Contacts of the helix formed by residues 425 - 438 (chain B) in PDB entry 5OC9
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 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419B ILE* 3.0 18.3 + - + +
423B LEU* 4.2 15.0 - - + +
424B LYS* 1.3 72.9 - - - +
426B MET* 1.3 58.0 + - - +
427B LYS* 3.4 11.8 + - - +
428B LEU* 3.2 36.9 + - + +
429B LEU* 3.0 22.3 + - - +
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Residues in contact with MET 426 (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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420B ALA* 3.4 26.9 - - - +
424B LYS* 3.7 17.5 + - + +
425B ASP* 1.3 69.9 + - - +
427B LYS* 1.4 58.0 + - - +
429B LEU* 3.8 15.6 - - - +
430B ARG* 3.0 52.7 + - - +
514B VAL* 4.0 30.1 - - + +
573B LEU* 3.9 15.7 - - + +
576B MET* 4.6 12.1 - - + -
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Residues in contact with LYS 427 (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 ASP* 3.3 9.8 + - - +
426B MET* 1.4 78.3 - - - +
428B LEU* 1.4 55.0 + - - +
430B ARG* 3.5 13.4 + - - +
431B GLN* 3.2 26.5 + - - +
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Residues in contact with LEU 428 (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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337B PHE* 5.5 2.0 - - + -
340B GLU* 5.7 5.8 - - - +
419B ILE* 3.8 32.3 - - + -
423B LEU* 4.3 13.0 - - + -
425B ASP* 3.2 33.4 + - - +
427B LYS* 1.4 72.4 - - - +
429B LEU* 1.4 55.8 + - - +
431B GLN* 3.4 8.8 + - + +
432B SER* 2.7 41.6 + - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.5 44.6 - - + +
419B ILE* 3.5 11.8 - - + +
420B ALA* 3.7 21.8 - - + +
425B ASP 3.0 16.6 + - - +
426B MET* 3.8 11.4 - - - +
427B LYS 3.4 0.2 - - - -
428B LEU* 1.4 73.4 - - - +
430B ARG* 1.4 58.7 + - - +
432B SER* 3.2 5.5 + - - -
433B LEU* 2.9 43.8 + - + +
511B PHE* 3.8 21.3 - - + -
514B VAL* 3.7 26.5 - - + -
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Residues in contact with ARG 430 (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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238B GLU* 3.2 29.6 + - - -
243B TYR* 4.5 4.9 + - - -
426B MET* 3.0 36.3 + - - +
427B LYS* 3.7 10.3 - - - +
429B LEU* 1.4 74.4 - - - +
431B GLN* 1.4 51.1 + - - +
433B LEU* 3.3 3.2 + - - -
434B ALA* 2.8 30.7 + - - +
513B CYS 4.9 0.2 + - - -
514B VAL* 2.9 45.5 + - + +
515B TYR* 3.3 28.2 - - + -
516B PRO* 5.7 0.2 - - - +
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Residues in contact with GLN 431 (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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427B LYS 3.2 15.1 + - - +
428B LEU* 3.7 11.4 - - + +
430B ARG* 1.4 77.0 - - - +
432B SER* 1.4 59.4 + - - +
434B ALA* 3.5 8.0 + - - +
435B THR* 3.0 29.6 + - - -
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Residues in contact with SER 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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416B LEU* 4.2 20.6 - - - -
419B ILE* 3.5 19.3 - - - +
428B LEU* 2.7 29.6 + - - +
429B LEU* 3.4 8.7 - - - -
431B GLN* 1.4 75.7 - - - +
433B LEU* 1.4 60.5 + - - +
435B THR* 3.5 7.4 + - - -
436B LEU* 3.2 27.5 + - - +
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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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416B LEU* 3.9 14.8 - - + -
429B LEU* 2.9 40.3 + - + +
430B ARG* 3.7 3.8 - - - +
432B SER* 1.4 73.2 - - - +
434B ALA* 1.4 54.6 + - - +
436B LEU* 3.3 6.0 + - - +
437B LEU* 2.8 44.7 + - + +
507B TYR* 3.8 41.7 - - + +
511B PHE* 3.8 26.2 - - + -
514B VAL* 5.0 0.4 - - + -
515B TYR* 3.8 33.7 - - + +
518B ALA* 6.2 0.2 - - + -
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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
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430B ARG 2.8 16.9 + - - +
431B GLN* 3.7 11.0 - - - +
432B SER 3.4 0.2 - - - -
433B LEU* 1.4 73.4 - - - +
435B THR* 1.4 58.9 - - - +
437B LEU* 4.9 0.2 - - - -
438B ILE* 2.9 42.1 + - + +
439B THR* 4.9 0.2 + - - -
515B TYR* 3.4 27.3 - - + +
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Residues in contact with THR 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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431B GLN 3.0 16.9 + - - -
432B SER* 3.7 6.7 - - - -
433B LEU 3.3 0.4 - - - -
434B ALA* 1.4 76.5 - - - +
436B LEU* 1.4 57.7 + - + +
439B THR* 3.3 24.8 + - + -
440B SER* 2.8 36.1 + - - +
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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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412B CYS* 4.6 9.9 - - - +
416B LEU* 3.8 29.2 - - + -
432B SER 3.2 18.1 + - - +
433B LEU* 3.3 9.2 + - - +
435B THR* 1.4 79.4 - - - +
437B LEU* 1.3 57.2 + - + +
440B SER* 3.4 21.8 - - - +
441B GLN* 3.4 18.0 - - - +
507B TYR* 3.5 49.5 + - + +
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Residues in contact with LEU 437 (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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433B LEU* 2.8 30.4 + - + +
434B ALA* 4.4 2.0 - - - +
436B LEU* 1.3 73.1 - - - +
438B ILE* 1.3 60.7 + - - +
441B GLN* 2.8 38.3 + - - +
504B GLN* 5.2 3.6 - - + +
507B TYR* 3.8 34.8 - - + -
508B VAL* 5.6 0.2 - - + -
515B TYR* 3.7 26.7 - - + -
518B ALA* 3.7 33.7 - - + +
521B PHE* 4.1 20.7 - - + +
522B ALA* 4.6 9.2 - - + +
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Residues in contact with ILE 438 (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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434B ALA* 2.9 26.1 + - + +
437B LEU* 1.3 80.4 - - - +
439B THR* 1.4 69.3 + - - +
440B SER 3.4 0.7 - - - -
441B GLN* 3.2 5.4 + - - +
442B ILE* 3.1 42.5 + - + +
515B TYR* 3.6 20.9 - - - +
521B PHE* 3.9 33.7 - - + -
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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