Contacts of the strand formed by residues 446 - 456 (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 GLN 446 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C HIS* 4.0 9.0 - - + -
402C PRO* 3.7 27.6 - - + +
411C ARG* 5.5 0.7 + - - -
444C VAL* 3.8 3.4 - - - +
445C SER* 1.3 90.5 - - - +
447C ALA* 1.3 63.8 + - - +
448C PHE* 4.6 15.8 - - + -
473C ARG 4.4 0.9 - - - -
474C ALA* 3.5 0.7 - - - -
475C VAL* 3.1 37.7 + - + +
477C THR* 4.5 6.3 + - - -
522C ILE* 3.8 35.2 - - - +
523C GLU* 4.6 5.7 - - - +
528C PO4 5.7 1.0 + - - -
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Residues in contact with ALA 447 (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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401C HIS* 4.1 11.3 + - - +
431C PHE* 4.2 6.7 - - + -
432C ILE* 3.4 17.3 - - + +
435C LEU* 3.4 31.6 - - + -
441C TYR* 5.7 0.2 - - - -
444C VAL* 3.9 12.8 - - + -
446C GLN* 1.3 79.9 - - - +
448C PHE* 1.3 64.3 + - - +
473C ARG 3.2 10.1 - - - +
474C ALA* 4.4 5.4 - - + -
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Residues in contact with PHE 448 (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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411C ARG* 3.2 48.2 - - - +
428C ASP* 3.7 13.2 - - - +
431C PHE* 3.8 7.0 - - - -
446C GLN* 4.6 11.2 - - + -
447C ALA* 1.3 82.3 - - - +
449C THR* 1.3 66.3 + - - +
450C VAL* 3.6 22.7 - - + -
473C ARG* 2.8 63.2 + - + +
475C VAL* 6.2 0.2 - - + -
522C ILE* 3.7 23.3 - - + -
523C GLU* 3.7 28.3 - - - -
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Residues in contact with THR 449 (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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411C ARG* 4.0 8.1 + - - +
424C LEU* 3.4 34.4 - - + +
427C ALA* 4.2 8.2 + - + -
428C ASP* 2.9 32.0 + - - -
431C PHE* 3.6 4.5 - - - +
448C PHE* 1.3 83.6 - - - +
450C VAL* 1.3 64.9 + - - +
470C VAL* 3.8 23.6 - - + -
471C SER 3.3 11.7 - - - +
472C LEU* 3.6 20.5 - - + +
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Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ARG* 3.5 12.8 - - - +
413C LEU* 3.6 26.2 - - + -
424C LEU* 4.1 2.7 - - - -
448C PHE* 3.6 29.2 - - + -
449C THR* 1.3 73.7 - - - +
451C PHE* 1.3 62.6 + - - +
452C LEU* 3.6 22.1 + - + -
470C VAL* 3.3 7.6 - - - +
471C SER* 2.8 40.6 + - - +
473C ARG* 5.1 2.2 - - + -
524C TRP* 4.0 26.7 - - + +
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Residues in contact with PHE 451 (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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411C ARG 2.9 16.2 + - - +
412C VAL* 3.9 17.5 - - + -
413C LEU* 3.3 23.2 + - - +
420C TYR* 3.6 53.6 - + + -
423C LEU* 3.9 21.1 - - + -
424C LEU* 4.0 15.8 - - + +
450C VAL* 1.3 72.7 - - - +
452C LEU* 1.3 70.4 + - - +
453C PRO* 3.4 19.9 - - + +
468C TRP* 3.7 40.2 - + + -
469C VAL 4.2 1.3 - - - -
470C VAL* 4.3 15.5 - - + -
507C ILE* 5.8 0.2 - - + -
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Residues in contact with LEU 452 (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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452A LEU* 3.7 29.2 - - + -
454A VAL* 4.6 5.6 - - + -
413C LEU* 4.0 5.2 - - + -
450C VAL* 3.6 20.6 - - + -
451C PHE* 1.3 81.8 - - - +
453C PRO* 1.3 61.0 - - + +
454C VAL* 2.9 27.9 + - + +
468C TRP* 4.0 0.2 - - - -
469C VAL* 3.0 44.5 + - + +
471C SER* 4.2 16.6 - - - +
511C VAL* 4.4 5.4 - - + -
524C TRP* 3.5 35.7 - - + -
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Residues in contact with PRO 453 (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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453A PRO* 5.5 1.5 - - - +
454A VAL* 3.9 16.4 - - + -
413C LEU* 3.4 33.2 - - + +
414C GLY* 4.9 4.5 - - - -
415C GLU 6.0 0.7 - - - +
420C TYR* 5.6 4.9 - - + -
451C PHE* 3.4 24.5 - - + +
452C LEU* 1.3 78.2 - - - +
454C VAL* 1.3 66.3 + - - +
468C TRP* 3.9 15.3 - - + -
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Residues in contact with VAL 454 (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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413A LEU* 3.7 24.2 - - + -
452A LEU* 4.8 4.0 - - + -
453A PRO* 3.6 30.1 - - + -
454A VAL* 3.6 22.9 - - + -
524A TRP* 4.8 3.4 - - + -
452C LEU* 2.9 23.2 + - + +
453C PRO* 1.3 80.5 - - - +
455C ARG* 1.3 62.4 + - - +
468C TRP* 3.6 6.5 - - - -
469C VAL* 3.4 35.3 + - + +
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Residues in contact with ARG 455 (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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413A LEU* 3.8 24.4 - - - +
524A TRP 4.4 1.0 - - - +
525A GLU* 5.1 3.3 - - - +
419C GLU* 4.8 2.2 + - - -
454C VAL* 1.3 77.7 - - - +
456C SER* 1.3 64.0 + - - +
464C ARG* 5.1 5.3 - - - +
466C TYR* 2.5 53.6 + - + -
467C ASP* 3.0 29.8 + - - +
468C TRP* 3.4 46.0 - - + +
469C VAL* 4.3 1.3 - - - -
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Residues in contact with SER 456 (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* 3.4 16.7 + - - -
525A GLU* 5.9 0.2 - - - -
455C ARG* 1.3 75.8 - - - +
457C VAL* 1.3 64.3 + - - +
465C LYS 3.1 2.1 - - - +
466C TYR* 3.2 4.8 - - - -
467C ASP 2.7 28.3 + - - -
469C VAL* 4.0 15.5 - - - -
508C SER* 3.0 19.3 + - - -
509C ARG* 2.7 39.0 + - - +
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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