Contacts of the strand formed by residues 448 - 457 (chain B) in PDB entry 3HIG
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 GLN 448 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLY* 3.8 15.2 - - - +
300A PRO* 3.1 25.5 + - - +
309B ARG* 3.7 17.0 - - - +
319B TYR* 3.8 3.8 - - - +
420B GLU* 3.4 29.6 - - - +
421B MET* 3.1 8.7 - - - -
422B PRO* 3.1 24.2 - - - +
423B THR* 4.2 1.9 + - - +
427B LEU* 5.6 0.4 - - - +
446B LYS* 3.6 28.7 + - + +
447B GLY* 1.3 78.1 - - - +
449B VAL* 1.3 66.9 + - - +
470B TYR* 4.6 1.0 - - - -
471B PRO* 3.1 31.8 - - + +
712B ASP* 5.3 1.8 - - - +
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Residues in contact with VAL 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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319B TYR* 4.0 7.0 - - - -
419B PHE 3.8 0.5 - - - +
420B GLU* 3.2 3.6 - - - +
421B MET* 2.9 53.3 + - + +
423B THR* 3.7 15.9 - - + -
448B GLN* 1.3 75.2 - - - +
450B LEU* 1.3 62.1 + - - +
451B VAL* 4.2 9.6 - - + -
468B ILE* 4.0 11.4 - - + -
469B PHE 3.5 7.4 - - - +
470B TYR* 3.1 52.3 - - + -
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.5 34.8 - - + -
317B VAL* 4.0 19.7 - - + -
319B TYR* 3.7 43.2 - - + -
324B PHE* 4.1 7.6 - - + -
418B LEU* 4.1 16.4 - - + -
419B PHE 3.4 16.4 - - - +
420B GLU* 4.2 2.2 - - - +
449B VAL* 1.3 73.2 - - - +
451B VAL* 1.3 60.1 + - - +
452B LEU 4.2 0.2 - - - -
468B ILE* 3.2 6.1 - - - +
469B PHE* 2.8 56.3 + - + +
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B CYS 3.8 1.2 - - - +
418B LEU* 3.3 8.8 - - - +
419B PHE* 2.7 78.2 + - + +
421B MET* 4.3 6.7 - - + -
449B VAL* 4.2 16.8 - - + -
450B LEU* 1.3 77.2 - - - +
452B LEU* 1.3 65.1 + - - +
453B ARG* 4.2 5.2 - - + +
466B ASP* 4.1 28.9 - - + +
467B PHE 3.5 5.2 - - - +
468B ILE* 4.2 12.6 - - + -
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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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324B PHE* 4.4 6.5 - - + -
326B PHE* 3.7 31.6 - - + -
334B LEU* 4.2 20.2 - - + +
336B VAL* 3.7 29.6 - - + -
398B LEU* 5.4 1.1 - - + -
416B LEU* 4.4 20.2 - - + -
417B CYS 3.5 11.9 - - - +
418B LEU* 3.7 23.3 - - + +
450B LEU 4.2 0.2 - - - -
451B VAL* 1.3 71.2 - - - +
453B ARG* 1.3 62.2 + - - +
465B TRP 3.8 0.5 - - - +
466B ASP* 3.4 3.5 - - - -
467B PHE* 2.8 41.5 + - + +
469B PHE* 4.6 6.6 - - + -
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Residues in contact with ARG 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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424A GLY 2.6 27.5 + - - -
425A VAL* 4.0 16.0 - - - +
426A PRO* 4.5 0.4 - - - +
334B LEU* 4.6 3.4 - - - -
385B LEU* 4.3 8.4 - - + +
390B ASP 2.6 36.9 + - - -
391B CYS* 4.0 9.8 - - - +
416B LEU* 3.2 10.0 - - - +
417B CYS* 2.9 42.6 + - - -
419B PHE* 3.9 19.6 - - - -
421B MET* 6.2 0.2 - - - -
451B VAL* 4.2 6.3 - - + +
452B LEU* 1.3 77.0 - - - +
454B THR* 1.3 74.7 + - - +
464B ILE* 3.4 17.4 - - + +
465B TRP 3.2 4.5 - - - -
466B ASP* 2.7 42.0 + - - +
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Residues in contact with THR 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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328B LEU* 4.2 13.5 - - + +
333B GLY* 6.1 0.4 - - - -
334B LEU* 4.0 30.9 - - + +
382B THR* 3.5 16.2 - - + +
385B LEU* 5.0 1.1 - - - -
415B ALA 2.8 23.3 + - - -
416B LEU* 4.5 8.5 - - - -
453B ARG* 1.3 83.4 - - - +
455B THR* 1.3 69.6 + - - +
464B ILE* 3.7 0.3 - - - -
465B TRP* 2.8 49.6 + - + +
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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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429A ARG* 4.2 25.4 + - - +
378B LEU 4.7 0.2 - - - +
381B VAL 4.4 0.5 + - - -
382B THR* 3.5 24.3 - - - +
383B HIS 3.8 25.3 + - - -
385B LEU* 3.5 27.2 - - + +
390B ASP* 5.6 0.4 - - - -
415B ALA 4.4 1.2 + - - -
453B ARG* 5.2 0.4 - - + -
454B THR* 1.3 82.1 + - - +
456B SER* 1.3 67.4 + - - +
457B THR* 4.8 0.7 + - - -
462B ASP* 5.9 0.9 - - + -
463B TYR 3.0 12.6 - - - +
464B ILE* 4.3 17.0 - - + -
465B TRP* 4.0 4.9 - - - -
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Residues in contact with SER 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.1 43.9 - - - +
381B VAL* 3.5 9.6 - - - -
455B THR* 1.3 74.9 - - - +
457B THR* 1.3 63.1 + - - +
458B VAL* 3.8 2.7 + - - +
461B TPQ 3.6 2.3 - - - +
462B ASP* 3.5 1.4 - - - -
463B TYR* 2.7 42.0 + - - +
465B TRP* 3.1 20.1 + - - -
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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
----------------------------------------------------------
429A ARG* 3.6 11.1 + - - -
430A HIS* 4.1 0.7 - - + -
431A PHE* 3.5 28.1 - - + +
433A SER* 6.0 2.7 - - - -
435A PHE* 5.8 0.7 - - - -
381B VAL* 3.1 28.1 + - - +
383B HIS* 4.3 11.0 - - - +
455B THR* 4.8 1.2 + - - -
456B SER* 1.3 73.1 - - - +
458B VAL* 1.3 64.8 + - - +
459B TYR 3.6 16.8 - - - +
461B TPQ 3.3 11.7 - - - +
462B ASP* 2.6 36.3 + - - +
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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