Contacts of the helix formed by residues 424 - 437 (chain C) in PDB entry 1O23
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 SER 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418C ASP* 3.6 11.4 - - - -
419C GLY* 4.3 1.1 - - - +
422C GLY 3.6 2.7 + - - -
423C ILE* 1.3 75.6 - - - +
425C LEU* 1.3 65.9 + - - +
426C LEU* 3.6 11.2 + - - +
427C GLU* 2.8 36.6 + - - +
428C TRP* 3.0 23.0 + - - -
517C LEU* 5.3 1.4 - - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C SER* 3.8 14.5 + - - +
414C ILE* 3.9 36.8 - - + +
415C LYS* 3.2 46.2 - - + +
417C ILE* 4.7 2.5 - - + -
418C ASP* 3.6 40.7 + - + +
424C SER* 1.3 71.6 - - - +
426C LEU* 1.3 65.4 + - + +
428C TRP* 3.2 3.4 + - + +
429C ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C SER* 3.2 9.1 + - - +
425C LEU* 1.3 81.3 - - + +
427C GLU* 1.3 64.2 + - - +
429C ALA* 3.1 5.6 + - - +
430C CYS* 3.0 19.6 + - - +
517C LEU* 3.7 35.9 - - + +
518C GLU* 3.8 11.0 - - - +
520C TRP* 3.5 10.4 - - - +
521C ARG* 3.2 70.4 - - + +
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Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLY 3.8 5.1 - - - +
423C ILE* 3.6 18.6 - - + +
424C SER* 2.8 41.5 + - - +
426C LEU* 1.3 80.2 - - - +
428C TRP* 1.3 56.9 + - - +
430C CYS* 3.3 3.2 + - - +
431C VAL* 2.9 33.6 + - - +
509C TYR* 2.6 41.2 + - + -
513C CYS* 4.3 1.9 - - - +
517C LEU* 3.8 34.6 - - + +
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Residues in contact with TRP 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ILE* 3.7 17.7 - - + -
417C ILE* 3.4 46.9 + - + +
423C ILE* 3.4 37.2 + - + +
424C SER 3.0 15.8 + - - +
425C LEU* 3.8 6.7 - - - +
426C LEU 3.1 0.2 - - - -
427C GLU* 1.3 74.7 - - - +
429C ALA* 1.3 57.8 + - - +
431C VAL* 3.1 15.9 + - + -
432C LEU* 2.7 51.8 + - + +
455C PHE* 3.3 33.4 - + - -
498C LEU* 3.8 19.4 - - + +
503C ILE* 4.2 8.1 - - + -
506C TRP* 3.6 43.5 - + - -
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LYS* 4.2 8.1 - - + +
410C VAL* 5.1 5.8 - - + -
411C SER* 4.4 9.2 - - - +
414C ILE* 5.1 1.0 - - - +
425C LEU 2.9 13.8 + - - +
426C LEU 3.1 8.3 + - - +
428C TRP* 1.3 75.3 - - - +
430C CYS* 1.3 63.7 + - - +
432C LEU* 4.9 1.1 - - - -
433C PHE* 3.0 14.7 + - - +
438C TYR* 2.9 33.4 + - + +
520C TRP* 3.6 26.0 - - + +
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Residues in contact with CYS 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C LEU 3.0 8.0 + - - +
427C GLU* 3.4 8.3 - - - +
429C ALA* 1.3 78.9 - - - +
431C VAL* 1.3 61.3 + - - +
433C PHE* 3.3 2.1 + - - +
434C HIS* 3.1 34.7 + - - -
512C MET 3.2 16.2 - - - -
513C CYS* 2.0 47.6 - - + -
517C LEU* 4.7 0.2 - - + -
520C TRP* 3.5 43.9 - - + +
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Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ILE* 6.0 0.2 - - + -
427C GLU* 2.9 22.6 + - + +
428C TRP* 3.6 17.7 - - + +
430C CYS* 1.3 74.1 - - - +
432C LEU* 1.3 56.5 + - + +
434C HIS* 3.1 4.7 + - - +
435C THR* 2.7 52.7 + - - +
503C ILE* 5.0 6.5 - - + -
506C TRP* 3.8 29.8 - - + -
508C ALA* 4.7 2.2 - - + +
509C TYR* 3.8 31.9 - - + +
513C CYS* 3.7 17.3 - - - -
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 3.5 15.9 - - + -
414C ILE* 3.5 31.6 - - + -
428C TRP* 2.7 31.2 + - + +
431C VAL* 1.3 74.1 - - + +
433C PHE* 1.3 62.4 + - - +
435C THR* 4.3 3.6 - - - -
436C SER* 3.0 26.7 + - - -
437C GLY 3.4 1.6 + - - -
438C TYR* 3.7 16.7 + - + -
454C LEU* 3.4 33.7 - - + +
455C PHE* 3.6 39.3 - - + -
506C TRP* 5.1 0.9 - - - +
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Residues in contact with PHE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C ALA 3.0 19.6 + - - +
430C CYS 3.6 3.8 - - - +
431C VAL 3.1 0.2 - - - -
432C LEU* 1.3 78.0 - - - +
434C HIS* 1.3 70.7 + + - +
437C GLY* 2.8 28.7 + - - +
438C TYR* 3.4 37.8 - + - +
520C TRP* 3.7 22.7 - + + -
814C PG4 3.2 48.0 - - - +
682D PHE* 4.2 9.6 - + - -
687D PRO* 3.8 25.4 - - + -
688D TYR* 3.7 25.6 - + - -
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Residues in contact with HIS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C CYS* 3.1 24.1 + - - +
431C VAL 3.9 0.2 - - - +
433C PHE* 1.3 91.6 - + - +
435C THR* 1.3 61.7 - - - +
508C ALA* 3.8 20.6 - - + -
512C MET* 3.3 54.0 - - + +
513C CYS* 4.4 0.2 - - - -
520C TRP* 4.0 24.7 - + - -
814C PG4 3.6 19.0 - - - +
688D TYR* 3.5 26.4 - + - -
690D GLN* 6.2 0.4 - - - -
721D ASP* 5.2 2.0 - - - -
761D ARG* 3.9 1.0 + - - -
762D PHE* 3.5 21.9 - + + -
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Residues in contact with THR 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C VAL* 2.7 41.6 + - - +
432C LEU* 4.0 5.6 - - - -
434C HIS* 1.3 76.2 - - - +
436C SER* 1.3 58.1 + - - +
444C VAL* 5.6 0.9 - - - +
451C GLU* 5.6 0.4 - - - +
454C LEU 4.4 1.8 - - - +
455C PHE 3.9 12.1 - - - +
456C GLN* 3.3 39.7 - - + +
506C TRP* 3.7 12.8 - - + +
508C ALA* 4.3 8.3 - - - +
814C PG4 3.6 11.0 - - - +
761D ARG* 4.5 4.9 + - - -
762D PHE* 4.9 6.9 - - + -
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Residues in contact with SER 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU 3.0 8.9 + - - -
435C THR* 1.3 77.0 - - - +
437C GLY* 1.3 65.1 + - - +
438C TYR 3.4 6.4 + - - -
439C ASP* 3.0 24.1 + - - +
442C ALA* 4.0 4.7 - - - -
453C GLY 3.6 16.4 - - - -
454C LEU* 2.7 35.1 + - - +
456C GLN* 4.0 4.7 - - - -
814C PG4 3.6 21.2 - - - +
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Residues in contact with GLY 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C GLU* 5.2 6.9 - - - +
405C LEU 4.9 0.5 - - - +
432C LEU 3.4 0.4 + - - -
433C PHE* 2.8 31.3 + - - -
436C SER* 1.3 72.5 - - - +
438C TYR* 1.3 73.2 + - - +
439C ASP* 3.1 3.6 + - - +
814C PG4 3.4 38.3 + - - -
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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