Contacts of the helix formed by residues 449 - 460 (chain A) in PDB entry 1GPU
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 ALA 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A GLU* 3.5 13.7 - - + +
419A HIS* 3.4 30.3 - - + +
422A GLY* 4.8 0.9 - - - -
446A VAL 2.8 8.7 + - - +
448A TYR* 1.3 79.8 - - - +
450A ALA* 1.3 62.5 + - - +
451A GLY 3.1 3.6 - - - -
452A ALA* 3.0 13.5 + - - -
453A VAL* 3.0 12.5 + - + +
465A TRP* 3.5 25.1 - - + -
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A VAL 3.6 3.0 + - - -
447A SER* 3.3 17.6 + - - +
448A TYR 3.5 1.2 + - - -
449A ALA* 1.3 77.1 - - - +
451A GLY* 1.3 63.6 + - - +
453A VAL* 3.9 8.0 - - - +
454A ARG* 3.0 26.5 + - - +
489A HIS* 4.1 25.6 - - + +
490A PHE* 4.8 3.7 - - + -
447B SER* 3.6 26.9 + - - +
450B ALA* 5.0 1.3 - - + -
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Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 5.4 1.9 - - - +
120A GLN* 3.5 9.1 - - - +
419A HIS* 3.6 13.7 + - - -
448A TYR 5.3 0.2 + - - -
449A ALA 3.0 1.6 + - - -
450A ALA* 1.3 78.6 - - - +
452A ALA* 1.3 60.3 + - - +
454A ARG* 3.7 6.6 - - - +
455A LEU* 3.7 19.9 + - - +
447B SER* 4.7 4.6 + - - -
448B TYR* 3.7 28.5 - - - +
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Residues in contact with ALA 452 (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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120A GLN* 3.5 23.3 - - - +
419A HIS* 3.3 19.6 + - + +
422A GLY* 3.7 7.0 - - - -
423A ALA* 3.5 28.0 - - - +
426A ASN* 3.3 12.1 + - - +
449A ALA 3.0 4.9 + - - +
451A GLY* 1.3 72.3 - - - +
453A VAL* 1.3 67.8 + - - +
454A ARG 3.1 1.6 - - - -
455A LEU* 3.0 4.8 + - - -
456A SER* 3.0 17.1 + - - -
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A VAL* 4.3 13.7 - - + -
449A ALA 3.0 18.2 + - - +
450A ALA 3.9 3.8 - - - +
452A ALA* 1.3 76.2 - - - +
454A ARG* 1.3 63.2 + - - +
456A SER* 3.0 20.2 + - - -
457A ALA* 3.1 12.3 + - - +
465A TRP* 3.8 36.1 - - + +
490A PHE* 3.5 28.7 - - + -
493A LEU* 4.4 1.6 - - + -
496A ILE* 3.6 24.9 - - + +
523A ILE* 4.6 2.7 - - + -
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Residues in contact with ARG 454 (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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450A ALA 3.0 17.7 + - - +
451A GLY* 3.7 8.3 - - - +
453A VAL* 1.3 77.6 - - - +
455A LEU* 1.3 62.4 + - + +
457A ALA* 3.3 4.3 + - - +
458A LEU* 2.9 29.8 + - + +
490A PHE* 5.7 0.2 - - - -
493A LEU* 4.1 18.3 - - + +
444B ASN* 3.2 35.4 + - - +
447B SER* 5.8 3.6 - - - -
479B PRO 3.0 23.4 + - - -
480B THR* 4.2 4.9 + - - +
482B GLN 2.9 23.8 + - - -
484B ILE* 3.7 5.9 - - - +
485B GLU* 2.8 39.6 + - - +
636B PHE* 4.0 23.2 - - + -
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Residues in contact with LEU 455 (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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114A THR* 3.5 42.4 - - + +
117A PRO* 4.1 23.3 - - + -
120A GLN* 3.6 37.5 - - + +
124A ASN* 5.4 1.8 - - - +
426A ASN* 4.4 8.3 - - - +
451A GLY 3.7 9.1 + - - +
452A ALA 3.0 9.4 + - - +
454A ARG* 1.3 79.0 - - + +
456A SER* 1.3 60.3 + - - +
458A LEU* 4.1 17.0 - - + +
459A SER* 2.8 39.2 + - - +
461A HIS* 4.6 1.8 - - + -
480B THR* 4.3 2.9 - - + -
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Residues in contact with SER 456 (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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422A GLY 4.6 1.4 + - - -
426A ASN* 2.6 34.3 + - - +
452A ALA 3.0 8.0 + - - -
453A VAL* 3.0 16.3 + - - -
455A LEU* 1.3 76.0 - - - +
457A ALA* 1.3 58.4 + - - +
460A GLY* 2.9 8.7 + - - -
461A HIS* 2.8 33.1 + - - -
463A VAL* 3.6 9.5 - - - +
465A TRP* 5.1 1.4 + - - -
521A PRO* 3.6 25.3 - - - +
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Residues in contact with ALA 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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453A VAL 3.1 2.9 + - - +
454A ARG 3.6 7.4 - - - +
455A LEU 3.1 0.2 - - - -
456A SER* 1.3 79.4 - - - +
458A LEU* 1.3 65.6 + - - +
460A GLY 3.5 1.2 + - - -
493A LEU* 3.7 21.3 - - + -
494A PRO 3.2 24.2 - - - +
495A ASN* 2.8 42.1 + - - +
496A ILE* 4.4 0.7 - - + -
521A PRO* 3.7 6.0 - - + +
636B PHE* 3.7 5.9 - - + -
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Residues in contact with LEU 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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105A GLU* 5.9 4.9 - - + +
114A THR* 4.2 7.9 - - + +
454A ARG* 2.9 23.8 + - + +
455A LEU* 4.1 14.4 - - + +
457A ALA* 1.3 76.3 - - - +
459A SER* 1.3 62.2 + - - +
460A GLY* 4.6 0.2 - - - -
495A ASN* 5.3 0.2 + - - -
479B PRO* 4.1 18.4 - - + +
480B THR* 3.7 41.7 - - + +
636B PHE* 3.5 41.9 - - + -
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.4 27.4 - - - +
107A GLU 5.6 0.3 + - - -
114A THR* 2.5 40.5 + - - -
455A LEU* 2.8 22.5 + - - +
458A LEU* 1.3 74.6 - - - +
460A GLY* 1.3 59.3 + - - +
461A HIS* 3.4 24.3 + - - -
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Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 4.8 5.4 - - - -
456A SER 2.9 10.5 + - - -
457A ALA 3.5 0.2 + - - -
458A LEU 3.3 2.4 - - - -
459A SER* 1.3 80.8 - - - +
461A HIS* 1.3 61.9 + - - +
462A PRO* 3.1 13.2 - - - +
495A ASN* 4.0 6.5 - - - -
518A LYS 3.7 1.4 - - - +
519A HIS* 3.0 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