
528B SER 3.4 27.7 + - - -
529B ASN* 3.9 12.3 - - - +
530B ILE* 4.5 2.7 - - + +
531B PHE* 3.6 33.9 - + + -
771B MET* 5.3 0.2 - - - -
901B 7FA 3.8 50.5 - - + -
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Residues in contact with ALA 429 (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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425B VAL 2.8 13.9 + - - +
426B ASP 3.3 12.1 - - - +
427B LEU 3.1 0.2 - - - -
428B TRP* 1.3 76.3 - - - +
430B LEU* 1.3 56.6 + - - +
432B LEU* 3.9 2.2 - - - +
433B GLU* 3.0 29.6 + - - +
521B CYS* 3.4 28.1 - - - +
522B PHE* 3.4 26.9 - - + -
525B ALA* 3.6 12.2 - - + +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TYR* 3.5 50.0 - - + +
411B GLU* 3.8 16.2 - - + +
412B LEU* 3.6 31.9 - - + -
426B ASP 3.5 9.2 - - - +
427B LEU* 2.9 8.7 + - - +
429B ALA* 1.3 72.7 - - - +
431B VAL* 1.3 66.3 + - - +
433B GLU* 3.3 8.5 + - - +
434B SER* 3.0 23.2 + - - -
519B ARG* 3.4 30.3 - - - +
522B PHE* 3.9 13.2 - - + -
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B VAL* 4.2 11.0 - - + -
400B PHE* 4.9 14.6 - - + -
408B TYR* 4.0 20.4 - - + -
427B LEU* 3.0 32.8 + - + +
428B TRP* 3.3 35.7 - - + +
430B LEU* 1.3 75.5 - - - +
432B LEU* 1.3 62.1 + - - +
434B SER* 3.1 4.0 + - - -
435B MET* 2.8 40.4 + - - +
585B LEU* 5.2 5.8 - - + -
901B 7FA 4.7 10.5 - - + -
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Residues in contact with LEU 432 (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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365B TRP* 3.7 50.5 - - + +
428B TRP* 2.9 46.8 + - + +
429B ALA 3.9 2.9 - - - +
431B VAL* 1.3 80.2 - - - +
433B GLU* 1.3 55.6 + - - +
435B MET* 3.3 8.6 + - + +
436B LEU* 3.0 49.1 + - + +
521B CYS* 5.2 1.8 - - + +
524B GLU* 4.3 20.4 - - + +
525B ALA* 4.6 2.2 - - - +
528B SER* 3.9 10.3 - - - +
771B MET* 4.8 6.5 - - - -
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Residues in contact with GLU 433 (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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429B ALA 3.0 18.7 + - - +
430B LEU* 3.5 9.1 - - - +
432B LEU* 1.3 77.4 - - - +
434B SER* 1.3 55.6 + - - +
436B LEU* 4.6 1.6 - - - -
437B HIS* 2.8 51.2 + - + +
439B GLN 3.8 10.1 - - - +
440B VAL* 3.6 9.9 + - - +
441B MET* 2.8 25.9 + - + +
519B ARG* 2.8 41.2 + - - -
521B CYS* 3.5 25.6 - - + +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LYS* 4.9 8.3 - - - -
399B VAL* 3.4 13.0 - - - +
404B ARG* 3.7 20.8 + - - -
408B TYR* 3.0 31.2 + - - -
430B LEU 3.0 8.5 + - - -
431B VAL 3.4 6.1 - - - -
433B GLU* 1.3 76.3 - - - +
435B MET* 1.3 55.6 + - - +
437B HIS 2.3 26.3 - - - +
438B GLY* 4.5 2.9 + - - -
439B GLN* 4.9 6.5 - - - +
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Residues in contact with MET 435 (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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391B HIS* 4.0 8.1 - - - +
392B LEU* 5.5 1.2 - - - +
394B LYS* 6.0 0.9 - - - +
396B LYS* 3.6 53.1 + - + -
399B VAL* 4.1 17.3 - - + -
400B PHE* 5.6 4.5 - - + -
428B TRP* 4.7 10.5 - - - -
431B VAL* 2.8 36.7 + - - +
432B LEU* 3.7 10.3 - - + +
434B SER* 1.3 72.5 - - - +
436B LEU* 1.3 62.8 + - + +
437B HIS 4.1 0.6 - - - +
771B MET* 3.2 51.9 - - + +
901B 7FA 4.8 13.7 - - + -
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Residues in contact with LEU 436 (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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335B MET* 4.1 20.0 - - + -
365B TRP* 4.1 39.9 - - + +
387B TYR* 3.7 5.2 - - - -
388B ALA* 6.0 0.3 - - - -
391B HIS* 3.6 20.8 - - - +
392B LEU* 6.1 0.7 - - + -
432B LEU* 3.0 32.5 + - + +
433B GLU* 5.4 0.9 - - - -
435B MET* 1.3 80.5 - - - +
437B HIS* 1.3 88.8 + - + +
524B GLU* 3.6 25.1 - - - +
771B MET* 4.8 7.0 - - + -
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Residues in contact with HIS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS* 3.8 28.0 - + + -
387B TYR* 2.7 27.3 + + - +
391B HIS* 3.7 14.0 - - - -
394B LYS* 5.1 1.6 - - - -
433B GLU* 2.8 26.4 + - + +
434B SER 2.3 32.7 - - - +
435B MET 4.1 0.3 - - - -
436B LEU* 1.3 103.9 + - + +
438B GLY* 1.3 59.4 + - - +
439B GLN* 3.2 17.3 - - + +
441B MET* 3.3 30.8 - - + +
520B ILE* 6.4 0.2 - - - +
521B CYS* 6.2 0.2 - - + -
524B GLU* 5.1 7.2 + - - -
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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
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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