Contacts of the helix formed by residues 418 - 434 (chain B) in PDB entry 2OFV
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 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ILE* 3.6 22.5 - - + +
410B GLU* 4.8 2.1 + - - -
416B THR* 4.3 14.4 - - - +
417B PHE* 1.3 80.0 - - - +
419B ILE* 1.3 67.6 + - - +
420B LYS* 3.1 25.4 + - - +
421B SER* 2.9 21.8 + - - -
422B ASP 3.2 8.0 + - - -
481B PRO* 5.0 2.1 - - + +
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B MET* 4.4 4.5 - - + -
355B ILE* 4.5 0.2 - - + -
356B GLU* 3.3 51.4 - - + +
360B TYR 4.3 11.0 - - - +
361B ILE* 4.2 6.9 - - + +
418B THR* 1.3 75.6 - - - +
420B LYS* 1.3 78.0 + - + +
422B ASP* 3.2 18.7 + - - +
423B VAL* 3.0 25.7 + - + +
487B PHE* 3.4 30.7 - - + -
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 5.1 1.2 + - - -
418B THR* 3.0 11.8 - - - +
419B ILE* 1.3 93.8 - - + +
421B SER* 1.3 61.8 + - - +
423B VAL* 3.2 8.9 + - + +
424B TRP 3.1 13.5 + - - -
481B PRO* 3.1 43.5 - - + +
482B GLU* 4.3 19.1 + - + +
484B ARG* 2.8 50.5 + - + +
485B PRO 3.9 1.2 + - - -
486B THR* 3.8 29.3 - - - +
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Residues in contact with SER 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR* 6.1 0.4 - - - -
408B ALA* 4.1 13.8 + - - +
410B GLU* 3.6 7.3 + - - -
411B ALA* 4.7 2.5 - - - -
416B THR 3.3 14.6 + - - -
417B PHE* 4.1 16.8 - - - -
418B THR* 2.9 30.6 + - - -
420B LYS* 1.3 75.4 - - - +
422B ASP* 1.3 68.2 + - - +
424B TRP* 3.2 5.4 + - - +
425B SER* 3.0 24.1 + - - -
484B ARG* 3.6 10.1 - - - +
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B MET* 3.7 21.7 - - + +
361B ILE* 3.6 11.9 - - - +
362B HIS* 2.9 32.5 + - - +
363B ARG* 2.7 30.5 + - - -
365B LEU* 3.6 7.4 - - + +
418B THR 3.2 6.3 + - - +
419B ILE* 3.2 14.7 + - - +
421B SER* 1.3 80.3 - - - +
423B VAL* 1.3 50.9 + - - +
425B SER* 3.0 10.0 + - - -
426B PHE* 2.8 35.0 + - - +
487B PHE* 3.6 4.3 - - + -
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 5.3 0.2 - - - +
419B ILE* 3.0 23.7 + - + +
420B LYS* 3.3 20.6 - - + +
422B ASP* 1.3 76.1 - - - +
424B TRP* 1.3 62.5 + - - +
426B PHE* 3.3 3.3 + - - +
427B GLY 3.1 17.3 + - - -
476B CYS* 3.6 13.7 - - - +
484B ARG* 3.8 20.0 - - + -
485B PRO* 3.5 29.8 - - + +
486B THR* 5.1 1.1 - - - -
487B PHE* 3.6 26.2 - - + +
490B LEU* 4.2 13.0 - - + -
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Residues in contact with TRP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LYS 4.8 0.6 + - - -
406B TRP 3.7 15.1 + - - -
407B THR 3.8 9.7 + - - -
408B ALA* 3.8 9.9 - - + -
409B PRO* 3.5 35.4 - - + -
420B LYS 3.1 6.3 + - - -
421B SER 3.2 8.5 + - - +
423B VAL* 1.3 78.9 - - - +
425B SER* 1.3 63.1 + - - +
427B GLY 3.1 2.6 + - - -
428B ILE* 3.1 33.8 + - + +
441B TYR* 4.2 6.8 + - - -
454B GLU* 3.7 26.7 - - - -
458B ARG* 3.7 22.9 - - - -
476B CYS 3.6 12.3 + - - +
477B TRP* 3.5 45.9 + + + -
478B LYS 4.1 4.7 - - - -
479B GLU* 5.1 0.9 - - - -
484B ARG* 3.7 30.3 - - - +
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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
----------------------------------------------------------
363B ARG 5.1 5.2 + - - -
365B LEU* 3.4 35.8 + - - +
406B TRP* 2.6 28.6 + - - +
407B THR* 4.5 2.1 - - - -
421B SER 3.0 12.7 + - - -
422B ASP* 3.0 13.0 + - - -
424B TRP* 1.3 74.9 - - - +
426B PHE* 1.3 54.2 + - - +
428B ILE* 3.0 7.2 + - - +
429B LEU* 2.7 33.4 + - - +
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Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 3.5 19.7 - - - -
348B ILE* 3.8 31.9 - - + -
349B ALA* 3.9 12.1 - - + -
352B MET* 5.2 0.9 - - + -
365B LEU* 3.9 15.8 - - + +
422B ASP 2.8 15.4 + - - +
423B VAL 3.5 8.5 - - - +
424B TRP 3.2 0.2 - - - -
425B SER* 1.3 70.5 - - - +
427B GLY* 1.3 68.0 + - - +
429B LEU* 2.8 16.1 + - + +
430B LEU* 2.8 46.6 + - + +
476B CYS* 4.7 1.3 - - - -
487B PHE* 3.6 16.2 - + + -
490B LEU* 3.7 29.4 - - + -
494B LEU* 3.6 21.8 - - + -
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Residues in contact with GLY 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B VAL 3.1 8.5 + - - -
424B TRP 3.1 2.2 + - - -
426B PHE* 1.3 79.5 - - - +
428B ILE* 1.3 61.8 + - - +
430B LEU* 3.4 19.8 + - - +
431B THR* 3.7 3.6 + - - +
473B MET* 4.2 3.9 - - - +
476B CYS* 3.5 32.0 - - - -
477B TRP* 3.3 20.7 - - - -
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Residues in contact with ILE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LYS 3.5 17.5 - - - +
406B TRP* 3.3 29.6 - - + +
424B TRP* 3.1 29.8 + - + +
425B SER 3.0 8.1 + - - +
427B GLY* 1.3 75.4 - - - +
429B LEU* 1.3 64.0 + - - +
431B THR* 2.5 26.3 + - - -
432B GLU* 3.5 3.2 + - + +
440B PRO* 3.9 18.2 - - + -
441B TYR* 3.4 25.8 - - - +
459B MET* 3.5 15.0 - - + -
477B TRP* 3.5 17.3 - - + +
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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
----------------------------------------------------------
324B LEU* 4.7 3.8 - - + -
348B ILE* 4.1 17.9 - - + -
365B LEU* 3.8 30.1 - - + -
366B ARG* 4.0 9.6 - - - -
367B ALA* 3.3 31.9 - - + +
370B ILE* 3.9 17.3 - - + -
406B TRP* 4.3 0.9 - - - +
425B SER 2.7 16.5 + - - +
426B PHE* 3.2 16.4 - - + +
428B ILE* 1.3 72.5 - - - +
430B LEU* 1.3 62.8 + - - +
432B GLU* 3.0 25.0 + - + +
433B ILE* 3.2 18.6 + - + +
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Residues in contact with LEU 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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342B LEU* 5.7 1.1 - - + -
345B ALA* 3.7 30.3 - - + -
426B PHE* 2.8 44.0 + - + +
427B GLY* 3.5 13.2 - - - +
428B ILE 3.1 0.4 - - - -
429B LEU* 1.3 76.4 - - - +
431B THR* 1.3 61.3 + - - +
433B ILE* 3.0 21.8 + - + +
434B VAL* 3.2 18.5 + - + +
469B LEU* 4.5 19.1 - - + -
472B LEU* 4.8 7.9 - - + -
473B MET* 3.6 29.4 - - + -
476B CYS* 4.8 6.3 - - - -
490B LEU* 5.6 1.3 - - + -
494B LEU* 4.4 8.1 - - + -
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLY 3.8 1.8 - - - +
428B ILE* 2.5 18.5 + - - +
430B LEU* 1.3 77.5 - - - +
432B GLU* 1.3 53.3 + - - +
433B ILE 3.3 0.2 + - - -
434B VAL* 3.5 8.2 - - - +
435B THR* 2.2 38.7 + - - +
438B ARG* 4.8 5.3 + - - -
440B PRO* 4.3 6.6 - - - +
459B MET* 3.7 24.5 - - - +
462B PRO* 4.4 12.6 - - + -
473B MET* 3.7 25.8 - - - -
477B TRP* 3.8 26.5 - - + -
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Residues in contact with GLU 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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325B VAL* 4.1 11.4 - - - +
328B LEU* 3.4 3.3 - - - +
367B ALA* 2.8 47.1 + - + +
368B ALA 4.6 0.7 + - - -
406B TRP* 3.0 40.9 + - + +
428B ILE 4.0 6.5 - - - +
429B LEU* 3.0 18.0 + - + +
431B THR* 1.3 79.4 + - - +
433B ILE* 1.3 60.6 + - - +
435B THR* 3.1 8.3 + - - -
437B GLY* 2.6 38.7 + - - +
438B ARG 4.0 15.2 - - - +
439B ILE* 5.9 0.3 - - - -
440B PRO* 4.7 2.9 - - + +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 3.9 21.1 - - + -
328B LEU* 3.7 7.6 - - + +
334B ILE* 3.9 7.1 - - - +
341B LEU* 3.6 51.3 - - + +
342B LEU* 5.0 5.8 - - + -
344B MET* 4.8 2.2 - - + -
345B ALA* 3.9 28.0 - - + +
348B ILE* 3.9 23.8 - - + -
426B PHE* 5.9 0.2 - - + -
429B LEU* 3.2 15.3 + - + +
430B LEU* 3.0 19.4 + - + +
432B GLU* 1.3 78.0 - - - +
434B VAL* 1.3 64.9 + - + +
435B THR 3.2 5.1 + - - -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ILE* 5.6 2.4 - - - +
338B ILE* 6.5 0.4 - - + -
341B LEU* 4.6 12.2 - - + +
342B LEU* 5.3 1.3 - - + -
430B LEU 3.2 12.1 + - - +
431B THR* 3.5 13.0 - - - +
433B ILE* 1.3 83.1 - - + +
435B THR* 1.3 59.8 + - - +
436B HIS 3.7 0.4 - - - -
462B PRO* 3.6 30.7 - - + -
463B ASP 4.6 10.4 - - - +
464B ASN* 5.3 3.6 - - - +
465B CYS* 4.0 17.5 - - + +
466B PRO* 5.5 0.9 - - + -
469B LEU* 3.5 31.6 - - + -
473B MET* 4.4 4.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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