Contacts of the helix formed by residues 443 - 454 (chain B) in PDB entry 3OPY
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 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430B VAL* 4.6 3.4 - - - -
441B PRO 3.9 0.4 + - - -
442B ILE* 1.3 75.7 - - - +
444B CYS* 1.3 63.0 + - - +
445B ASP* 3.4 12.8 + - - +
446B GLN* 3.0 44.5 + - - +
447B VAL* 3.3 24.8 + - - +
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Residues in contact with CYS 444 (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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371B ILE* 3.6 29.3 - - + +
373B GLU* 3.4 51.4 - - - +
430B VAL* 4.1 12.9 - - - +
443B SER* 1.3 72.4 - - - +
445B ASP* 1.3 60.2 + - - +
447B VAL* 3.3 7.5 + - - +
448B LYS* 2.7 35.3 + - - +
461B VAL* 5.2 9.2 - - + -
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Residues in contact with ASP 445 (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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443B SER* 3.8 10.6 + - - +
444B CYS* 1.3 77.3 + - - +
446B GLN* 1.4 56.5 + - - +
448B LYS* 3.2 10.2 + - - +
449B ASP* 2.9 47.8 + - - +
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Residues in contact with GLN 446 (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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407B TRP* 3.9 12.6 + - + -
441B PRO 3.6 12.6 + - - +
442B ILE* 3.5 24.6 - - + +
443B SER* 3.0 43.1 + - - +
445B ASP* 1.4 76.8 - - - +
447B VAL* 1.4 60.9 + - - +
449B ASP* 3.5 7.6 + - - +
450B VAL* 3.4 24.6 + - - +
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Residues in contact with VAL 447 (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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371B ILE* 3.7 15.9 - - + -
396B LEU* 3.9 13.7 - - + -
407B TRP* 3.8 24.7 - - + -
411B MET* 3.6 18.8 - - + +
428B VAL* 3.8 15.5 - - + -
430B VAL* 3.9 16.2 - - + -
442B ILE* 3.8 11.0 - - + -
443B SER 3.3 13.2 + - - +
444B CYS 3.3 8.0 + - - +
446B GLN* 1.4 76.4 - - - +
448B LYS* 1.4 63.4 + - - +
450B VAL* 3.3 5.0 + - - +
451B LEU* 3.3 24.8 + - + +
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Residues in contact with LYS 448 (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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371B ILE* 3.6 15.4 - - + +
444B CYS 2.7 22.0 + - - +
445B ASP* 3.2 12.1 + - - +
447B VAL* 1.4 71.1 - - - +
449B ASP* 1.3 63.7 + - - +
451B LEU* 3.3 5.8 + - - +
452B VAL* 2.9 39.3 + - + +
459B THR* 2.8 40.3 + - - +
461B VAL* 5.0 13.2 - - + +
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Residues in contact with ASP 449 (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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445B ASP* 2.9 32.7 + - - +
446B GLN* 3.9 7.0 + - - +
447B VAL 3.4 0.4 - - - -
448B LYS* 1.3 78.3 - - - +
450B VAL* 1.3 58.2 + - + +
452B VAL* 4.4 5.9 - - - +
453B ASN* 2.6 51.3 + - - +
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Residues in contact with VAL 450 (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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407B TRP* 3.7 19.3 - - + -
408B GLN* 3.8 24.9 - - + +
411B MET* 4.4 13.5 - - - -
412B CYS* 3.6 27.8 - - - -
446B GLN 3.4 14.6 + - - +
447B VAL 3.3 8.0 + - - +
448B LYS 3.3 0.6 - - - -
449B ASP* 1.3 75.2 - - + +
451B LEU* 1.3 57.9 + - - +
453B ASN* 5.4 0.2 - - - -
454B ARG* 2.8 41.9 + - + +
455B LEU* 3.4 3.5 + - - +
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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
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369B ALA* 4.2 8.1 - - + -
370B PHE 5.6 0.4 - - - +
371B ILE* 4.0 15.3 - - + -
411B MET* 4.1 19.3 - - + -
415B VAL* 4.6 7.9 - - + -
426B THR* 5.6 0.4 - - - +
428B VAL* 4.3 17.7 - - + -
447B VAL* 3.3 22.0 + - + +
448B LYS 3.3 3.1 + - - +
450B VAL* 1.3 78.6 - - + +
452B VAL* 1.3 51.7 + - - +
455B LEU* 2.8 37.9 - - + +
457B LEU* 3.3 39.5 + - + +
459B THR* 3.4 32.8 - - + +
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Residues in contact with VAL 452 (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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448B LYS* 2.9 34.0 + - + +
449B ASP* 4.1 5.4 - - - +
451B LEU* 1.3 73.0 - - - +
453B ASN* 1.3 74.4 + - - +
455B LEU 2.9 15.1 - - - +
456B GLY* 4.3 5.5 - - - -
457B LEU 3.2 19.7 - - - +
458B ASP* 4.9 1.6 - - - +
459B THR* 3.4 19.3 - - - +
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Residues in contact with ASN 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 ASP* 2.6 36.1 + - - +
450B VAL* 5.4 0.2 - - - -
452B VAL* 1.3 92.8 + - - +
454B ARG* 1.4 61.6 + - - +
455B LEU 3.4 3.2 + - - +
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Residues in contact with ARG 454 (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 GLU* 4.0 6.9 + - - -
408B GLN* 3.4 25.6 - - - +
409B ASP* 2.9 46.2 + - - +
412B CYS* 3.3 27.0 - - - +
449B ASP 4.0 0.2 + - - -
450B VAL* 2.8 25.4 + - + +
453B ASN* 1.4 73.6 - - - +
455B LEU* 1.3 63.8 + - + +
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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