Contacts of the strand formed by residues 462 - 467 (chain A) in PDB entry 3HO5
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 SER 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A SER* 3.6 2.9 - - - -
454A ASP* 2.9 32.5 + - - +
456A ASN* 2.8 26.1 + - - -
461A SER* 1.3 74.8 - - - +
463A ALA* 1.3 59.8 + - - +
464A ARG* 3.9 7.3 + - - -
482A GLU* 3.4 30.1 + - - +
483A PHE 3.7 9.2 - - - -
484A LYS* 3.8 14.3 - - - +
486A PHE* 3.9 5.0 - - - -
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Residues in contact with ALA 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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451A LEU* 4.1 7.2 - - + -
452A CYS 3.2 8.5 - - - +
462A SER* 1.3 74.7 - - - +
464A ARG* 1.3 63.3 + - - +
482A GLU* 3.4 3.8 - - - +
483A PHE* 2.8 67.3 + - + +
485A PRO* 3.9 2.0 - - + +
486A PHE* 3.6 24.1 - - + -
521A LEU* 5.7 0.2 - - + -
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Residues in contact with ARG 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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428A GLY* 4.2 8.6 + - - -
429A LEU* 3.8 21.5 - - + -
430A HIS* 3.2 22.5 + - - -
450A ILE* 4.1 0.9 - - - +
451A LEU* 3.5 2.4 - - - +
452A CYS* 2.7 46.5 + - + +
454A ASP* 2.7 28.2 + - + +
456A ASN* 2.8 29.5 + - - -
462A SER* 3.9 7.6 + - - +
463A ALA* 1.3 78.9 - - - +
465A ILE* 1.3 59.7 + - - +
480A LEU* 4.2 25.3 + - + +
481A LEU 3.3 7.6 - - - +
482A GLU* 3.3 35.9 + - + +
483A PHE* 4.6 0.9 - - - -
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Residues in contact with ILE 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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449A THR* 3.8 20.6 - - + -
450A ILE 3.6 3.6 - - - +
451A LEU* 4.1 11.9 - - + +
464A ARG* 1.3 75.4 - - - +
466A LEU* 1.3 63.6 + - - +
467A GLN* 3.7 26.4 + - + +
479A SER 4.0 2.1 - - - +
480A LEU* 3.7 7.4 - - - -
481A LEU* 2.8 57.7 + - + +
483A PHE* 3.7 17.7 - - + -
523A GLN* 5.8 0.4 - - - +
530A TRP* 3.6 33.4 - - + +
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Residues in contact with LEU 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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366A TYR* 5.2 2.5 - - + -
392A VAL* 4.3 21.1 - - + -
425A PHE* 3.7 36.1 - - + -
426A ALA* 4.0 20.9 - - + -
448A LEU 3.9 0.5 - - - +
449A THR* 3.3 4.0 - - - +
450A ILE* 2.7 68.5 + - + +
465A ILE* 1.3 74.4 - - - +
467A GLN* 1.3 67.5 + - - +
468A ILE* 5.0 4.1 - - + +
478A PRO* 4.3 12.8 - - + -
479A SER 4.2 15.7 - - - +
480A LEU* 4.2 9.0 - - + -
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Residues in contact with GLN 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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425A PHE* 5.7 0.3 - - - -
440A HIS* 5.9 0.2 + - - -
448A LEU 3.4 5.4 - - - +
449A THR* 3.5 27.3 + - + +
465A ILE* 3.7 25.5 + - + +
466A LEU* 1.3 83.8 - - - +
468A ILE* 1.3 64.3 + - - +
469A ILE* 3.6 10.5 - - + +
474A TYR* 4.4 2.4 + - - -
478A PRO* 4.9 7.8 - - - +
479A SER 5.6 1.0 + - - -
523A GLN* 4.7 14.3 + - - +
530A TRP* 5.0 1.0 - - - -
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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