Contacts of the helix formed by residues 407 - 420 (chain B) in PDB entry 2O8F
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 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405B SER 5.5 1.6 - - - +
406B CYS* 1.3 75.7 - - - +
408B PRO* 1.3 76.6 - - + +
410B MET* 2.8 15.5 + - - +
411B ARG* 2.8 19.8 + - - +
504B LYS* 4.9 2.5 - - - +
13E T 2.7 37.7 + - - -
14E A 3.4 36.6 - - - +
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Residues in contact with PRO 408 (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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406B CYS 3.9 0.2 - - - -
407B THR* 1.3 87.0 - - + +
409B GLY* 1.3 61.2 + - - +
411B ARG* 3.4 4.0 + - - +
412B LYS* 3.4 19.6 + - - +
504B LYS* 3.7 50.5 - - + +
505B TYR* 3.7 21.2 - - + +
507B ARG* 5.4 2.2 - - + +
508B VAL* 3.7 22.3 - - + +
13E T 3.4 10.5 - - + +
14E A 6.0 0.2 - - - +
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Residues in contact with GLY 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PRO* 1.3 73.9 - - - +
410B MET* 1.3 60.2 + - - +
412B LYS* 3.6 2.3 + - - -
413B TRP* 3.5 6.4 + - - +
427B TYR* 2.8 35.0 + - - -
508B VAL* 4.0 11.8 - - - +
511B ARG* 5.1 4.9 - - - -
12E C 4.2 5.2 - - - -
13E T 2.8 25.5 + - - -
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Residues in contact with MET 410 (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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406B CYS* 4.3 7.6 - - + -
407B THR* 2.8 25.1 + - - +
409B GLY* 1.3 75.0 - - - +
411B ARG* 1.3 66.4 + - - +
412B LYS 3.2 0.2 - - - -
413B TRP* 3.2 16.3 + - - +
414B TRP* 3.2 34.5 + - + +
436B TYR* 3.7 40.2 - - + -
437B HIS* 4.1 18.2 - - - +
456B TRP* 3.9 26.2 - - + -
13E T 3.2 7.4 + - - +
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Residues in contact with ARG 411 (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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400B GLU 4.9 0.2 + - - -
403B LEU* 3.4 47.0 + - + +
404B ASN* 2.8 28.9 + - - -
406B CYS* 3.8 11.8 - - + +
407B THR 2.8 13.5 + - - +
408B PRO 3.7 5.6 - - - +
409B GLY 3.4 0.2 - - - -
410B MET* 1.3 75.1 - - - +
412B LYS* 1.3 63.7 + - - +
414B TRP* 3.3 7.0 + - - +
415B GLN* 3.2 49.2 + - - +
505B TYR* 3.5 44.6 - - + +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PRO 3.4 9.8 + - - +
409B GLY* 3.7 4.3 - - - +
411B ARG* 1.3 80.5 - - - +
413B TRP* 1.3 60.3 + - - +
415B GLN* 3.4 25.5 + - - +
416B ILE* 3.1 43.5 + - + +
427B TYR* 3.4 22.9 - - + +
508B VAL* 5.7 7.0 - - + -
509B VAL 6.0 1.1 - - - +
510B ARG* 6.1 2.3 - - - +
511B ARG* 3.4 33.9 + - + +
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Residues in contact with TRP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLY 3.5 4.9 + - - +
410B MET* 3.2 17.5 + - - +
412B LYS* 1.3 77.4 - - - +
414B TRP* 1.3 104.1 + + - +
416B ILE* 3.1 5.7 + - + +
417B LYS* 2.9 55.5 + - + +
425B ILE* 3.8 25.5 + - + +
427B TYR* 3.4 42.8 + + + +
436B TYR* 3.6 42.8 - + + +
437B HIS* 3.6 18.8 - + + -
438B MET* 3.9 14.4 - - - -
439B ASP* 4.0 5.6 - - - -
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Residues in contact with TRP 414 (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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366B TYR* 6.1 0.4 - - - -
367B HIS* 5.0 0.2 - - + -
370B LEU* 4.1 21.1 - - + -
372B TRP* 3.5 32.3 - + - -
373B LEU* 4.6 4.7 - - + -
396B LEU* 4.3 10.1 - - + -
398B VAL* 4.0 14.6 - - + +
402B PHE* 3.6 27.5 - + - -
403B LEU* 3.8 16.6 - - + -
406B CYS* 3.9 10.5 - - - -
410B MET* 3.2 28.2 + - + +
411B ARG 3.3 6.9 + - - +
413B TRP* 1.3 98.2 - + - +
415B GLN* 1.3 55.9 + - - +
417B LYS* 3.6 11.9 - - + +
418B SER* 2.7 37.9 + - - -
437B HIS* 3.7 33.0 + + - -
438B MET* 4.5 15.0 - - + -
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Residues in contact with GLN 415 (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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403B LEU* 4.5 15.4 - - + +
411B ARG* 3.2 53.8 + - - +
412B LYS* 3.4 36.5 + - + +
413B TRP 3.2 0.2 - - - -
414B TRP* 1.3 75.3 - - - +
416B ILE* 1.3 64.3 + - + +
418B SER* 2.8 20.7 + - - -
419B GLN* 3.2 18.8 + - + +
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Residues in contact with ILE 416 (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 LYS* 3.1 40.4 - - - +
413B TRP* 3.1 9.5 + - - +
415B GLN* 1.3 78.0 - - + +
417B LYS* 1.3 57.6 + - - +
419B GLN* 3.4 5.2 + - + -
420B ASN* 3.0 30.5 + - - +
425B ILE* 3.7 18.8 - - + -
427B TYR* 4.8 9.4 - - + -
483B VAL* 4.3 11.2 - - + -
511B ARG 4.8 5.8 - - - +
512B GLU* 5.3 7.0 - - + -
513B ILE* 4.1 31.0 - - + +
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Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 4.7 1.8 - - + -
413B TRP* 2.9 51.9 + - + +
414B TRP* 3.2 17.7 + - + +
416B ILE* 1.3 75.5 - - - +
418B SER* 1.3 57.5 + - - +
419B GLN 3.1 4.9 - - - -
420B ASN 3.1 7.2 + - - +
421B PHE* 3.0 60.3 + - + +
423B LEU 3.2 14.6 + - - -
425B ILE* 3.7 12.3 - - + +
438B MET* 3.7 15.7 - - - +
439B ASP* 3.0 32.8 + - - -
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 4.5 6.7 - - - +
395B THR* 3.4 10.6 - - - +
396B LEU* 3.2 45.0 + - - +
398B VAL* 3.8 18.3 - - - +
414B TRP 2.7 19.0 + - - -
415B GLN* 2.8 25.1 + - - -
417B LYS* 1.3 73.9 - - - +
419B GLN* 1.3 59.7 + - - +
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Residues in contact with GLN 419 (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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381B GLU* 3.1 26.7 + - - +
394B SER* 3.5 11.5 + - - +
395B THR* 3.6 11.8 - - - +
415B GLN 3.2 18.8 + - - +
416B ILE* 3.7 7.9 - - + +
417B LYS 3.1 0.4 - - - -
418B SER* 1.3 80.9 + - - +
420B ASN* 1.3 77.0 + - - +
693B LYS* 5.5 0.2 + - - -
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Residues in contact with ASN 420 (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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394B SER 3.5 2.7 - - - -
416B ILE* 3.0 19.1 + - - +
417B LYS* 3.1 12.6 - - - +
419B GLN* 1.3 92.1 - - - +
421B PHE* 1.3 58.8 - - - +
422B ASP* 3.1 10.2 - - - +
423B LEU* 3.3 44.6 + - + +
425B ILE* 4.6 4.4 - - + +
513B ILE* 3.4 24.5 - - + +
516B ILE* 4.7 0.2 - - - +
693B LYS* 3.2 27.0 + - - -
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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