Contacts of the strand formed by residues 467 - 479 (chain C) 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 ASP 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455C ARG* 3.0 15.1 + - - +
456C SER 2.7 32.0 + - - -
459C VAL* 4.2 11.2 - - + +
464C ARG* 3.0 52.2 + - - +
465C LYS 3.7 0.6 + - - -
466C TYR* 1.3 76.3 - - - +
468C TRP* 1.3 62.2 + - - +
506C GLY* 3.3 28.1 + - - +
507C ILE 4.3 0.3 + - - -
508C SER* 3.1 24.7 + - - +
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Residues in contact with TRP 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLU* 2.9 20.2 + - - -
420C TYR* 3.6 32.9 - + - -
423C LEU* 3.6 17.9 - - + -
451C PHE* 3.7 29.2 - + + -
452C LEU 4.0 0.2 - - - -
453C PRO* 3.9 24.0 - - + -
454C VAL* 3.6 24.9 - - - -
455C ARG* 3.4 45.8 - - + +
464C ARG* 5.9 1.9 - - - +
467C ASP* 1.3 75.5 - - - +
469C VAL* 1.3 62.5 + - - +
506C GLY* 2.9 26.4 + - - +
507C ILE* 3.5 7.3 - - + +
508C SER* 2.9 26.9 + - - -
509C ARG 3.6 1.7 + - - -
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A TRP* 4.0 15.7 - - + -
451C PHE* 4.0 2.9 - - - -
452C LEU* 3.0 35.7 + - + +
454C VAL* 3.4 36.4 + - + +
455C ARG 4.3 0.2 - - - -
456C SER* 4.0 24.5 - - - -
468C TRP* 1.3 77.7 - - - +
470C VAL* 1.3 79.5 + - - +
509C ARG* 3.3 19.5 - - + +
511C VAL* 4.2 17.9 - - + -
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Residues in contact with VAL 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LEU* 4.8 3.8 - - + -
427C ALA* 4.5 4.0 - - + -
449C THR* 3.8 19.3 - - + -
450C VAL 3.3 12.8 - - - +
451C PHE* 4.3 16.2 - - + -
452C LEU* 4.4 2.2 - - - +
469C VAL* 1.3 82.9 - - - +
471C SER* 1.3 60.3 + - - +
472C LEU* 5.2 0.2 - - + -
500C ILE* 4.3 10.3 - - + -
507C ILE* 3.7 30.7 - - + -
509C ARG 3.2 2.5 + - - +
510C VAL* 3.6 29.8 - - + -
511C VAL* 3.0 27.4 + - - +
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Residues in contact with SER 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A VAL* 3.9 0.5 - - - +
449C THR* 3.3 5.4 - - - +
450C VAL* 2.8 39.3 + - - +
452C LEU* 4.2 6.7 - - - +
470C VAL* 1.3 76.0 - - - +
472C LEU* 1.3 65.7 + - - +
473C ARG* 3.9 0.8 + - - -
511C VAL* 3.3 23.8 - - - +
513C ASP* 3.9 12.3 + - - +
524C TRP* 3.4 33.5 + - - -
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.3 14.1 - - + -
431C PHE* 3.9 29.2 - - + -
448C PHE 4.0 1.6 - - - -
449C THR* 3.6 26.0 - - + +
470C VAL* 5.2 1.1 - - + -
471C SER* 1.3 76.3 - - - +
473C ARG* 1.3 60.2 + - - +
493C LEU* 4.6 7.6 - - + -
496C VAL* 3.7 26.7 - - + -
500C ILE* 4.2 14.4 - - + -
510C VAL* 3.9 16.4 - - + -
511C VAL 2.9 15.3 + - - +
512C TYR* 3.3 18.1 - - + -
513C ASP* 2.9 27.4 + - - +
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Residues in contact with ARG 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A ARG* 3.4 4.2 - - - +
431C PHE* 4.0 2.1 - - - -
446C GLN 4.1 0.2 - - - +
447C ALA* 3.2 3.8 - - - -
448C PHE* 2.8 80.1 + - + +
450C VAL* 5.1 1.8 - - + -
471C SER 3.9 2.2 + - - +
472C LEU* 1.3 73.8 - - - +
474C ALA* 1.3 63.6 + - - +
475C VAL* 3.5 26.8 - - + +
485C TRP* 3.7 13.1 - - - +
513C ASP* 3.2 33.8 + - + +
515C SER 2.9 30.9 + - - -
516C GLY 4.9 3.2 - - - -
517C LYS* 5.3 1.2 - - - +
521C THR 2.7 29.9 + - - -
522C ILE* 3.0 17.7 + - - +
524C TRP* 4.8 5.2 - - - +
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Residues in contact with ALA 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C PHE* 4.3 8.3 - - + -
435C LEU* 5.7 0.2 - - + -
444C VAL* 4.4 8.1 - - + -
446C GLN 3.5 8.3 - - - +
447C ALA* 4.4 2.7 - - + -
473C ARG* 1.3 78.3 + - - +
475C VAL* 1.3 67.5 + - - +
485C TRP* 3.6 3.1 - - - +
486C ALA* 2.8 27.4 + - + -
488C LEU* 3.7 30.3 - - + -
512C TYR* 3.4 15.2 + - + +
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C VAL* 3.6 5.0 - - - +
445C SER* 2.8 27.0 + - - -
446C GLN* 3.1 32.7 + - + +
473C ARG* 3.5 39.2 - - + +
474C ALA* 1.3 81.1 - - - +
476C GLU* 1.3 64.9 + - - +
477C THR* 4.0 0.7 - - - +
483C ALA* 4.4 9.4 - - + -
484C HIS 3.1 14.8 - - - +
485C TRP* 4.2 1.6 - - - +
486C ALA 4.0 0.4 - - - +
522C ILE* 4.0 28.3 - - + -
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Residues in contact with GLU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C LYS 3.9 21.5 - - - +
444C VAL* 4.5 2.2 - - - +
445C SER* 3.7 4.5 - - - +
475C VAL* 1.3 77.3 - - - +
477C THR* 1.3 64.8 + - - +
478C ILE* 3.5 11.8 + - + +
483C ALA* 4.4 1.6 - - - -
484C HIS* 2.7 44.9 + - + +
485C TRP 5.4 0.2 - - - -
486C ALA* 3.5 29.4 - - + +
487C HIS* 4.1 5.4 + - - +
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Residues in contact with THR 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C SER* 2.7 33.1 + - - -
446C GLN* 4.5 9.9 + - - -
475C VAL* 4.9 0.5 - - - +
476C GLU* 1.3 72.1 - - - +
478C ILE* 1.3 68.0 + - - +
479C ASP* 3.7 23.6 - - - +
480C PHE* 5.5 0.9 - - - -
482C THR 4.1 3.6 - - - +
483C ALA* 4.3 9.6 - - + +
522C ILE* 4.8 3.9 - - + +
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Residues in contact with ILE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C GLU* 3.7 17.7 - - + +
477C THR* 1.3 82.6 - - - +
479C ASP* 1.3 61.8 + - + +
482C THR* 2.9 22.4 + - - +
484C HIS* 3.9 38.4 - - + +
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Residues in contact with ASP 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN* 3.8 19.9 + - - +
477C THR* 3.7 14.2 - - - +
478C ILE* 1.3 81.5 - - + +
480C PHE* 1.3 81.1 + - - +
481C MET* 2.9 33.1 + - - +
482C THR* 2.8 33.8 + - - +
517C LYS* 5.9 0.2 - - - -
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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