Contacts of the strand formed by residues 451 - 456 (chain B) in PDB entry 3INB
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 VAL 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B SER* 2.7 33.0 + - - +
448B HIS* 3.0 22.7 + - + +
449B ASN 4.2 4.0 - - - +
450B ASN* 1.3 85.1 - - - +
452B TYR* 1.3 84.3 + - - +
453B TRP* 6.2 0.4 - - + -
469B THR* 4.6 9.6 - - + -
470B LEU 3.1 8.5 - - - +
471B GLU* 3.4 26.7 - - + +
67C TYR* 4.1 27.8 - - + -
69C ARG* 4.5 8.7 - - - -
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Residues in contact with TYR 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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357B VAL* 3.7 28.8 - - + +
359B ALA* 4.5 8.0 + - - +
364B LYS* 4.4 13.0 - - + +
443B LEU* 4.4 15.3 - - + -
444B TYR 3.4 5.8 - - - +
445B LYS* 3.5 43.8 + - + +
446B SER* 4.6 0.2 - - - -
450B ASN 5.3 3.6 - - - -
451B VAL* 1.3 101.2 - - - +
453B TRP* 1.3 67.3 + - - +
469B THR* 3.3 5.7 - - - -
470B LEU* 2.5 59.3 + - + -
472B TRP* 3.2 37.2 - + - -
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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
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442B ASP 3.9 0.3 - - - +
443B LEU* 3.4 5.7 - - - +
444B TYR* 2.8 38.6 + - + +
445B LYS 3.9 5.4 - - - -
446B SER* 3.3 38.5 - - - +
447B ASN 4.7 0.8 - - - +
448B HIS* 6.1 2.2 - + - -
451B VAL* 6.5 0.2 - - + -
452B TYR* 1.3 71.7 - - - +
454B LEU* 1.3 59.5 + - - +
455B THR* 3.9 2.3 + - + -
467B ILE* 3.8 9.4 - - + -
468B ASN 3.5 17.7 - - - +
469B THR* 3.6 19.7 - - + -
481B TYR* 3.7 31.2 - + - -
516B ILE* 3.4 45.3 - - + +
522B LEU* 3.4 38.0 - - + +
67C TYR* 4.2 22.2 - + + -
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Residues in contact with LEU 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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366B ALA* 3.9 17.0 - - + -
410B TYR* 3.3 48.5 - - + -
412B VAL* 5.4 0.4 - - + -
441B MET* 3.9 20.4 - - + -
442B ASP 3.5 4.5 - - - -
443B LEU* 3.8 13.2 - - + -
452B TYR 3.6 1.4 + - - -
453B TRP* 1.3 71.0 - - - +
455B THR* 1.3 62.6 + - - +
456B ILE* 4.5 5.2 - - + -
466B VAL* 4.2 0.9 - - - +
467B ILE* 3.9 0.3 - - - -
468B ASN* 2.8 47.0 + - + +
470B LEU* 4.6 17.5 - - + +
478B VAL* 3.9 12.8 - - + -
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Residues in contact with THR 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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441B MET* 3.3 7.4 - - - +
442B ASP* 3.2 38.0 + - - +
444B TYR* 4.7 2.5 - - + -
453B TRP* 4.5 4.0 - - + +
454B LEU* 1.3 75.4 - - - +
456B ILE* 1.3 66.7 + - - +
457B PRO* 4.4 0.7 - - - +
466B VAL 3.4 8.1 - - - -
467B ILE* 4.4 12.3 - - + -
514B LEU* 2.7 34.9 + - + +
516B ILE* 3.5 40.2 - - + -
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Residues in contact with ILE 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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410B TYR* 4.5 14.1 - - + +
435B ILE* 3.9 21.5 - - + -
437B HIS* 3.6 22.0 - - + +
440B GLY 3.8 11.4 - - - +
441B MET* 3.9 27.1 - - + -
454B LEU* 4.5 3.4 - - + -
455B THR* 1.3 80.1 - - - +
457B PRO* 1.3 86.7 - - + +
465B GLY* 3.0 19.8 - - - -
466B VAL* 2.9 35.9 + - + +
514B LEU* 4.0 9.1 - - - +
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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