Contacts of the strand formed by residues 450 - 455 (chain A) in PDB entry 3D8F
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 ILE 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A LEU* 4.4 14.6 - - + -
445A GLN* 3.7 26.9 - - + -
447A ILE* 3.0 42.8 + - + +
448A ILE 4.5 3.1 - - - +
449A SER* 1.3 76.0 - - - +
451A ARG* 1.3 67.6 + - - +
452A VAL* 3.7 21.5 - - - +
453A TRP* 4.3 16.2 - - + -
467A TYR* 3.9 18.2 - - + -
468A VAL 3.4 11.2 - - - +
469A ALA* 4.5 0.9 - - - -
495A LEU* 4.3 16.8 - - + -
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Residues in contact with ARG 451 (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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1A PO4 3.0 39.9 + - - +
382A GLU* 2.7 44.8 + - - -
385A LEU* 3.5 25.2 + - + +
449A SER 4.5 4.0 - - - +
450A ILE* 1.3 76.1 - - - +
452A VAL* 1.3 77.8 + - + +
468A VAL* 2.5 24.6 + - + +
469A ALA* 4.8 1.3 - - - -
477A LEU* 3.7 18.7 - - + +
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Residues in contact with VAL 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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385A LEU* 4.2 19.1 - - + +
390A SER* 4.0 23.8 - - - +
394A VAL* 4.5 7.0 - - + -
450A ILE* 3.5 6.9 - - - +
451A ARG* 1.3 94.6 - - + +
453A TRP* 1.3 70.5 + - - +
467A TYR* 3.4 2.3 - - - -
468A VAL* 3.0 36.5 + - + +
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Residues in contact with TRP 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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394A VAL* 4.7 11.8 - - - +
447A ILE* 5.1 2.5 - - + -
450A ILE* 4.3 23.3 - - + -
452A VAL* 1.3 84.1 - - - +
454A GLY* 1.3 65.3 + - - +
465A PHE* 3.7 13.5 - + + -
466A ALA 3.2 15.7 - - - +
467A TYR* 4.3 3.1 - - + -
492A ALA* 4.1 17.7 + - + +
495A LEU* 3.4 41.5 - - + -
496A HIS* 3.3 56.0 + + - -
499A CYS* 3.6 29.2 - - + -
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Residues in contact with GLY 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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394A VAL* 4.9 9.0 - - - -
398A ILE* 4.9 2.7 - - - -
453A TRP* 1.3 86.9 - - - +
455A VAL* 1.3 66.2 + - - +
465A PHE* 3.1 26.2 - - - -
466A ALA 3.1 12.5 + - - -
492A ALA* 5.7 0.2 - - - -
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Residues in contact with VAL 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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395A ASN* 3.6 6.8 - - - +
398A ILE* 4.1 3.8 - - - +
454A GLY* 1.3 80.4 - - - +
456A GLY* 1.3 62.8 + - - +
457A ARG* 2.9 18.1 + - + +
461A ARG 5.0 1.6 - - - +
462A GLU* 5.3 2.7 - - - +
464A ASP 3.3 7.2 - - - -
488A ALA* 3.1 43.1 - - + +
489A LYS* 3.8 12.8 - - + +
492A ALA* 4.1 10.5 - - + -
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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