Contacts of the helix formed by residues 448 - 457 (chain B) in PDB entry 2I91
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 ALA 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLN* 4.5 0.8 + - - +
446B ASP* 2.9 10.3 + - - +
447B CYS* 1.3 77.4 - - - +
449B LEU* 1.3 67.0 + - - +
450B PRO* 3.2 4.3 - - - -
451B MET* 3.4 5.1 + - - -
452B LEU* 3.1 24.9 + - + +
476B ASP* 3.9 7.9 - - - +
477B VAL* 3.4 25.6 - - + +
479B PRO* 3.7 20.2 - - + -
482B ALA* 3.8 12.9 - - + +
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Residues in contact with LEU 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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415B PHE* 4.2 5.2 - - + -
416B SER 3.6 5.8 - - - +
417B ASP 3.4 8.7 - - - +
418B GLU* 3.1 46.2 - - - +
419B MET* 3.7 17.9 - - + +
446B ASP* 3.1 39.3 - - + +
448B ALA* 1.3 79.1 - - - +
450B PRO* 1.3 58.8 - - + +
452B LEU* 3.2 8.6 + - + +
453B TRP* 2.5 39.5 + - - +
476B ASP* 4.5 4.7 - - - +
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Residues in contact with PRO 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.4 12.2 - - + +
374B ALA* 3.5 33.4 - - + -
413B VAL* 5.3 1.3 - - + -
415B PHE* 3.7 21.8 - - + -
419B MET* 4.3 6.9 - - + -
446B ASP 4.3 0.2 - - - +
447B CYS 3.9 12.1 - - - +
448B ALA 3.3 4.9 - - - -
449B LEU* 1.3 92.9 - - + +
451B MET* 1.3 72.9 + - - +
453B TRP* 3.1 7.5 + - + +
454B ALA* 2.8 26.0 + - - +
464B PHE* 4.7 2.2 - - + -
466B VAL* 4.6 9.4 - - + -
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Residues in contact with MET 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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447B CYS 3.6 23.8 - - - +
448B ALA* 3.4 2.8 + - - -
450B PRO* 1.3 85.7 - - - +
452B LEU* 1.3 64.5 + - - +
454B ALA* 3.1 4.5 + - - +
455B GLN* 3.0 21.6 + - - +
464B PHE* 3.2 42.6 - - + -
466B VAL* 4.6 5.4 - - + -
479B PRO* 3.6 28.0 - - + +
482B ALA* 3.7 23.6 - - + +
483B LEU* 3.7 20.6 - - + -
486B TYR* 3.8 7.2 - - + -
496B LEU* 4.3 24.2 - - + -
508B ILE* 5.3 0.9 - - + -
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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
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448B ALA* 3.1 24.1 + - + +
449B LEU* 3.5 13.5 - - + +
451B MET* 1.3 80.4 - - - +
453B TRP* 1.3 63.1 + - - +
455B GLN* 3.3 11.0 + - - +
456B LYS* 3.2 25.3 + - + +
476B ASP* 3.1 31.9 - - - +
477B VAL* 4.3 8.1 - - + -
482B ALA* 4.1 17.5 - - + +
485B GLN* 4.2 19.3 - - - +
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Residues in contact with TRP 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.8 27.6 - - + -
411B HIS* 4.0 28.7 - + - -
413B VAL* 4.3 6.1 - - + -
419B MET* 3.3 46.4 - - + +
449B LEU 2.5 21.5 + - - +
450B PRO 3.5 4.5 - - - +
452B LEU* 1.3 71.8 - - - +
454B ALA* 1.3 72.2 + - + +
456B LYS* 3.2 8.9 + - + +
457B THR* 2.4 60.8 + - + +
459B THR* 3.7 28.0 - - + -
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Residues in contact with ALA 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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372B LEU* 5.1 4.5 - - + -
450B PRO 2.8 12.0 + - - +
451B MET 3.2 9.0 - - - +
453B TRP* 1.3 94.0 - - + +
455B GLN* 1.3 58.9 + - - +
457B THR* 3.9 0.7 - - - -
458B ASN 3.3 1.6 + - - -
459B THR* 2.8 41.3 + - + +
464B PHE* 3.7 16.4 - - + -
486B TYR* 3.6 18.7 - - + -
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Residues in contact with GLN 455 (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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451B MET 3.0 12.0 + - - +
452B LEU* 3.9 12.9 - - - +
453B TRP 3.3 0.4 - - - -
454B ALA* 1.3 75.7 - - - +
456B LYS* 1.3 64.0 + - - +
458B ASN* 2.9 21.1 + - - +
482B ALA 5.4 0.5 - - - +
485B GLN* 3.7 29.6 + - - +
486B TYR* 3.7 17.5 + - + -
489B LYS* 3.4 51.5 - - + +
490B MET* 4.2 8.8 - - - +
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Residues in contact with LYS 456 (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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452B LEU 3.2 11.5 + - - +
453B TRP* 3.2 12.9 + - + +
455B GLN* 1.3 82.3 - - + +
457B THR* 1.3 58.5 + - + +
458B ASN* 3.1 7.5 + - - +
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Residues in contact with THR 457 (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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453B TRP* 2.4 65.1 + - + +
454B ALA 3.8 0.7 + - - -
456B LYS* 1.3 76.5 - - + +
458B ASN* 1.3 71.4 + - - +
459B THR* 2.8 18.3 + - - -
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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