Contacts of the strand formed by residues 452 - 456 (chain A) in PDB entry 5H65
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 452 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A VAL* 3.0 43.3 + - + +
451A CYS* 1.3 75.6 - - - +
453A LEU* 1.3 70.4 + - - +
454A LEU* 4.3 0.7 - - + -
472A SER* 3.1 42.0 - - - +
474A ILE* 3.8 24.0 - - + -
493A LEU* 3.9 15.0 - - + -
515A LEU* 4.0 7.4 - - + -
524A TRP* 3.4 58.9 - - + +
529A VAL* 5.6 0.7 - - + -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A VAL* 4.0 17.0 - - + -
437A HIS 3.3 2.9 - - - +
438A PHE* 3.3 38.6 - - + -
451A CYS* 4.0 2.7 - - - -
452A LEU* 1.3 83.3 - - - +
454A LEU* 1.3 64.4 + - - +
455A ILE* 5.7 0.7 - - + -
466A LEU* 3.8 29.2 - - + -
470A PHE* 3.6 48.2 - - + -
472A SER 2.9 11.0 + - - +
473A VAL* 3.2 10.1 - - + -
474A ILE 2.8 25.8 + - - -
275B ALA* 5.0 0.2 - - + -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A TYR* 3.9 16.2 - - + -
436A VAL* 3.5 2.4 - - - +
437A HIS* 2.7 60.2 + - + +
439A VAL* 4.0 12.6 - - + -
452A LEU* 4.3 6.1 - - + -
453A LEU* 1.3 75.8 - - - +
455A ILE* 1.3 60.8 + - - +
474A ILE* 3.4 38.1 - - + -
476A VAL* 3.9 15.0 - - + -
483A LEU* 4.0 6.7 - - + -
512A ILE* 3.7 31.2 - - + -
515A LEU* 4.1 13.0 - - + -
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Residues in contact with ILE 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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434A VAL* 4.0 13.0 - - + -
435A ALA 3.3 9.9 - - - +
436A VAL* 4.2 7.4 - - + -
453A LEU* 5.5 0.9 - - + -
454A LEU* 1.3 75.2 - - - +
456A GLU* 1.3 70.5 + - - +
457A GLY 4.3 0.5 + - - -
458A GLY* 3.8 23.5 + - - +
462A GLU* 5.3 1.6 - - + -
463A ILE* 3.9 17.7 - - + -
466A LEU* 3.6 28.5 - - + -
473A VAL* 3.5 28.7 - - + -
474A ILE 3.0 7.1 + - - +
475A PRO* 3.6 7.6 - - + +
476A VAL* 2.8 28.9 + - - +
486A LEU* 5.9 0.2 - - - +
279B LEU* 4.8 4.0 - - + -
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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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408A THR 5.1 0.2 - - - -
409A PRO* 3.5 24.5 - - + +
410A ASP 5.0 1.2 + - - +
414A GLN* 5.3 0.5 - - - +
433A LYS 4.6 1.1 - - - -
434A VAL* 3.4 5.5 - - - +
435A ALA* 2.9 41.1 + - + +
437A HIS* 2.8 28.9 + - - +
455A ILE* 1.3 71.3 - - - +
457A GLY* 1.3 63.3 + - - +
458A GLY 3.3 3.5 + - - -
476A VAL* 3.5 32.8 - - + +
477A ARG* 4.2 1.2 - - - -
478A SER* 2.7 32.5 + - - -
483A LEU* 3.4 13.3 - - - +
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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
------------------------------------------------------------
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