Contacts of the helix formed by residues 456 - 469 (chain A) in PDB entry 1GM5
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 THR 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ALA 4.2 4.3 - - - +
455A THR* 1.3 73.2 - - - +
457A PRO* 1.3 67.4 - - - -
458A SER* 3.2 7.9 + - - -
459A GLU* 2.7 40.9 + - + +
460A LYS* 2.9 7.9 + - - -
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Residues in contact with PRO 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A THR 3.7 0.2 - - - -
456A THR* 1.3 86.0 - - - -
458A SER* 1.3 68.5 + - - +
460A LYS* 2.9 35.5 - - + +
461A GLU* 3.0 13.4 + - - +
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Residues in contact with SER 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A THR* 2.9 13.4 + - - -
457A PRO* 1.3 75.0 - - - +
459A GLU* 1.3 61.3 + - - +
460A LYS 2.5 0.9 + - - -
461A GLU* 2.1 54.2 + - - +
462A LYS* 2.8 4.1 + - - -
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A THR* 4.1 23.8 - - + +
456A THR* 2.7 26.5 + - + +
458A SER* 1.3 79.6 + - - +
460A LYS* 1.3 53.2 + - - +
462A LYS* 3.2 33.4 + - - +
463A ILE* 2.3 51.2 + - + +
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Residues in contact with LYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 5.0 17.9 - - + +
453A GLY* 3.5 30.8 + - - +
455A THR* 2.2 46.2 + - - +
456A THR 2.9 11.4 + - - +
457A PRO* 2.9 31.9 - - + +
458A SER 2.5 3.8 + - - -
459A GLU* 1.3 73.2 - - - +
461A GLU* 1.3 51.3 - - + +
463A ILE* 2.6 29.1 + - - +
464A LYS* 2.7 34.4 + - + +
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PRO* 3.2 15.5 - - - +
458A SER* 2.1 30.0 + - - +
460A LYS* 1.3 74.8 - - + +
462A LYS* 1.3 50.2 + - - +
463A ILE 2.9 0.9 + - - -
464A LYS* 3.9 10.5 - - + +
465A SER* 2.5 37.8 + - - -
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Residues in contact with LYS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A SER 2.8 6.9 + - - +
459A GLU* 3.5 33.7 + - - +
461A GLU* 1.3 77.0 - - - +
463A ILE* 1.3 64.9 + - + +
465A SER* 2.7 15.3 + - - -
466A GLY* 3.2 9.5 + - - -
472A ILE* 4.5 1.6 - - - +
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ALA* 3.9 27.1 - - + -
450A LEU* 4.1 18.8 - - + +
451A LEU* 4.1 19.1 - - + -
455A THR* 5.8 0.7 - - + -
459A GLU* 2.3 49.8 - - + +
460A LYS* 2.6 12.0 + - - +
462A LYS* 1.3 84.1 - - + +
464A LYS* 1.3 70.7 + - - +
466A GLY* 2.5 18.5 + - - -
467A LEU* 3.0 9.2 + - + +
472A ILE* 3.3 15.8 - - + +
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Residues in contact with LYS 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 4.5 16.3 - - + +
460A LYS* 2.7 31.6 + - + +
461A GLU* 3.9 9.6 - - + +
463A ILE* 1.3 76.6 - - - +
465A SER* 1.3 51.8 - - - +
467A LEU* 2.5 37.1 + - - +
468A ARG* 3.0 11.2 + - - -
484A GLU* 4.7 21.9 + - - +
485A ASP 5.6 4.2 + - - -
486A VAL* 4.4 24.7 - - + +
487A HIS 4.4 1.4 + - - +
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Residues in contact with SER 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A GLU 2.5 22.7 + - - -
462A LYS* 2.7 12.7 + - - -
464A LYS* 1.3 69.3 - - - +
466A GLY* 1.3 71.9 + - - -
467A LEU 2.9 5.8 + - - -
468A ARG* 3.3 19.4 + - - +
469A ASN* 3.5 14.0 + - - +
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Residues in contact with GLY 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A LYS 3.7 5.2 - - - -
463A ILE 2.5 16.7 + - - -
465A SER* 1.3 80.7 + - - +
467A LEU* 1.3 54.4 + - - -
469A ASN 3.2 16.2 - - - +
470A GLY 4.0 0.3 + - - -
471A GLN 4.1 1.2 + - - -
472A ILE* 3.2 39.0 + - - +
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A GLN* 4.4 7.2 - - - +
451A LEU* 4.9 4.0 - - + -
463A ILE* 3.0 18.7 + - + +
464A LYS* 2.5 26.2 + - - +
466A GLY* 1.3 71.1 - - - +
468A ARG* 1.3 47.5 + - - +
469A ASN* 2.7 16.0 + - - -
472A ILE* 2.1 67.3 - - + +
475A VAL* 3.5 39.7 - - + -
486A VAL* 4.8 10.1 - - + -
487A HIS 3.2 14.1 - - - +
488A PHE* 2.9 36.7 - - + +
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Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LYS 3.0 6.1 + - - +
465A SER* 3.6 19.5 - - - +
467A LEU* 1.3 72.3 - - - +
469A ASN* 1.3 84.0 + - + +
487A HIS* 3.1 51.1 + - + +
488A PHE* 4.1 5.5 - - - -
489A LYS* 3.4 33.0 + - - +
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Residues in contact with ASN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A SER 3.5 8.8 + - - +
466A GLY* 3.2 15.0 - - - +
467A LEU 2.7 3.7 + - - -
468A ARG* 1.3 108.6 + - + +
470A GLY* 1.3 59.3 + - - +
471A GLN 4.2 0.2 + - - -
488A PHE* 5.4 2.7 - - - -
489A LYS* 5.3 9.3 - - - +
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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