Contacts of the helix formed by residues 451 - 465 (chain A) in PDB entry 2P6U
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 LEU 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A LEU* 5.4 0.7 - - + -
410A GLY* 4.8 8.1 - - - +
415A LEU* 4.0 27.1 - - + -
435A GLU* 6.3 0.2 - - - +
438A PHE* 4.3 17.9 - - + +
443A PHE* 3.7 41.3 - - + -
449A ILE* 3.4 14.4 + - + +
450A SER* 1.3 73.0 + - - +
452A SER* 1.3 54.9 + - - +
453A TYR 2.8 5.2 + - - -
454A GLU* 3.1 29.6 + - + +
455A LEU* 2.6 50.4 + - + +
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Residues in contact with SER 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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431A LEU* 4.8 0.2 - - - +
435A GLU* 2.7 48.2 + - - +
450A SER* 2.6 23.6 + - - -
451A LEU* 1.3 77.0 - - - +
453A TYR* 1.3 65.5 + - - +
455A LEU* 4.0 3.7 - - - +
456A GLU* 3.0 22.0 + - - +
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Residues in contact with TYR 453 (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 SER 4.8 1.4 + - - +
451A LEU 2.8 1.6 + - - -
452A SER* 1.3 76.9 - - - +
454A GLU* 1.3 79.1 + - - +
456A GLU* 2.8 41.1 + - - +
457A ARG* 3.1 48.4 + - + +
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Residues in contact with GLU 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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410A GLY 5.6 0.2 - - - +
412A GLU* 5.4 4.9 - - + -
415A LEU* 4.1 18.4 - - + -
449A ILE* 5.7 0.4 - - - +
450A SER 3.8 5.4 - - - +
451A LEU* 3.2 49.9 - - + +
453A TYR* 1.3 102.2 - - + +
455A LEU* 1.3 55.3 + - - +
457A ARG* 2.8 28.9 + - - +
458A VAL* 2.8 32.6 + - + +
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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
----------------------------------------------------------
415A LEU* 3.9 38.4 - - + -
419A SER* 4.4 10.3 - - - +
431A LEU* 4.0 7.0 - - + +
434A LEU* 3.7 30.3 - - + -
435A GLU* 3.9 21.8 - - + -
438A PHE* 3.8 22.4 - - + -
451A LEU* 2.6 34.2 + - + +
452A SER* 4.1 4.9 - - - +
454A GLU* 1.3 74.0 - - - +
456A GLU* 1.3 59.4 - - - +
458A VAL* 3.6 5.2 - - + +
459A VAL* 3.3 28.6 + - - +
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Residues in contact with GLU 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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431A LEU* 3.8 27.7 - - + +
452A SER 3.0 14.4 + - - +
453A TYR* 2.8 26.2 + - - +
455A LEU* 1.3 74.1 - - - +
457A ARG* 1.3 64.5 + - - +
459A VAL* 3.5 3.8 + - - +
460A ARG* 3.2 38.1 + - + +
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 3.4 39.4 + - - +
453A TYR* 3.1 49.0 + - + +
454A GLU* 2.8 24.2 + - - +
456A GLU* 1.3 79.0 + - - +
458A VAL* 1.3 66.2 - - - +
460A ARG* 3.2 20.3 + - - +
461A GLN* 3.0 19.5 + - - +
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Residues in contact with VAL 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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412A GLU* 4.7 6.1 - - + +
415A LEU* 4.2 13.5 - - + -
416A ARG* 3.9 34.1 - - + +
419A SER* 3.7 30.3 - - - +
454A GLU* 2.8 16.3 + - + +
455A LEU* 3.6 11.9 - - - +
457A ARG* 1.3 73.4 - - + +
459A VAL* 1.3 58.1 + - + +
460A ARG 2.7 12.8 + - - -
461A GLN* 2.7 23.0 + - - +
462A LEU* 2.8 24.1 + - + +
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Residues in contact with VAL 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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423A ILE* 4.1 9.4 - - + -
431A LEU* 4.2 9.9 - - + -
434A LEU* 3.4 27.6 - - + -
455A LEU 3.3 18.2 + - - +
456A GLU* 3.5 5.4 + - - +
458A VAL* 1.3 78.4 - - + +
460A ARG* 1.3 60.3 + - + +
462A LEU* 3.7 8.2 - - - +
463A GLU* 3.1 26.4 + - - +
468A VAL* 4.5 8.3 - - + -
474A LEU* 3.6 36.3 - - + -
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Residues in contact with ARG 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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456A GLU* 3.2 32.9 + - + +
457A ARG* 3.5 20.9 + - - +
458A VAL 2.7 5.7 + - - -
459A VAL* 1.3 73.3 - - + +
461A GLN* 1.3 50.0 + - - +
463A GLU* 2.7 22.1 + - - +
464A ASN* 2.6 47.5 + - - +
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Residues in contact with GLN 461 (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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416A ARG* 3.4 31.3 + - - +
457A ARG 3.0 8.8 + - - +
458A VAL* 2.7 16.4 + - - +
460A ARG* 1.3 76.4 - - - +
462A LEU* 1.3 56.8 + - + +
464A ASN* 3.9 12.1 + - + +
465A TRP* 3.0 68.6 + - + +
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Residues in contact with LEU 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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416A ARG* 3.7 33.0 - - + +
420A LEU* 3.7 37.5 - - + +
423A ILE* 4.0 9.6 - - + -
458A VAL* 2.8 30.0 + - + +
459A VAL* 3.7 6.1 - - - +
461A GLN* 1.3 78.3 - - + +
463A GLU* 1.3 60.0 + - - +
465A TRP* 3.7 8.4 + - + +
466A GLY 3.5 2.3 + - - -
467A MET* 2.9 33.0 + - + +
468A VAL* 3.1 29.8 + - + -
490A PRO* 4.7 10.8 - - + -
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Residues in contact with GLU 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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459A VAL* 3.1 25.5 + - - +
460A ARG* 2.7 25.4 + - - +
462A LEU* 1.3 75.1 - - - +
464A ASN* 1.3 58.4 + - - +
466A GLY* 2.7 26.0 + - - -
468A VAL* 3.1 31.9 - - + +
469A VAL* 4.4 2.0 - - - +
470A GLU* 3.0 36.5 - - - +
474A LEU* 3.4 15.4 - - - +
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Residues in contact with ASN 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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460A ARG* 2.6 32.2 + - - +
461A GLN* 3.7 16.0 + - + +
462A LEU 3.4 0.2 - - - -
463A GLU* 1.3 76.5 - - - +
465A TRP* 1.3 66.2 + - + +
466A GLY* 2.9 6.4 + - - -
494A PHE* 4.9 2.1 - - - -
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Residues in contact with TRP 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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416A ARG* 3.9 20.0 - - - -
461A GLN* 3.0 56.0 + - + +
462A LEU* 4.0 9.0 - - + +
463A GLU 3.2 0.4 - - - -
464A ASN* 1.3 80.9 - - + +
466A GLY* 1.3 61.0 + - - +
467A MET* 3.3 13.6 + - + +
479A LEU* 3.7 15.8 - - - +
490A PRO* 3.7 20.4 - - + -
491A LEU* 3.4 53.2 - - + -
494A PHE* 3.5 52.0 - + + -
497A HIS* 5.2 2.4 - - - -
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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