Contacts of the strand formed by residues 455 - 461 (chain B) in PDB entry 4DN5
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 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B LEU* 3.7 27.4 - - + -
382B LEU* 3.7 18.9 - - + +
441B LEU* 3.8 15.9 - - + -
444B CYS* 3.8 40.1 + - - +
445B ALA* 4.0 16.4 - - + -
446B GLY 5.5 0.6 + - - +
453B VAL* 3.6 3.7 + - + -
454B PRO* 1.3 72.2 - - - +
456B TYR* 1.3 65.3 + - - +
457B GLY 4.0 8.1 - - - +
467B ILE* 3.7 24.2 - - + -
468B PHE 3.3 16.2 - - - +
469B MET* 4.4 5.2 - - + +
1002B EDO 5.1 3.1 - - - -
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B LEU* 3.9 2.9 - - - +
382B LEU* 2.9 24.8 + - - +
383B THR* 3.6 31.5 + - + +
386B LEU* 3.9 15.2 - - + +
424B PHE* 3.5 34.9 - + - -
425B GLN 5.1 0.4 - - - -
426B CYS* 3.7 14.8 - - + -
454B PRO* 4.2 20.9 - - + +
455B LEU* 1.3 80.1 - - - +
457B GLY* 1.3 56.1 + - - +
468B PHE* 2.9 15.5 + - + +
469B MET* 3.4 26.5 - - - -
470B GLU* 3.6 28.8 - - + +
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Residues in contact with GLY 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.1 14.8 - - - -
380B VAL 3.5 12.8 - - - -
381B LEU* 4.4 1.1 - - - -
382B LEU* 4.2 4.0 - - - +
455B LEU* 3.4 9.0 + - - +
456B TYR* 1.3 80.1 - - - +
458B ALA* 1.3 58.6 + - - +
467B ILE* 3.9 0.3 - - - -
468B PHE* 2.8 39.4 + - - +
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B LEU* 3.7 17.3 - - + +
360B TRP* 3.6 12.8 - - + -
379B GLY* 3.2 19.8 - - - -
380B VAL 3.2 12.7 + - - -
381B LEU* 4.6 0.2 - - - +
441B LEU* 3.8 23.3 - - + -
457B GLY* 1.3 75.6 - - - +
459B VAL* 1.3 63.2 + - - +
466B ASN 3.2 13.2 - - - +
467B ILE* 4.3 9.4 - - + -
468B PHE* 4.0 2.4 - - - -
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL* 3.8 22.0 - - + -
360B TRP* 4.0 5.4 - - - -
377B ASN* 4.9 1.1 - - - +
378B GLU 3.3 8.1 - - - +
379B GLY* 3.8 7.2 - - - -
381B LEU* 3.6 24.9 - - + -
393B TYR* 4.0 24.7 - - + +
399B TRP* 4.8 2.2 - - - +
458B ALA* 1.3 79.5 - - - +
460B ARG* 1.3 63.1 + - - +
461B GLU* 5.5 1.1 - - + -
465B VAL* 3.8 0.3 - - - -
466B ASN* 2.9 41.5 + - - +
468B PHE* 3.7 24.0 - - + -
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Residues in contact with ARG 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B TRP* 3.4 42.0 - - + +
363B ARG* 3.7 38.1 - - - +
376B ASP* 3.4 32.1 + - - +
377B ASN* 2.7 29.5 + - - -
378B GLU* 2.6 60.3 + - + +
433B LEU* 4.2 10.3 - - - +
459B VAL* 1.3 73.5 - - - +
461B GLU* 1.3 55.9 + - - +
462B GLY* 2.8 32.5 + - - +
464B TRP 3.5 2.7 - - - -
465B VAL* 3.9 15.7 - - + -
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ARG* 5.7 0.2 + - - -
408A ARG* 3.3 25.9 + - - +
375B GLU* 3.6 15.5 - - - +
376B ASP 3.6 4.0 - - - -
377B ASN* 3.5 20.9 - - - +
393B TYR 4.0 3.0 - - - +
394B ARG* 3.2 21.1 + - + +
395B GLU* 2.6 42.9 + - - +
399B TRP* 4.2 7.1 + - - -
459B VAL* 4.1 1.7 + - + +
460B ARG* 1.3 70.3 - - - +
462B GLY* 1.3 60.7 + - - +
463B PRO* 3.5 0.2 - - - +
464B TRP* 2.9 41.0 + - + +
466B ASN* 4.3 7.4 - - - +
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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