Contacts of the helix formed by residues 423 - 435 (chain B) 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 CYS 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B GLY* 3.7 24.9 - - - -
263B SER* 3.1 19.7 - - - +
276B ASP 4.1 4.3 - - - -
277B THR* 3.3 20.3 + - + +
279B VAL 4.3 0.8 + - - -
281B PHE* 4.0 7.4 - - - -
422B THR* 1.3 73.4 - - - +
424B GLU* 1.3 63.8 + - - +
426B ALA 3.4 0.2 + - - -
427B SER* 3.0 24.3 + - - -
498B MET* 3.5 24.0 - - - +
500B TRP* 3.6 31.4 - - - -
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Residues in contact with GLU 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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168B ARG* 2.8 29.0 + - - +
263B SER* 3.5 15.3 - - - +
271B ARG* 3.8 5.9 + - - +
273B SER* 3.4 13.2 + - - +
277B THR* 2.8 29.8 + - - +
278B LYS* 3.1 33.9 + - - +
368B GLU* 4.1 11.0 - - - +
422B THR* 3.1 6.7 - - - +
423B CYS* 1.3 75.6 - - - +
425B SER* 1.3 65.1 + - - +
427B SER* 2.6 23.7 + - - -
428B VAL* 3.4 8.0 + - - +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ALA* 3.8 12.5 - - - +
368B GLU* 3.7 18.2 + - - -
369B TYR 2.9 40.3 + - - -
421B VAL* 3.6 3.4 - - - +
422B THR* 2.8 39.7 + - - -
424B GLU* 1.3 75.8 - - - +
426B ALA* 1.3 62.6 + - - +
428B VAL* 3.1 16.6 + - - +
429B MET* 3.3 8.2 + - - -
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 5.3 1.1 - - + -
421B VAL* 4.1 12.8 - - + -
422B THR 2.9 17.2 + - - +
423B CYS 3.7 3.4 - - - +
425B SER* 1.3 76.6 + - - +
427B SER* 1.3 56.7 + - - +
429B MET* 3.0 18.0 + - - +
430B ALA* 2.9 28.4 + - - +
488B LEU* 4.1 5.0 - - + +
498B MET* 3.7 35.9 - - + -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER* 3.4 35.5 - - - -
264B VAL 4.2 1.2 + - - -
265B CYS* 3.5 18.3 + - - +
271B ARG* 4.6 3.3 + - - -
423B CYS 3.0 13.7 + - - -
424B GLU* 2.6 20.4 + - - -
426B ALA* 1.3 77.1 - - - +
428B VAL* 1.3 57.3 + - - +
430B ALA* 3.5 2.2 + - - +
431B ALA* 3.0 27.7 + - - +
496B GLY 3.8 3.9 - - - +
497B MET 4.2 10.8 - - - -
498B MET* 4.1 4.0 - - - +
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS* 4.1 10.8 - - - -
271B ARG* 3.4 37.5 - - - +
364B MET 3.6 5.6 - - - +
365B ALA 3.5 31.9 - - - +
366B GLY 3.8 2.0 - - - +
368B GLU* 4.4 2.7 - - - -
424B GLU 3.7 5.4 - - - +
425B SER 3.1 7.5 + - - +
427B SER* 1.3 75.9 + - - +
429B MET* 1.3 66.2 + - - +
431B ALA* 3.0 4.5 + - - +
432B THR* 2.8 23.6 + - - -
439B CYS* 3.9 14.1 - - - -
440B PRO* 4.1 6.9 - - + +
441B ILE* 4.2 13.7 - - + -
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Residues in contact with MET 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 5.2 2.0 - - - -
290B LEU* 4.3 25.4 - - + -
361B LEU* 3.6 36.3 - - + +
364B MET* 3.3 24.0 + - + +
365B ALA* 3.6 21.5 - - + +
369B TYR 5.2 0.2 - - - +
370B VAL* 3.7 25.1 - - + -
421B VAL* 4.0 19.7 - - + -
425B SER 3.3 3.1 + - - +
426B ALA* 3.0 19.5 + - - +
428B VAL* 1.3 77.3 - - - +
430B ALA* 1.3 58.2 + - - +
432B THR* 2.9 25.2 + - - -
433B LEU* 3.3 11.2 + - - +
488B LEU* 5.3 4.0 - - + -
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA 2.9 17.3 + - - +
427B SER 3.7 1.1 - - - +
429B MET* 1.3 71.9 - - - +
431B ALA* 1.3 58.8 + - - +
433B LEU* 3.0 14.8 + - - +
434B ALA* 2.9 22.7 + - - +
488B LEU* 4.1 13.6 - - + +
489B LEU 3.8 5.8 - - - +
490B VAL* 3.5 13.3 - - + +
496B GLY* 3.6 4.3 - - - -
497B MET 3.6 34.5 - - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS* 3.3 31.0 - - + +
266B THR 4.2 3.4 - - - +
267B ALA* 5.1 0.5 - - - -
427B SER 3.0 13.1 + - - +
428B VAL 3.0 9.2 + - - +
430B ALA* 1.3 76.0 - - - +
432B THR* 1.3 57.1 + - - +
434B ALA* 3.4 4.0 - - - +
435B ASN* 2.8 32.4 + - - +
440B PRO* 3.5 19.2 - - + +
496B GLY* 3.4 10.2 - - - +
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Residues in contact with THR 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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364B MET* 2.7 45.7 + - + -
428B VAL 2.8 10.0 + - - -
429B MET* 2.9 12.3 + - - -
431B ALA* 1.3 76.4 - - - +
433B LEU* 1.3 57.6 + - - +
435B ASN 3.2 4.5 + - - -
437B GLY* 2.9 56.1 + - - +
438B PHE 3.9 13.2 - - - -
439B CYS* 3.7 4.4 - - - +
440B PRO* 3.7 9.4 - - - +
446B VAL* 4.3 5.6 - - + -
447B LEU* 4.9 5.8 - - + -
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Residues in contact with LEU 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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531A ASN* 5.0 0.5 + - - -
289B PRO* 5.4 0.7 - - + -
290B LEU* 4.3 22.9 - - + -
293B ALA* 5.2 3.4 - - + -
364B MET* 5.5 1.3 - - - -
429B MET 3.3 9.6 + - - +
430B ALA* 3.0 12.9 + - - +
432B THR* 1.3 71.0 - - - +
434B ALA* 1.3 66.1 + - - +
435B ASN 3.0 2.3 + - - -
436B GLY 3.6 3.6 + - - -
447B LEU* 4.0 16.4 - - + -
452B VAL* 3.2 47.8 - - + +
455B THR* 4.6 15.3 - - + -
456B LEU* 3.9 23.1 - - + +
459B MET* 4.5 22.0 - - - -
488B LEU* 4.8 6.5 - - + -
490B VAL* 4.0 8.7 - - + -
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ASN* 3.3 8.9 + - - -
267B ALA* 4.8 2.8 - - + +
430B ALA 2.9 10.1 + - - +
431B ALA* 3.2 9.6 + - + +
433B LEU* 1.3 77.3 - - - +
435B ASN* 1.3 56.8 + - - +
436B GLY 3.5 0.2 - - - -
490B VAL* 3.7 16.9 - - + +
491B VAL 3.9 6.3 - - - +
492B PRO* 4.2 3.7 - - - +
493B ASN* 3.1 26.0 + - - -
494B VAL 4.9 0.7 - - - +
495B MET* 3.4 38.4 - - - +
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Residues in contact with ASN 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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531A ASN* 3.7 7.0 - - - +
533A ARG* 3.2 25.9 + - - +
534A HIS* 3.2 21.2 + - - -
267B ALA* 3.6 26.5 + - + +
431B ALA 2.8 15.8 + - - +
432B THR 3.2 0.8 + - - +
433B LEU 3.0 1.2 - - - -
434B ALA* 1.3 77.2 - - - +
436B GLY* 1.3 60.3 + - - +
437B GLY 3.0 5.7 + - - -
438B PHE* 2.7 40.4 + - - +
440B PRO* 4.2 9.7 - - + +
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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