Contacts of the strand formed by residues 445 - 455 (chain B) in PDB entry 3TQI
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 445 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B ARG* 4.7 3.4 - - - +
400B HIS* 3.6 19.8 - - - +
401B PRO* 2.8 42.8 + - + +
410B ARG* 4.0 6.4 + - - +
443B VAL* 3.3 4.3 - - - +
444B SER* 1.3 82.2 - - - +
446B ALA* 1.3 82.0 + - - +
447B PHE* 3.7 30.3 - - + -
472B ARG* 6.0 0.4 - - + -
473B ALA* 3.3 3.7 - - - +
474B VAL* 3.1 42.5 + - + +
521B ILE* 5.3 7.0 - - + -
522B GLU* 4.7 4.9 - - - +
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Residues in contact with ALA 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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266B ARG* 3.1 14.9 + - - -
400B HIS* 3.4 21.4 - - + +
430B PHE* 4.0 15.9 - - + -
431B ILE* 4.5 5.8 - - + +
434B LEU* 4.1 19.7 - - + -
443B VAL* 4.5 5.4 - - + -
445B GLN* 1.3 83.7 + - - +
447B PHE* 1.3 67.5 + - - +
472B ARG 3.2 9.6 - - - +
473B ALA* 4.4 4.9 - - + -
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Residues in contact with PHE 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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266B ARG* 3.5 7.2 - - - +
410B ARG* 3.1 41.3 - - + +
427B ASP* 3.8 1.1 - - - -
430B PHE* 3.8 12.2 - - - -
431B ILE* 5.5 0.4 - - - -
445B GLN* 3.7 22.9 - - + -
446B ALA* 1.3 79.1 - - - +
448B ALA* 1.3 71.6 + - - +
449B VAL* 3.5 19.1 - - + -
471B LEU* 3.7 1.0 - - - -
472B ARG* 2.8 66.6 + - + +
521B ILE* 3.7 16.6 - - + -
522B GLU* 3.2 29.2 - - + -
523B TRP* 4.6 3.8 - + - -
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Residues in contact with ALA 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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410B ARG* 3.7 10.6 - - - +
423B LEU* 3.5 23.4 - - + +
426B ALA* 4.3 0.9 - - + -
427B ASP* 3.2 31.8 + - - +
430B PHE* 4.3 0.8 - - - -
447B PHE* 1.3 80.7 - - - +
449B VAL* 1.3 69.1 + - - +
469B ILE* 4.2 9.6 - - + -
470B ALA 3.4 6.1 - - - +
471B LEU* 3.6 19.7 - - + -
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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
----------------------------------------------------------
409B ILE* 6.2 0.2 - - + -
410B ARG* 3.2 24.9 - - + +
412B LEU* 5.6 2.7 - - + -
423B LEU* 3.9 4.0 - - - -
447B PHE* 3.5 25.1 - - + -
448B ALA* 1.3 79.9 - - - +
450B PHE* 1.3 60.0 + - - +
451B MET* 4.0 2.2 + - + -
469B ILE* 3.5 5.9 - - - +
470B ALA* 2.7 67.6 + - + +
471B LEU 5.9 0.4 - - - -
472B ARG* 5.4 0.9 - - + -
523B TRP* 3.6 39.0 - - + +
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Residues in contact with PHE 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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410B ARG 2.7 15.0 + - - +
411B ILE* 4.1 11.9 - - + -
412B LEU* 3.2 27.7 + - - +
419B TYR* 3.3 52.9 - + + -
422B ILE* 4.1 25.1 - - + -
423B LEU* 3.8 14.1 - - + +
449B VAL* 1.3 71.8 - - - +
451B MET* 1.3 62.5 + - - +
452B PRO* 3.8 19.6 - - + +
467B TYR* 3.5 43.3 - + + -
468B ILE 4.6 0.2 - - - -
469B ILE* 3.8 22.0 - - + -
506B VAL* 6.1 0.2 - - + -
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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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451A MET* 3.8 29.8 - - + +
453A LEU* 3.6 14.8 - - + -
468A ILE* 4.7 2.9 - - + -
510A VAL* 5.0 0.9 - - + -
412B LEU* 3.9 13.9 - - + -
449B VAL* 4.6 3.6 - - + +
450B PHE* 1.3 77.6 - - - +
452B PRO* 1.3 60.9 - - - +
453B LEU* 3.0 11.9 + - + +
467B TYR* 3.8 6.1 - - - +
468B ILE* 2.9 40.8 + - + +
469B ILE 4.5 0.9 - - - -
470B ALA* 2.9 37.5 - - + +
510B VAL* 3.6 18.4 - - + -
523B TRP* 3.5 20.4 - - + -
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Residues in contact with PRO 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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453A LEU* 3.6 28.3 - - + -
412B LEU* 4.1 7.4 - - + -
413B GLY* 4.2 17.7 - - - +
419B TYR* 4.3 20.1 + - + +
450B PHE* 3.8 27.5 - - + +
451B MET* 1.3 80.0 - - - +
453B LEU* 1.3 61.7 + - - +
454B LYS* 5.0 0.3 - - - +
467B TYR* 3.8 15.9 - - + -
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Residues in contact with LEU 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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412A LEU* 3.8 23.1 - - + +
413A GLY* 5.3 4.5 - - - +
451A MET* 3.8 15.7 - - + -
452A PRO* 3.7 33.7 - - + -
453A LEU* 3.3 41.3 - - + -
451B MET* 3.0 7.1 + - + +
452B PRO* 1.3 80.9 - - + +
454B LYS* 1.3 78.9 + - - +
467B TYR* 4.0 0.2 - - - -
468B ILE* 4.6 6.3 - - + -
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Residues in contact with LYS 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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412A LEU* 3.7 16.8 - - - +
452B PRO 5.9 0.4 - - - -
453B LEU* 1.3 86.4 - - - +
455B SER* 1.3 63.5 + - - +
465B TYR* 4.2 34.5 + - + +
466B GLY* 2.9 20.2 - - - +
467B TYR* 3.4 46.0 + - + +
468B ILE* 4.0 7.0 - - - +
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Residues in contact with SER 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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412A LEU* 4.5 1.6 - - - -
523A TRP* 4.3 21.1 - - - -
454B LYS* 1.3 76.4 - - - +
456B VAL* 1.3 62.4 + - - +
465B TYR* 3.1 8.4 - - - -
466B GLY 2.9 25.9 + - - -
468B ILE* 4.2 13.3 - - - +
507B SER* 3.2 14.7 + - - -
508B ARG* 2.8 35.1 + - - +
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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