Contacts of the strand formed by residues 465 - 479 (chain B) in PDB entry 1GPM
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 LYS 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457B VAL* 3.6 8.8 - - - +
458B GLY* 2.7 29.8 + - - +
463B GLY 3.9 4.5 + - - +
464B ARG* 1.3 71.7 - - - +
466B TYR* 1.3 73.0 + - + +
305D GLU* 2.9 42.2 + - - +
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Residues in contact with TYR 466 (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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455B ARG* 3.9 35.3 - - + -
456B SER* 3.2 26.2 - - - +
457B VAL* 3.5 27.2 - - + +
464B ARG* 4.0 8.0 - - - +
465B LYS* 1.3 95.0 - - + +
467B ASP* 1.3 67.0 + - - +
303D ASP* 3.9 13.7 - - - -
304D PRO* 3.2 39.7 - - + +
305D GLU* 3.4 26.8 + - + +
524D TRP 4.6 3.1 - - - -
525D GLU* 4.5 5.1 + - - -
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Residues in contact with ASP 467 (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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455B ARG* 3.0 10.0 - - - -
456B SER 3.0 22.2 + - - -
458B GLY* 4.1 11.6 - - - -
459B VAL* 4.1 3.3 + - - +
462B ASP* 3.6 17.9 - - - +
464B ARG* 3.5 26.9 - - - +
465B LYS 4.3 0.2 + - - -
466B TYR* 1.3 75.4 - - - +
468B TRP* 1.3 66.6 + - - +
506B GLY* 3.3 27.0 - - - +
507B ILE 4.0 2.8 + - - +
508B SER* 2.9 34.3 + - - +
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Residues in contact with TRP 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU* 3.3 19.0 + - - -
420B TYR* 3.8 28.4 - + - -
423B LEU* 3.8 22.2 - - + -
451B PHE* 3.4 25.4 - + + -
452B LEU 3.7 3.1 - - - -
453B PRO* 3.1 34.1 - - + -
454B VAL* 3.2 34.8 - - - -
455B ARG* 3.9 21.8 - - + -
467B ASP* 1.3 79.9 - - - +
469B VAL* 1.3 61.9 + - - +
506B GLY* 3.1 13.9 + - - +
507B ILE* 3.3 8.2 - - + +
508B SER* 2.9 25.8 + - - -
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Residues in contact with VAL 469 (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 PHE* 4.0 2.3 - - - -
452B LEU* 2.7 56.1 + - + +
454B VAL* 3.5 25.6 + - + +
456B SER* 3.7 27.8 - - - +
467B ASP 4.4 0.2 - - - +
468B TRP* 1.3 80.3 - - - +
470B VAL* 1.3 73.0 + - - +
508B SER* 4.2 0.4 - - - +
509B ARG* 3.6 25.4 - - + +
511B VAL* 4.3 9.9 - - + -
524D TRP* 4.4 7.4 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 4.9 2.9 - - + -
427B ALA* 4.7 2.9 - - + -
449B THR* 3.8 19.7 - - + -
450B VAL 3.2 13.2 - - - +
451B PHE* 4.0 17.0 - - + -
452B LEU* 4.3 2.0 - - - +
469B VAL* 1.3 87.0 - - - +
471B SER* 1.3 60.7 + - - +
500B ILE* 4.2 15.5 - - + -
507B ILE* 3.6 24.7 - - + -
509B ARG 3.4 2.7 + - - +
510B VAL* 3.3 30.3 - - + -
511B VAL* 3.0 22.7 + - - +
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Residues in contact with SER 471 (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 PHE 3.9 0.2 - - - +
449B THR* 3.3 4.0 - - - -
450B VAL* 2.8 40.3 + - - +
452B LEU* 4.6 3.8 - - - -
470B VAL* 1.3 75.3 - - - +
472B LEU* 1.3 72.6 + - - +
511B VAL* 3.1 25.8 + - - +
512B TYR 4.1 0.2 - - - -
513B ASP 3.7 5.5 + - - -
524B TRP* 3.3 34.7 - - - -
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Residues in contact with LEU 472 (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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431B PHE* 3.9 29.6 - - + -
448B PHE 3.6 3.1 - - - -
449B THR* 3.8 21.8 - - + +
470B VAL* 5.2 0.2 - - + -
471B SER* 1.3 78.9 + - - +
473B ARG* 1.3 62.6 + - - +
493B LEU* 4.3 20.0 - - + -
496B VAL* 3.7 24.2 - - + -
500B ILE* 3.9 22.7 - - + -
510B VAL* 4.0 15.3 - - + -
511B VAL 2.9 9.5 + - - +
512B TYR* 3.4 14.6 - - + -
513B ASP* 3.1 25.1 + - - +
514D ILE* 4.4 8.7 - - + -
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Residues in contact with ARG 473 (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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431B PHE* 4.2 1.5 - - - -
446B GLN 3.8 0.3 - - - +
447B ALA* 3.0 5.0 - - - +
448B PHE* 2.8 74.5 + - + +
450B VAL* 4.7 2.7 - - + -
472B LEU* 1.3 78.4 - - - +
474B ALA* 1.3 62.7 + - - +
475B VAL* 3.8 23.2 - - + +
483B ALA* 6.1 0.6 - - - +
484B HIS 5.6 0.2 - - - -
485B TRP* 4.3 11.5 - - - +
512B TYR* 4.4 1.3 - - - -
513B ASP* 3.4 31.5 + - + +
515B SER 2.7 30.0 + - - -
516B GLY 4.9 3.6 + - - -
517B LYS* 5.2 0.8 - - - +
520B ALA* 4.5 2.0 - - - +
521B THR 2.7 29.1 + - - -
522B ILE* 2.9 19.3 + - - +
524B TRP* 4.5 7.6 - - - +
509D ARG* 3.4 4.8 - - - +
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Residues in contact with ALA 474 (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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431B PHE* 4.6 3.1 - - + -
435B LEU* 6.0 0.2 - - + -
444B VAL* 4.0 12.3 - - + -
446B GLN 3.3 5.8 - - - +
447B ALA* 4.4 6.5 - - + -
473B ARG* 1.3 78.2 + - - +
475B VAL* 1.3 66.1 + - - +
485B TRP* 3.9 4.0 - - - +
486B ALA* 3.0 31.4 + - + -
488B LEU* 3.8 18.2 - - + -
512B TYR* 3.4 23.9 + - + +
513B ASP 5.4 0.2 - - - +
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Residues in contact with VAL 475 (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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444B VAL* 3.8 4.7 - - - +
445B SER* 3.0 23.6 + - - -
446B GLN* 3.0 35.0 + - + +
448B PHE* 5.7 0.2 - - + -
473B ARG* 3.8 33.0 - - + +
474B ALA* 1.3 78.1 - - - +
476B GLU* 1.3 68.8 + - - +
477B THR* 3.9 7.9 - - - +
483B ALA* 4.4 6.7 - - + -
484B HIS 3.3 9.6 - - - +
486B ALA 4.3 0.2 - - - +
522B ILE* 3.9 36.8 - - + -
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Residues in contact with GLU 476 (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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443B LYS 4.6 15.1 - - - +
444B VAL* 5.0 1.8 - - + +
445B SER* 3.3 8.1 - - - +
475B VAL* 1.3 80.4 - - - +
477B THR* 1.3 61.3 + - - +
478B ILE* 2.8 24.0 + - + +
483B ALA* 4.3 0.2 - - - -
484B HIS* 2.9 41.6 + - + +
485B TRP 5.1 1.8 - - - -
486B ALA* 3.5 29.2 - - + +
487B HIS* 4.0 5.9 + - - +
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Residues in contact with THR 477 (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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445B SER* 3.0 24.6 + - - -
446B GLN* 5.7 0.5 - - - +
475B VAL* 4.1 1.7 - - - +
476B GLU* 1.3 67.9 - - - +
478B ILE* 1.3 65.5 + - - +
479B ASP 2.9 28.6 - - - +
480B PHE* 4.6 7.9 - - - +
482B THR 4.4 1.8 - - - +
483B ALA* 3.8 13.4 - - + +
522B ILE* 3.7 23.4 - - + +
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Residues in contact with ILE 478 (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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476B GLU* 2.8 31.4 + - + +
477B THR* 1.3 75.0 - - - +
479B ASP* 1.3 62.4 + - + +
482B THR* 3.0 9.3 + - + +
484B HIS* 3.6 37.2 - - + +
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Residues in contact with ASP 479 (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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18B GLN* 4.2 12.5 + - - +
477B THR* 2.9 23.0 - - - +
478B ILE* 1.3 79.5 - - + +
480B PHE* 1.3 77.8 + - - +
481B MET* 2.8 35.1 + - - +
482B THR* 2.9 32.0 + - + +
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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