Contacts of the helix formed by residues 422 - 435 (chain A) in PDB entry 5I94
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 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A THR 3.4 12.4 + - - -
278A LYS* 3.7 24.5 - - + +
279A VAL 3.9 8.1 - - - +
280A PRO* 4.1 5.4 - - + -
281A PHE* 4.1 5.6 - - - -
369A TYR* 3.8 26.7 - - + +
421A VAL* 1.3 81.5 - - - +
423A CYS* 1.3 66.1 + - - +
424A GLU* 3.3 7.4 + - - +
425A SER* 2.9 25.4 + - - -
426A ALA* 3.0 23.2 + - - +
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Residues in contact with CYS 423 (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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261A GLY* 3.6 33.0 - - - -
263A SER* 3.1 25.6 - - - +
276A ASP 4.3 3.6 - - - -
277A THR* 3.2 20.2 + - + +
279A VAL 4.6 0.4 + - - -
281A PHE* 3.9 8.8 - - - -
422A THR* 1.3 71.9 - - - +
424A GLU* 1.3 64.7 + - - +
427A SER* 3.0 18.7 + - - -
498A MET* 3.6 22.4 - - - +
500A TRP* 3.6 23.1 - - - -
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Residues in contact with GLU 424 (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 ARG* 2.8 35.2 + - - +
263A SER* 3.3 15.0 - - - +
271A ARG* 3.7 6.8 + - - +
273A SER* 3.0 13.7 + - - +
277A THR* 3.0 31.1 + - - +
278A LYS* 3.1 34.5 + - + +
368A GLU* 4.0 11.5 - - - +
422A THR* 3.1 5.5 - - - +
423A CYS* 1.3 75.7 - - - +
425A SER* 1.3 64.3 + - - +
427A SER* 2.5 23.3 + - - -
428A VAL 3.4 2.6 + - - -
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ALA* 3.7 13.1 - - - +
368A GLU* 3.7 17.5 + - - -
369A TYR 2.7 46.8 + - - -
421A VAL* 3.5 5.0 - - - +
422A THR* 2.9 26.3 + - - -
424A GLU* 1.3 78.5 - - - +
426A ALA* 1.3 66.3 + - - +
428A VAL* 3.2 14.9 + - - +
429A MET* 3.4 7.8 + - - -
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.9 1.6 - - + -
421A VAL* 3.9 16.2 - - + -
422A THR 3.0 14.6 + - - +
425A SER* 1.3 82.0 + - - +
427A SER* 1.3 58.1 + - - +
429A MET* 3.1 17.3 + - - +
430A ALA 2.9 23.6 + - - -
488A LEU* 3.5 9.5 - - + +
498A MET* 3.7 34.1 - - + -
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 3.4 34.1 - - - -
264A VAL 4.4 1.4 + - - -
265A CYS* 3.5 16.2 - - - +
271A ARG* 4.5 2.4 + - - -
423A CYS 3.0 15.7 + - - -
424A GLU* 2.5 20.6 + - - -
426A ALA* 1.3 73.9 - - - +
428A VAL* 1.3 60.8 + - - +
430A ALA* 3.7 2.4 - - - +
431A ALA* 3.0 24.1 + - - +
496A GLY 3.7 3.3 - - - -
497A MET* 4.0 13.7 - - - -
498A MET* 3.8 5.8 - - - +
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Residues in contact with VAL 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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265A CYS* 4.2 8.1 - - - -
271A ARG* 3.3 41.1 - - - +
364A MET 3.5 12.8 - - - +
365A ALA* 3.8 17.3 - - - +
366A GLY 4.0 0.2 - - - +
368A GLU* 4.4 7.6 - - - -
424A GLU 3.7 4.9 - - - +
425A SER 3.2 7.8 + - - +
426A ALA 3.1 0.6 - - - -
427A SER* 1.3 75.8 - - - +
429A MET* 1.3 54.1 + - - +
431A ALA* 2.7 26.1 + - - +
432A THR* 2.7 19.5 + - - +
439A CYS* 4.0 16.6 - - - -
440A PRO* 4.6 5.4 - - + -
441A ILE* 4.3 9.9 - - + -
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Residues in contact with MET 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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283A LEU* 5.1 2.0 - - + -
290A LEU* 3.7 32.0 - - + +
361A LEU* 3.7 29.8 - - + +
364A MET* 3.2 22.6 + - + +
365A ALA* 3.7 20.6 - - + +
369A TYR 5.3 0.2 - - - +
370A VAL* 3.6 30.3 - - + -
421A VAL* 3.9 20.9 - - + -
425A SER 3.7 6.3 - - - +
426A ALA* 3.2 15.3 - - + +
428A VAL* 1.3 76.9 - - - +
430A ALA* 1.3 61.5 + - - +
432A THR* 3.2 16.6 + - - -
433A LEU* 3.4 13.7 + - - +
488A LEU* 5.2 3.8 - - + -
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Residues in contact with ALA 430 (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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426A ALA 2.9 12.2 + - - +
427A SER 3.7 2.0 - - - +
429A MET* 1.3 75.7 - - - +
431A ALA* 1.3 62.0 + - - +
433A LEU* 3.3 5.8 + - - +
434A ALA 3.2 15.2 + - - -
488A LEU* 3.6 16.5 - - + +
489A LEU 3.7 6.5 - - - +
490A VAL* 3.4 18.6 - - + +
496A GLY* 3.6 4.7 - - - -
497A MET 3.3 37.5 - - - +
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Residues in contact with ALA 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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265A CYS* 3.2 33.7 - - - +
266A THR 4.3 2.9 - - - +
267A ALA* 5.0 0.7 - - - -
427A SER 3.0 11.8 + - - +
428A VAL 2.7 15.4 + - - +
430A ALA* 1.3 70.5 - - - +
432A THR* 1.3 62.0 + - - -
433A LEU 3.2 0.2 - - - -
434A ALA* 3.3 4.9 + - - +
435A ASN* 3.1 25.6 + - - +
440A PRO* 3.5 20.3 - - + +
496A GLY* 3.6 8.9 - - - +
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Residues in contact with THR 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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364A MET* 2.8 44.3 + - + -
428A VAL 2.7 7.8 + - - -
429A MET* 3.3 11.2 - - - -
431A ALA* 1.3 79.0 - - - +
433A LEU* 1.3 58.7 + - - +
435A ASN 3.3 4.9 + - - -
437A GLY* 3.0 50.6 + - - +
438A PHE 4.0 6.7 - - - -
439A CYS* 3.8 3.8 - - - +
440A PRO* 3.8 15.5 - - - +
446A VAL* 4.2 9.0 - - + -
447A LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 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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289A PRO* 5.5 0.2 - - + -
290A LEU* 4.4 20.2 - - + -
293A ALA* 5.1 5.4 - - + -
364A MET* 5.4 2.7 - - - -
429A MET 3.4 11.6 + - - +
430A ALA* 3.3 9.3 + - - +
431A ALA 3.2 0.4 - - - -
432A THR* 1.3 76.6 - - + +
434A ALA* 1.3 62.7 + - - +
435A ASN 3.1 1.0 + - - -
436A GLY 3.9 1.7 + - - -
447A LEU* 3.9 28.0 - - + -
452A VAL* 3.2 37.1 - - + +
455A THR* 4.5 9.9 - - + -
456A LEU* 3.6 34.1 - - + +
459A MET* 4.5 15.9 - - + -
488A LEU* 5.3 3.8 - - + -
490A VAL* 4.1 10.3 - - + -
531B ASN* 5.3 0.3 + - - -
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Residues in contact with ALA 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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267A ALA* 4.8 3.9 - - + +
430A ALA 3.2 9.3 + - - +
431A ALA* 3.4 10.3 - - - +
432A THR 3.2 0.2 - - - -
433A LEU* 1.3 78.0 - - - +
435A ASN* 1.3 56.3 + - + +
436A GLY 3.5 0.9 - - - -
490A VAL* 3.9 10.5 - - + +
491A VAL 4.1 7.9 - - - +
492A PRO* 4.2 4.2 - - - +
493A ASN* 3.0 27.0 + - - +
494A VAL 5.0 0.7 - - - -
495A MET* 3.3 39.3 - - - +
531B ASN* 3.2 10.2 + - - -
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Residues in contact with ASN 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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267A ALA* 3.8 20.1 + - + +
431A ALA 3.1 15.8 + - - +
432A THR 3.3 0.4 + - - +
433A LEU 3.1 0.8 - - - -
434A ALA* 1.3 79.8 - - - +
436A GLY* 1.3 61.9 + - - +
437A GLY 3.0 4.3 + - - -
438A PHE* 2.8 41.4 + - - +
439A CYS 4.4 0.2 - - - -
440A PRO* 4.0 12.5 - - + +
531B ASN* 3.9 6.8 - - - +
533B ARG* 3.1 38.5 + - - +
534B HIS* 3.6 11.1 + - - -
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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