Contacts of the strand formed by residues 440 - 446 (chain E) in PDB entry 6T8B
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 PRO 440 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432E TYR* 3.4 30.5 - - + -
435E HIS* 3.4 28.7 - - + +
438E THR* 3.5 7.0 - - - +
439E VAL* 1.3 88.9 - - - +
441E LEU* 1.3 53.5 + - - +
442E ALA 3.5 0.4 - - - -
453E ILE* 4.2 7.9 - - + -
454E THR 3.4 8.1 - - - +
482E SER* 2.8 41.4 + - - +
483E ILE* 3.7 2.2 + - - +
486E LYS* 4.1 21.8 - - + -
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Residues in contact with LEU 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E VAL 3.4 16.8 - - - +
440E PRO* 1.3 68.6 - - - +
442E ALA* 1.3 60.1 + - - +
443E LEU* 2.9 27.1 + - + +
452E ILE 4.0 0.2 - - - +
453E ILE* 4.6 0.2 - - - -
454E THR* 2.8 33.0 + - - +
456E LEU* 3.5 22.7 - - + +
459E MET* 3.7 14.4 - - + -
462E LEU* 3.5 31.6 - - + -
479E MET* 3.8 29.6 - - + +
482E SER* 3.6 5.2 - - - +
483E ILE* 3.6 15.9 - - + -
627E ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E PHE* 3.7 18.1 - - + -
426E VAL* 3.7 24.5 - - + +
427E LEU* 4.5 5.8 - - + -
432E TYR* 3.9 21.5 - - + -
440E PRO 3.5 5.3 + - - -
441E LEU* 1.3 69.8 - - - +
443E LEU* 1.3 55.2 + - - +
444E GLY 3.4 7.5 + - - -
453E ILE* 3.7 25.9 - - + +
478E ALA* 4.8 3.4 - - - +
479E MET* 6.0 0.7 - - - -
482E SER* 3.7 12.8 + - - -
694E ALA* 5.1 0.3 - - - +
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Residues in contact with LEU 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E LEU* 2.9 25.2 + - + +
442E ALA* 1.3 70.8 - - - +
444E GLY* 1.3 58.2 + - - +
452E ILE* 3.4 21.9 + - + +
454E THR* 4.2 9.9 - - + +
478E ALA* 5.9 3.6 - - - -
479E MET* 4.2 21.8 - - + -
650E ILE* 3.8 27.6 - - + -
678E MET* 3.7 15.9 - - + +
680E TYR* 4.1 14.6 - - + -
691E VAL* 3.5 30.4 - - + +
692E HIS 3.7 3.8 - - - +
693E GLY* 3.8 8.0 - - - -
694E ALA* 4.5 7.4 - - - +
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Residues in contact with GLY 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E VAL* 4.1 4.3 - - - -
426E VAL* 3.8 24.8 - - - +
442E ALA 3.4 5.7 + - - -
443E LEU* 1.3 76.5 - - - +
445E HIS* 1.3 61.6 + - - +
451E PRO* 4.3 2.2 - - - -
452E ILE* 2.7 36.6 + - - +
692E HIS 3.4 7.6 - - - -
694E ALA* 4.2 4.4 - - - +
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Residues in contact with HIS 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E PRO* 4.8 7.2 - - + -
421E VAL* 3.4 40.1 - - + +
425E GLU* 3.3 48.0 + - + +
426E VAL* 4.5 2.2 - - + +
444E GLY* 1.3 76.2 - - - -
446E ASP* 1.3 62.5 + - - +
449E GLY* 3.1 32.6 + - - -
450E ARG 3.8 5.2 - - - -
451E PRO* 3.5 26.4 - - + +
452E ILE* 4.1 1.3 - - - -
691E VAL* 3.2 5.0 - - - +
692E HIS* 2.7 36.5 + - + -
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Residues in contact with ASP 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E PRO* 3.9 7.4 - - - +
445E HIS* 1.3 79.7 - - - +
447E ILE* 1.3 68.7 + - - +
448E GLY* 3.5 5.5 + - - -
449E GLY* 3.0 14.9 + - - -
450E ARG* 2.8 38.9 + - - +
452E ILE* 3.5 25.4 - - + +
689E ILE* 4.6 6.0 - - + +
690E ARG 3.6 17.7 - - - +
691E VAL* 4.3 0.9 - - - +
692E HIS* 4.1 5.8 + - - -
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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