Contacts of the helix formed by residues 481 - 494 (chain B) in PDB entry 1M2V
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 481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B CYS* 4.7 5.8 - - - -
479B GLN 3.7 3.2 + - - -
480B ASP* 1.3 71.8 + - - +
482B PHE* 1.3 56.0 + - - +
483B TYR 3.2 1.8 - - - -
484B LYS* 3.4 11.2 + - - +
485B ASN* 2.6 43.1 + - - +
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Residues in contact with PHE 482 (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 GLY* 3.8 29.4 - - - -
428B LEU* 4.2 11.0 - - + -
429B LYS* 4.2 23.8 - - + -
454B ILE* 4.0 22.7 - - + +
455B GLY* 4.3 9.9 - - - -
480B ASP* 2.5 25.3 + - - +
481B SER* 1.3 72.8 - - - +
483B TYR* 1.3 91.9 + + - +
485B ASN* 3.4 8.8 + - + +
486B PHE* 2.9 60.5 + + + +
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Residues in contact with TYR 483 (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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424B LEU* 4.0 16.7 - - + +
425B GLY 4.9 1.4 + - - -
450B PRO* 3.3 21.3 - - - +
455B GLY* 2.7 33.9 + - - -
457B LEU* 3.8 18.6 - - + -
478B CYS* 4.2 6.5 - - - -
480B ASP* 3.4 18.8 - - + +
481B SER 3.2 1.0 - - - -
482B PHE* 1.3 104.6 - + - +
484B LYS* 1.3 58.2 + - - +
486B PHE* 4.2 1.1 - - - -
487B THR* 3.3 22.5 + - - +
511B SER* 3.8 20.9 - - - +
512B LEU* 3.4 25.1 - - + -
514B ASN* 4.0 8.5 - - + +
515B LEU* 3.9 27.4 - - + +
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Residues in contact with LYS 484 (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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478B CYS* 3.9 28.4 - - + +
481B SER* 3.4 14.3 + - - +
482B PHE 3.1 0.4 - - - -
483B TYR* 1.3 77.9 - - - +
485B ASN* 1.3 68.0 + - - +
486B PHE 3.2 1.8 - - - -
487B THR* 2.6 25.7 + - - -
488B ILE* 3.4 12.5 + - + +
514B ASN* 3.7 28.9 - - + -
518B PHE* 5.0 13.0 - - + -
665B ASN* 5.6 3.8 + - - -
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Residues in contact with ASN 485 (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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481B SER* 2.6 33.7 + - - +
482B PHE* 3.4 7.8 + - + +
484B LYS* 1.3 80.7 - - - +
486B PHE* 1.3 62.5 + - - +
488B ILE* 3.1 26.8 + - + +
489B ASP* 3.1 21.3 + - - +
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Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 3.4 46.9 - - + -
429B LYS* 4.3 8.1 - - + -
432B TYR* 3.9 22.9 - + + -
442B ILE* 4.4 5.4 - - + -
482B PHE* 2.9 45.3 + + + +
483B TYR 4.5 0.7 - - - +
484B LYS 3.2 0.2 - - - -
485B ASN* 1.3 79.1 - - - +
487B THR* 1.3 56.6 + - - +
489B ASP* 3.3 13.4 + - + +
490B CYS* 3.0 51.9 + - - -
497B VAL* 4.0 13.0 - - + -
515B LEU* 3.6 26.0 - - + -
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Residues in contact with THR 487 (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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483B TYR 3.3 16.6 - - - +
484B LYS* 2.6 20.4 + - - -
486B PHE* 1.3 77.0 - - - +
488B ILE* 1.3 64.5 + - - +
490B CYS* 3.4 3.8 + - - +
491B SER* 3.3 19.8 + - - -
514B ASN 3.3 26.2 - - - +
515B LEU* 3.7 22.4 - - + +
518B PHE* 3.7 24.0 - - + +
519B THR* 3.9 15.9 - - + +
576B PHE* 4.2 7.4 - - - -
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Residues in contact with ILE 488 (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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484B LYS* 3.5 16.6 - - + +
485B ASN* 3.1 19.0 + - + +
487B THR* 1.3 78.3 + - - +
489B ASP* 1.3 62.5 + - - +
491B SER* 2.6 26.2 + - - +
492B LYS* 3.6 23.0 - - - +
576B PHE* 4.2 13.7 - - + -
578B ARG* 3.1 44.0 - - - +
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Residues in contact with ASP 489 (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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432B TYR* 3.3 30.5 - - + +
485B ASN* 3.1 20.1 + - - +
486B PHE* 3.3 13.9 + - + +
487B THR 3.3 0.2 - - - -
488B ILE* 1.3 77.7 - - - +
490B CYS* 1.3 58.4 + - - +
491B SER 3.1 0.2 - - - -
492B LYS* 3.0 46.8 + - - +
493B VAL 3.5 1.2 + - - -
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Residues in contact with CYS 490 (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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432B TYR* 4.2 9.6 - - - -
486B PHE* 3.0 56.7 + - - +
487B THR 3.7 6.1 - - - +
488B ILE 3.3 0.2 - - - -
489B ASP* 1.3 76.8 - - - +
491B SER* 1.3 58.0 + - - +
493B VAL* 3.5 2.9 + - - -
494B GLN* 2.9 24.8 + - - -
495B ILE* 2.9 47.0 + - + +
497B VAL* 4.6 5.8 - - - -
519B THR* 4.0 9.6 - - + -
586B SER* 3.6 1.3 + - - -
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Residues in contact with SER 491 (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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487B THR 3.3 12.4 + - - -
488B ILE* 2.6 23.3 + - - +
490B CYS* 1.3 76.7 - - - +
492B LYS* 1.3 61.0 + - - +
494B GLN* 2.9 26.7 + - - +
519B THR* 5.8 0.2 - - - +
576B PHE* 3.9 39.6 - - - -
584B ALA* 6.1 2.0 - - - -
586B SER* 4.3 8.7 - - - -
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Residues in contact with LYS 492 (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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432B TYR* 4.5 5.2 - - - +
488B ILE* 3.6 26.5 + - - +
489B ASP* 3.0 35.6 + - + +
491B SER* 1.3 81.4 + - - +
493B VAL* 1.3 66.4 + - + +
494B GLN* 4.0 6.6 + - - +
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Residues in contact with VAL 493 (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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432B TYR* 3.1 49.6 - - + +
436B GLY* 3.2 23.5 - - - +
437B GLY 5.3 0.2 - - - +
438B VAL 4.6 0.7 - - - -
439B GLY* 3.2 16.5 - - - -
489B ASP 3.5 0.2 + - - -
490B CYS 4.0 4.5 - - - +
491B SER 3.3 0.2 - - - -
492B LYS* 1.3 80.7 - - + +
494B GLN* 1.3 69.9 + - - +
495B ILE* 3.4 26.0 - - + -
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Residues in contact with GLN 494 (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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438B VAL 5.2 2.7 - - - +
439B GLY* 3.6 3.3 - - - -
440B GLY* 3.0 21.5 + - - +
490B CYS 2.9 5.3 + - - -
491B SER* 2.9 23.0 + - - +
492B LYS 4.0 7.7 + - - +
493B VAL* 1.3 79.7 - - - +
495B ILE* 1.3 56.2 + - - +
555B GLU* 4.3 31.5 - - + +
584B ALA* 5.7 4.3 - - - +
585B PHE 4.9 0.9 - - - +
586B SER* 3.3 43.6 + - - +
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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