Contacts of the strand formed by residues 447 - 449 (chain D) in PDB entry 7KHE
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 447 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D SER* 3.9 36.1 - - - +
354D VAL 2.9 10.8 + - - +
355D ILE* 3.2 14.1 - - + +
356D THR* 2.7 32.6 + - - +
366D CYS* 5.4 2.0 - - + -
367D GLY 3.4 10.8 - - - +
368D LEU* 5.1 2.9 - - + -
369D PRO* 3.9 18.4 - - + -
372D MET* 4.0 7.4 - - + -
423D LEU* 4.2 24.0 - - + -
445D LYS 4.1 0.6 + - - -
446D ALA* 1.3 72.0 - - - +
448D GLN* 1.3 64.0 + - - +
449D LEU* 3.9 2.1 + - + +
466D MET* 4.1 11.2 - - + +
468D VAL* 4.0 24.7 - - + -
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Residues in contact with GLN 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C TYR* 5.8 3.0 - - - -
1077C SER* 4.6 13.5 + - - -
1078C LYS* 6.1 1.2 - - - +
356D THR* 3.4 20.4 - - - +
358D GLY* 4.0 15.2 - - - +
360D TYR* 2.6 44.3 + - - -
361D LEU* 3.2 10.1 - - + +
366D CYS* 3.3 5.4 - - - +
367D GLY* 2.5 48.0 + - - +
442D ILE* 3.5 17.4 - - + +
446D ALA* 3.7 2.9 + - + +
447D ILE* 1.3 75.4 - - - +
449D LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ILE* 4.0 15.0 - - + -
356D THR 3.2 4.0 + - - +
357D VAL* 2.5 27.5 - - - +
361D LEU* 4.2 3.8 - - - -
366D CYS* 4.5 4.9 - - + -
423D LEU* 4.7 15.7 - - + -
437D PHE* 5.8 3.8 - - + -
447D ILE* 3.9 1.5 + - + -
448D GLN* 1.3 73.3 - - - +
450D HIS* 1.3 78.4 + - - +
451D PRO* 3.4 0.7 - - - +
453D VAL* 4.5 9.4 - - + -
454D CYS* 3.3 26.7 - - - -
457D TYR* 5.1 4.9 - - + -
461D PHE* 3.7 12.6 - - + -
466D MET* 3.2 45.5 - - + -
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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
------------------------------------------------------------
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