Contacts of the strand formed by residues 410 - 422 (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 VAL 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B PHE* 3.3 7.1 - - - -
402B HIS 2.9 38.1 + - - +
406B ALA* 3.7 17.9 - - + -
408B ASP 3.2 17.7 - - - +
409B PRO* 1.3 73.4 - - - +
411B HIS* 1.3 61.2 + - - +
412B TYR* 3.3 28.0 - - + +
748B TYR* 3.4 36.6 - - + +
749B ARG* 3.6 4.5 - - - +
750B PRO* 4.5 11.7 - - + -
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Residues in contact with HIS 411 (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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399B ASP* 2.9 39.6 + - + +
400B THR 3.7 6.7 - - - -
401B PHE* 3.6 40.1 - + + -
409B PRO 4.2 0.2 + - - -
410B VAL* 1.3 71.1 - - - +
412B TYR* 1.3 61.3 + - - +
413B PRO* 3.5 22.4 - - + +
748B TYR* 3.2 27.0 - - - +
749B ARG 2.8 20.5 + - - +
751B VAL* 3.8 16.5 - - + +
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Residues in contact with TYR 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER* 3.4 24.0 + - - -
381B VAL* 5.8 0.5 - - - +
382B THR* 3.5 27.6 - - - +
383B HIS* 3.6 30.3 + + - -
399B ASP* 3.4 2.1 - - - +
400B THR* 2.8 45.1 + - + +
402B HIS* 3.6 24.0 - + + +
410B VAL* 3.3 37.3 - - + +
411B HIS* 1.3 76.5 - - - +
413B PRO* 1.3 68.9 - - + +
415B ALA* 3.9 2.8 - - + +
748B TYR* 3.7 23.0 - + + -
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Residues in contact with PRO 413 (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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382B THR 5.0 0.2 - - - +
383B HIS 4.6 0.3 - - - -
384B GLU* 3.4 39.5 + - + +
399B ASP* 3.5 11.0 - - - +
411B HIS* 3.5 25.1 - - + +
412B TYR* 1.3 82.0 - - + +
414B ARG* 1.3 76.2 + - + +
415B ALA* 3.2 1.4 + - - -
745B ASN* 4.9 7.4 - - + -
747B THR 3.5 23.3 - - - +
748B TYR* 4.4 2.9 - - + -
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Residues in contact with ARG 414 (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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384B GLU* 2.9 26.7 + - + +
385B LEU* 3.0 45.8 + - - +
387B PRO* 3.3 29.0 - - - +
397B PHE* 3.8 27.9 - - + -
398B LEU 3.4 9.4 + - - -
399B ASP* 2.8 18.5 + - - +
413B PRO* 1.3 75.8 - - + +
415B ALA* 1.3 62.2 + - - +
416B LEU 3.3 6.7 - - - -
743B SER* 2.7 49.9 + - - +
744B TYR* 3.8 1.8 - - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.5 0.4 - - + -
382B THR* 3.6 32.9 - - - +
383B HIS 4.6 0.7 - - - +
385B LEU* 3.9 6.1 - - - +
398B LEU 2.8 8.4 + - - +
400B THR* 3.6 31.9 - - + -
412B TYR* 3.9 8.5 - - + +
413B PRO 3.2 1.4 + - - -
414B ARG* 1.3 75.3 - - - +
416B LEU* 1.3 61.7 + - + +
454B THR* 2.8 29.1 + - - -
455B THR 4.4 1.6 + - - -
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Residues in contact with LEU 416 (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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326B PHE* 4.1 25.6 - - + -
328B LEU* 4.1 23.8 - - + -
334B LEU* 3.9 28.3 - - + -
385B LEU* 3.4 8.3 - - - +
397B PHE* 3.5 2.1 - - - -
398B LEU* 2.8 55.5 + - + +
399B ASP 4.5 6.5 - - - +
400B THR* 4.5 4.3 - - - -
414B ARG 4.0 2.4 - - - -
415B ALA* 1.3 89.3 - - + +
417B CYS* 1.3 62.3 + - - +
452B LEU* 4.4 7.0 - - + -
453B ARG 3.2 13.5 - - - +
454B THR* 4.4 1.8 - - - +
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Residues in contact with CYS 417 (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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385B LEU* 3.8 1.1 - - + -
391B CYS* 2.1 49.8 - - + -
395B ALA* 4.3 2.9 - - + -
396B THR 3.2 12.6 - - - +
397B PHE* 3.8 14.6 - - + -
398B LEU* 4.6 2.5 - - - +
416B LEU* 1.3 77.3 - - - +
418B LEU* 1.3 60.9 + - - +
419B PHE* 3.7 16.4 - - - -
451B VAL 3.8 0.4 - - - +
452B LEU* 3.5 7.9 - - - +
453B ARG* 2.9 42.6 + - - +
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Residues in contact with LEU 418 (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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310B PHE* 3.6 33.2 - - + -
312B LEU* 3.9 19.1 - - + -
317B VAL* 3.6 30.7 - - + -
324B PHE* 4.9 1.6 - - + -
326B PHE* 5.0 2.9 - - + -
396B THR* 2.9 38.8 + - - +
398B LEU* 5.0 6.1 - - + -
417B CYS* 1.3 75.7 - - - +
419B PHE* 1.3 61.9 + - - +
450B LEU* 4.1 19.1 - - + -
451B VAL 3.3 14.8 - - - +
452B LEU* 3.7 28.9 - - + +
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Residues in contact with PHE 419 (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 4.0 5.4 - - - -
310B PHE* 4.1 5.6 - - - -
392B PRO* 3.5 37.0 - - + -
394B THR* 5.1 2.0 - - - +
395B ALA* 3.6 20.2 - - + +
417B CYS* 3.7 31.9 - - - -
418B LEU* 1.3 77.6 - - - +
420B GLU* 1.3 61.8 + - - +
421B MET* 3.7 35.4 - - + -
449B VAL 3.8 0.3 - - - +
450B LEU* 3.4 7.0 - - - +
451B VAL* 2.7 72.1 + - + -
453B ARG* 3.9 19.1 - - - -
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Residues in contact with GLU 420 (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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300A PRO* 3.4 32.0 - - + +
302B LEU* 4.6 4.9 - - - +
304B GLN* 4.8 7.4 + - - +
309B ARG* 2.9 55.0 + - - +
310B PHE* 4.0 16.7 - - + -
319B TYR* 2.7 30.9 + - + +
392B PRO* 5.3 0.2 - - - +
394B THR* 5.0 4.2 + - - -
419B PHE* 1.3 80.6 - - - +
421B MET* 1.3 66.1 + - - +
448B GLN* 3.4 15.9 - - + +
449B VAL 3.2 12.1 - - - +
450B LEU* 4.3 3.4 - - + +
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Residues in contact with MET 421 (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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421A MET* 4.7 4.0 - - + -
422A PRO* 4.1 8.3 - - + +
423A THR* 3.4 26.7 - - - +
424A GLY* 3.8 15.3 - - - +
302B LEU* 4.0 13.2 - - + -
392B PRO* 5.6 0.4 - - - -
419B PHE* 3.7 31.0 - - + -
420B GLU* 1.3 76.6 - - - +
422B PRO* 1.3 92.8 - - + +
423B THR* 3.5 3.9 + - - -
448B GLN* 3.1 4.9 - - - +
449B VAL* 2.9 46.5 + - + +
451B VAL* 4.3 5.8 - - + -
453B ARG* 6.2 0.2 - - - -
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Residues in contact with PRO 422 (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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300A PRO* 3.6 24.5 - - + +
301A ARG* 4.5 3.4 - - - -
302A LEU* 4.8 9.2 - - + +
421A MET* 4.1 5.2 - - - +
422A PRO 5.1 0.2 - - - +
302B LEU* 3.4 33.2 - - + +
421B MET* 1.3 102.8 - - + +
423B THR* 1.3 62.1 + - - +
424B GLY* 3.6 6.5 + - - +
446B LYS* 4.1 15.9 - - - -
447B GLY 3.3 14.8 - - - +
448B GLN* 3.1 7.8 - - - +
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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