Contacts of the helix formed by residues 508 - 518 (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 ASP 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B LEU* 3.8 8.1 - - + -
457B LEU* 3.7 8.6 - - + +
460B ARG* 2.6 21.9 + - - -
479B GLN* 2.7 23.1 - - - +
506B TYR* 3.0 35.3 + - + -
507B MET* 1.3 82.8 - - - +
509B VAL* 1.3 66.9 + - - +
510B ALA* 3.1 4.1 - - - +
511B SER* 2.5 28.4 + - - +
512B LEU* 3.1 17.0 + - - +
731B ASP* 3.0 7.4 + - - -
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Residues in contact with VAL 509 (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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501B LEU* 3.8 24.2 - - + -
507B MET* 3.4 2.9 - - + -
508B ASP* 1.3 72.3 - - - +
510B ALA* 1.3 59.7 + - - +
512B LEU 4.6 0.2 - - - +
513B SER* 2.4 44.8 + - - +
523B THR* 4.1 15.3 - - + -
525B PHE* 3.9 25.1 - - + -
731B ASP* 2.6 40.1 + - + +
734B ALA* 4.1 0.4 - - + -
735B SER* 4.0 29.4 - - - +
738B ASN* 5.7 0.9 - - + -
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Residues in contact with ALA 510 (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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460B ARG* 4.1 1.3 - - - +
475B LEU 3.3 26.0 - - - +
476B LEU* 3.5 24.1 - - + +
508B ASP* 3.1 7.6 - - - +
509B VAL* 1.3 81.7 - - - +
511B SER* 1.3 60.2 + - - +
513B SER* 3.8 9.6 - - - -
514B ASN* 3.6 9.7 + - - -
517B ARG* 4.7 3.3 + - - -
664B LEU* 5.6 3.9 - - - +
730B SER* 4.5 4.0 + - - +
731B ASP* 4.3 0.6 + - - -
734B ALA* 3.4 24.7 - - + +
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Residues in contact with SER 511 (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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457B LEU* 3.8 12.3 - - - +
460B ARG* 3.5 15.0 - - - -
478B CYS* 3.5 9.6 - - - +
479B GLN 3.5 19.6 + - - -
483B TYR* 3.8 13.9 - - - +
508B ASP* 2.5 30.7 + - - -
510B ALA* 1.3 75.2 - - - +
512B LEU* 1.3 64.5 + - - +
513B SER 3.3 1.8 - - - -
514B ASN* 2.7 26.8 + - - +
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Residues in contact with LEU 512 (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* 4.3 7.9 - - + -
448B THR 5.9 0.7 - - - +
450B PRO* 4.1 15.3 - - + -
457B LEU* 3.6 15.7 - - + -
483B TYR* 3.4 41.7 - - + +
499B LEU* 3.8 20.6 - - + +
501B LEU* 4.1 29.8 - - + -
507B MET* 3.8 15.9 - - + +
508B ASP 3.1 15.4 + - - +
509B VAL 4.3 2.0 - - - +
511B SER* 1.3 73.4 - - - +
513B SER* 1.3 66.4 + - - +
514B ASN 3.0 2.9 - - - -
515B LEU* 2.8 25.2 + - + +
516B SER 4.2 0.3 + - - -
523B THR* 4.6 0.2 - - - -
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Residues in contact with SER 513 (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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509B VAL* 2.4 38.1 + - - +
510B ALA* 3.8 8.5 + - - -
512B LEU* 1.3 77.1 - - - +
514B ASN* 1.3 63.5 + - - +
515B LEU 2.9 0.9 + - - -
516B SER* 3.1 4.3 + - - -
517B ARG* 2.8 50.7 + - - +
523B THR* 3.3 19.0 + - - +
734B ALA 4.9 1.7 + - - -
738B ASN* 4.4 9.1 - - - +
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Residues in contact with ASN 514 (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* 3.3 24.4 - - - +
483B TYR* 4.0 13.9 - - + +
484B LYS* 3.7 21.2 - - + -
487B THR* 3.3 7.3 - - - +
510B ALA 3.6 4.9 + - - -
511B SER* 2.7 33.0 + - - +
512B LEU 3.0 0.2 + - - -
513B SER* 1.3 79.1 - - - +
515B LEU* 1.3 61.0 + - - +
517B ARG* 3.7 14.1 + - - +
518B PHE* 3.1 47.7 + - + -
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Residues in contact with LEU 515 (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* 4.7 3.4 - - + -
428B LEU* 3.7 24.5 - - + -
444B VAL* 5.8 0.4 - - + -
482B PHE* 5.4 0.2 - - + -
483B TYR* 3.9 39.7 - - + +
486B PHE* 3.6 34.3 - - + -
487B THR* 3.7 6.0 - - + +
497B VAL* 3.9 21.2 - - + +
499B LEU* 4.0 18.6 - - + -
512B LEU* 2.8 17.2 + - - +
513B SER 2.9 0.4 + - - -
514B ASN* 1.3 80.4 - - - +
516B SER* 1.3 53.4 + - - +
519B THR* 2.8 37.1 + - - +
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Residues in contact with SER 516 (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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497B VAL 3.1 24.9 - - - -
499B LEU* 4.0 4.0 - - - -
513B SER* 3.1 2.8 + - - -
515B LEU* 1.3 78.8 - - - +
517B ARG* 1.3 66.9 + - - +
519B THR* 3.6 0.9 - - - -
520B ALA* 3.1 6.6 + - - -
521B GLY 2.7 27.2 + - - +
522B GLN* 3.1 27.7 + - - -
523B THR* 2.4 32.2 + - - -
574B HIS* 4.1 0.3 + - - +
738B ASN* 5.0 2.3 + - - -
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Residues in contact with ARG 517 (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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510B ALA 4.7 3.6 + - - -
513B SER* 2.8 39.9 + - - +
514B ASN* 3.7 22.2 + - - +
516B SER* 1.3 79.2 + - - +
518B PHE* 1.3 85.9 + - + +
519B THR 3.5 0.2 - - - -
573B GLY 4.1 2.9 - - - +
574B HIS* 3.3 24.3 - - + +
575B PHE 3.3 21.0 + - - +
664B LEU* 3.7 31.0 - - - +
734B ALA 5.2 1.4 + - - -
738B ASN* 3.4 22.2 + - - +
741B GLU* 2.6 32.9 + - - +
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Residues in contact with PHE 518 (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* 5.0 13.9 - - + -
487B THR* 3.7 25.8 - - + +
514B ASN* 3.1 48.8 + - + -
516B SER 3.2 0.4 - - - -
517B ARG* 1.3 100.6 - - + +
519B THR* 1.3 63.9 + - - +
520B ALA 3.6 1.6 - - - -
575B PHE 3.4 19.1 - - - +
576B PHE* 3.6 30.3 - + + +
577B ASN 6.1 0.7 - - - -
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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