Contacts of the helix formed by residues 440 - 457 (chain B) in PDB entry 3VRY
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 440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ILE* 3.7 19.9 - - + +
432B GLU* 4.4 6.4 + - - +
438B SER* 3.8 12.9 + - - +
439B PHE* 1.3 77.8 - - - +
441B ILE* 1.3 66.2 + - - +
442B LYS* 3.0 24.8 + - + +
443B SER* 2.6 29.1 + - - -
444B ASP* 3.3 6.2 + - - -
503B PRO* 5.0 2.0 - - + +
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 4.4 5.4 - - + -
377B ILE* 4.5 0.4 - - + -
378B GLU* 3.6 47.8 - - + +
382B TYR 3.6 24.2 - - - +
383B ILE* 4.5 5.9 - - + +
440B THR* 1.3 77.5 - - - +
442B LYS* 1.3 77.0 + - + +
444B ASP* 3.2 17.0 - - - +
445B VAL* 2.9 27.3 + - + +
509B PHE* 3.9 19.7 - - + -
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 5.9 0.9 - - - -
440B THR* 3.0 13.5 + - + +
441B ILE* 1.3 90.8 - - + +
443B SER* 1.3 58.6 + - - +
444B ASP 3.3 0.2 - - - -
445B VAL* 3.3 13.0 - - + +
446B TRP 3.0 18.2 + - - -
503B PRO* 3.4 40.8 - - + +
504B GLU* 4.7 8.0 + - - +
506B ARG* 2.5 51.3 + - + +
507B PRO 3.5 14.3 + - - -
508B THR* 3.9 14.2 - - - +
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Residues in contact with SER 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B THR* 6.1 0.4 - - - -
430B ALA* 3.8 19.8 - - - +
432B GLU* 4.0 8.7 - - - -
433B ALA* 4.4 7.6 - - - -
438B SER 4.3 5.6 - - - -
439B PHE* 3.2 13.3 - - - +
440B THR* 2.6 41.9 + - - -
442B LYS* 1.3 72.4 - - - +
444B ASP* 1.3 60.3 + - - +
446B TRP* 3.2 4.9 + - - +
447B SER* 2.8 32.1 + - - -
506B ARG* 3.7 8.4 - - - +
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 3.8 8.3 - - + +
383B ILE* 3.5 9.6 - - - +
384B HIS* 2.8 35.0 + - - +
385B ARG* 3.2 24.7 + - - -
386B ASP 4.7 0.3 + - - -
387B LEU* 4.3 6.4 - - + +
439B PHE* 5.8 0.5 - - - +
440B THR 3.3 10.6 + - - +
441B ILE* 3.2 14.2 - - - +
443B SER* 1.3 75.4 + - - +
445B VAL* 1.3 54.4 + - - +
447B SER* 3.1 10.3 + - - -
448B PHE* 2.7 35.0 + - - +
509B PHE* 3.7 17.4 - - + -
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 5.3 1.1 - - - +
441B ILE* 2.9 22.3 + - + +
442B LYS* 3.3 18.4 + - + +
444B ASP* 1.3 74.2 - - - +
446B TRP* 1.3 66.0 + - - +
448B PHE* 3.1 13.0 + - - +
449B GLY 3.1 8.7 + - - -
498B CYS* 3.4 27.2 - - - +
506B ARG* 3.7 22.0 - - + -
507B PRO* 3.4 25.1 - - + +
508B THR* 5.1 0.4 - - - -
509B PHE* 3.6 28.0 - - + +
512B ILE* 4.3 3.6 - - + -
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Residues in contact with TRP 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS 5.2 1.0 + - - -
428B TRP 3.6 17.5 + - - -
429B THR 3.7 7.9 + - - -
430B ALA* 3.5 19.5 - - + -
431B PRO* 3.8 25.8 - - + -
442B LYS 3.0 11.2 + - - +
443B SER 3.3 9.2 - - - +
445B VAL* 1.3 76.4 - - - +
447B SER* 1.3 64.4 + - - +
449B GLY 2.9 12.6 + - - -
450B ILE* 3.2 21.2 + - + +
463B TYR* 4.3 7.2 + - - -
475B LEU* 4.2 23.7 - - + +
480B ARG* 3.6 26.7 - - - -
498B CYS 3.2 12.1 + - - +
499B TRP* 3.4 51.6 + + + -
500B LYS 3.6 2.9 - - - -
501B ASN* 4.8 0.9 - - - -
506B ARG* 3.0 29.4 - - - +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ARG 5.6 2.6 + - - -
387B LEU* 3.4 38.0 + - - +
428B TRP* 3.0 25.2 + - - +
429B THR* 4.8 1.9 - - - -
443B SER 2.8 21.6 + - - -
444B ASP* 3.4 11.3 + - - -
446B TRP* 1.3 72.5 - - - +
448B PHE* 1.3 58.0 + - - +
450B ILE* 3.0 8.1 + - - +
451B LEU* 2.9 25.8 + - - +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 3.6 24.7 - - - -
370B ILE* 4.1 10.8 - - + -
371B ALA* 3.8 18.2 - - + -
387B LEU* 3.8 20.6 - - + +
444B ASP 2.7 16.1 + - - +
445B VAL* 3.1 9.4 + - - +
447B SER* 1.3 73.3 - - - +
449B GLY* 1.3 53.7 + - - +
451B LEU* 3.0 12.1 + - + +
452B LEU* 2.7 69.0 + - + +
494B ILE* 5.2 0.4 - - + -
498B CYS* 4.1 14.8 - - - -
509B PHE* 3.7 20.2 - + + -
512B ILE* 3.5 25.6 - - + -
516B LEU* 3.7 7.2 - - + -
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Residues in contact with GLY 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL 3.1 6.5 + - - -
446B TRP 2.9 9.4 + - - -
448B PHE* 1.3 75.9 - - - +
450B ILE* 1.3 61.4 + - - +
452B LEU* 3.2 19.1 + - - +
453B MET* 3.2 8.8 + - - +
495B MET* 4.1 6.4 - - - +
498B CYS* 3.7 18.2 - - - -
499B TRP* 3.3 24.3 - - - -
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS 3.5 20.2 - - - +
428B TRP* 3.4 31.6 - - + +
446B TRP* 3.2 21.9 + - + +
447B SER 3.0 7.1 + - - +
449B GLY* 1.3 75.5 - - - +
451B LEU* 1.3 61.4 + - - +
453B MET* 3.1 6.1 + - - +
454B GLU* 3.0 20.6 + - - +
462B PRO* 4.0 17.7 - - + -
463B TYR* 3.7 25.8 - - + +
481B MET* 4.3 6.1 - - + -
499B TRP* 3.2 32.5 - - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.5 4.0 - - + -
370B ILE* 3.8 26.2 - - + -
387B LEU* 3.7 28.5 - - + -
388B ARG* 4.4 9.9 - - - -
389B ALA* 3.3 37.2 - - + +
392B ILE* 4.2 8.5 - - + -
428B TRP* 4.7 0.4 - - - -
447B SER 2.9 12.6 + - - +
448B PHE* 3.0 13.4 + - + +
450B ILE* 1.3 76.9 - - - +
452B LEU* 1.3 57.6 + - - +
454B GLU* 3.3 8.8 + - - +
455B ILE* 2.8 47.7 + - + +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 3.6 24.0 - - - +
448B PHE* 2.7 45.8 + - + +
449B GLY* 3.2 11.0 - - - +
451B LEU* 1.3 77.2 - - - +
453B MET* 1.3 61.5 + - - +
455B ILE* 3.6 7.0 + - + +
456B VAL* 3.2 23.6 + - - +
491B LEU* 3.6 32.4 - - + +
494B ILE* 3.8 22.4 - - + -
495B MET* 3.7 25.9 - - + +
516B LEU* 4.1 4.5 - - + -
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Residues in contact with MET 453 (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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449B GLY 3.2 10.3 + - - +
450B ILE* 3.1 13.6 + - + +
451B LEU 3.1 0.4 - - - -
452B LEU* 1.3 76.0 - - - +
454B GLU* 1.3 56.5 + - - +
456B VAL* 3.1 5.0 + - - +
457B THR* 2.9 44.3 + - + +
460B ARG* 4.2 10.3 - - - +
462B PRO* 5.6 3.8 - - + -
481B MET* 3.7 46.2 - - + -
482B PRO 3.9 4.7 - - - +
484B PRO* 3.7 38.6 - - + -
492B TYR* 4.3 4.9 - - + -
495B MET* 3.7 24.9 - - - +
499B TRP* 3.9 8.5 - - + -
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Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.2 16.3 - - - +
350B LEU* 4.5 1.1 - - - -
388B ARG* 3.8 0.2 - - - +
389B ALA* 3.1 40.3 + - + +
390B ALA* 4.8 0.7 + - - +
428B TRP* 2.8 42.7 + - - +
450B ILE 3.0 6.5 + - - +
451B LEU* 3.3 13.1 - - - +
453B MET* 1.3 79.8 - - - +
455B ILE* 1.3 62.4 + - - +
457B THR* 3.3 8.1 + - - -
458B TYR 3.3 3.6 + - - -
459B GLY* 2.8 32.1 + - - +
460B ARG 3.9 17.5 - - - +
462B PRO* 4.1 10.5 - - + +
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Residues in contact with ILE 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.8 19.1 - - + -
350B LEU* 3.5 13.6 - - + +
363B LEU* 3.7 49.7 - - + +
366B PHE* 5.0 3.1 - - + -
367B SER* 3.9 22.9 - - - +
370B ILE* 3.7 21.8 - - + -
389B ALA* 5.5 0.4 - - + -
451B LEU* 2.8 40.7 + - + +
452B LEU* 3.8 6.5 - - + +
453B MET 3.2 0.2 - - - -
454B GLU* 1.3 77.4 - - - +
456B VAL* 1.3 58.7 + - + +
458B TYR* 3.2 18.2 + - - -
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 3.6 31.2 - - + -
363B LEU* 4.5 6.5 - - + -
452B LEU 3.2 11.3 + - - +
453B MET* 3.1 14.3 + - - +
455B ILE* 1.3 81.6 - - + +
457B THR* 1.3 59.2 + - - +
458B TYR* 3.3 8.1 + - - -
484B PRO* 3.9 14.8 - - + -
486B ASN* 3.2 31.7 + - - +
487B CYS* 3.8 31.6 - - + -
491B LEU* 4.0 20.4 - - + -
495B MET* 4.5 1.1 - - + -
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B MET* 2.9 24.2 + - - +
454B GLU* 3.3 10.0 + - - -
455B ILE 3.2 0.2 - - - -
456B VAL* 1.3 77.6 - - - +
458B TYR* 1.3 71.0 + - - +
459B GLY 3.1 1.1 + - - -
460B ARG* 3.1 65.5 + - - +
484B PRO* 4.1 24.0 - - + -
486B ASN* 5.1 2.0 - - - +
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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