Contacts of the helix formed by residues 453 - 463 (chain A) in PDB entry 1V9P
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 GLY 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A GLU 5.1 1.8 - - - -
451A GLY 2.6 12.9 + - - -
452A LEU* 1.3 74.7 - - - +
454A GLU* 1.3 64.1 + - - -
455A LYS* 2.9 7.6 - - - -
456A LEU* 2.8 19.7 + - - +
457A ILE* 3.0 10.8 + - - +
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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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435A PHE* 3.1 45.2 - - + -
439A ARG* 3.7 28.4 + - - +
452A LEU 3.8 1.2 + - - -
453A GLY* 1.3 70.8 - - - -
455A LYS* 1.3 63.5 + - + +
457A ILE* 3.8 7.1 + - - +
458A GLU* 3.6 21.5 + - - +
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Residues in contact with LYS 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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453A GLY* 2.9 1.2 - - - -
454A GLU* 1.3 80.2 - - + +
456A LEU* 1.3 59.9 + - - +
457A ILE 3.2 0.4 - - - -
458A GLU* 3.2 21.3 - - + +
459A ARG* 2.9 28.9 + - - +
485A ARG* 4.0 25.1 + - - +
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Residues in contact with LEU 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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451A GLY 4.2 8.3 - - - +
452A LEU* 4.2 4.5 - - + -
453A GLY* 2.8 15.6 + - - +
455A LYS* 1.3 76.4 - - - +
457A ILE* 1.3 57.9 + - - +
459A ARG* 3.9 5.2 - - + -
460A LEU* 2.7 70.6 + - + +
481A LEU* 4.8 0.7 - - + -
484A GLU* 4.0 6.5 - - + +
485A ARG* 4.3 15.0 - - - +
486A MET* 3.5 33.9 - - + -
494A LEU* 3.5 31.6 - - + -
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Residues in contact with ILE 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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435A PHE* 3.9 19.5 - - + +
438A ILE* 3.4 33.0 - - + -
439A ARG* 3.7 37.2 - - + -
442A ALA* 4.9 1.6 - - + -
452A LEU* 3.5 41.1 - - + +
453A GLY 3.0 14.3 + - - +
454A GLU* 4.0 7.4 - - - +
456A LEU* 1.3 78.1 - - - +
458A GLU* 1.3 55.8 + - - +
460A LEU* 3.9 2.8 - - - -
461A LEU* 2.8 42.4 + - + +
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Residues in contact with GLU 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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435A PHE* 4.6 14.3 - - + -
454A GLU* 3.6 12.9 + - - +
455A LYS* 3.2 32.1 - - - +
457A ILE* 1.3 77.8 - - - +
459A ARG* 1.3 58.7 + - - +
461A LEU* 3.7 8.1 - - - +
462A GLU* 3.0 32.1 + - - +
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Residues in contact with ARG 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 LYS 2.9 17.6 + - - +
456A LEU* 3.2 6.5 + - + +
458A GLU* 1.3 77.9 - - + +
460A LEU* 1.3 60.6 + - - +
461A LEU 3.1 1.1 - - - -
462A GLU* 3.1 35.3 - - - +
463A LYS* 3.0 47.3 + - - +
484A GLU* 3.5 34.1 - - + -
485A ARG* 3.5 19.1 - - - +
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Residues in contact with LEU 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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452A LEU* 3.6 21.8 - - + -
456A LEU* 2.7 49.9 + - + +
457A ILE* 4.1 4.7 - - - +
459A ARG* 1.3 71.7 - - - +
461A LEU* 1.3 60.7 + - + +
463A LYS* 4.1 2.2 - - - -
464A GLY 3.6 0.5 + - - -
465A LEU* 3.1 47.3 + - + -
466A VAL* 3.1 23.9 + - + -
472A LEU* 5.4 0.2 - - + -
475A LEU* 4.1 20.4 - - + -
481A LEU* 3.9 13.5 - - + -
484A GLU* 3.8 22.4 - - - +
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Residues in contact with LEU 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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434A ARG* 3.9 40.1 + - + +
435A PHE* 4.9 7.4 - - + +
438A ILE* 4.0 9.9 - - + -
457A ILE* 2.8 43.4 + - + +
458A GLU* 3.9 8.5 - - - +
459A ARG 3.1 0.2 - - - -
460A LEU* 1.3 78.4 - - + +
462A GLU* 1.3 61.1 + - - +
463A LYS 3.5 0.2 - - - -
464A GLY* 3.6 9.4 + - - -
466A VAL* 3.6 40.8 - - + +
467A ARG* 4.2 1.3 - - - -
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Residues in contact with GLU 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 GLU* 3.0 20.8 + - - +
459A ARG* 3.1 24.8 + - - +
461A LEU* 1.3 75.0 - - - +
463A LYS* 1.3 55.5 + - - +
464A GLY* 3.1 8.5 + - - -
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Residues in contact with LYS 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 ARG* 3.0 34.1 + - - +
460A LEU 4.7 0.4 - - - +
462A GLU* 1.3 76.8 - - - +
464A GLY* 1.3 60.3 + - - +
465A LEU* 3.3 26.3 + - + +
483A LEU* 3.3 47.5 + - - +
484A GLU* 3.8 20.1 + - + +
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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