Contacts of the strand formed by residues 480 - 486 (chain B) in PDB entry 5NEU
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 ARG 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430B GLY 4.2 9.6 - - - +
431B ASP* 4.1 14.5 + - - +
432B THR* 3.8 24.0 + - - +
476B GLU* 3.4 32.9 + - - +
477B ARG* 5.8 5.3 - - - +
478B ARG 4.0 0.2 - - - -
479B SER* 1.3 71.2 - - - +
481B HIS* 1.3 67.1 + - - +
482B ILE* 3.4 21.3 + - + -
495B LEU 3.0 8.3 - - - +
496B LEU* 3.3 2.1 - - - -
497B VAL* 2.9 35.7 + - + +
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Residues in contact with HIS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU 4.1 1.2 - - - +
430B GLY* 3.0 17.2 - - - +
479B SER* 3.1 25.7 + - - -
480B ARG* 1.3 77.6 - - - +
482B ILE* 1.3 61.5 + - - +
483B ILE* 3.8 15.2 + - + +
495B LEU 3.7 4.0 - - - -
496B LEU* 3.5 21.9 - - + +
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Residues in contact with ILE 482 (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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428B VAL* 3.7 16.4 - - + -
430B GLY 3.3 15.3 - - - +
431B ASP* 4.0 15.0 - - + -
432B THR* 4.9 3.6 - - - +
435B LEU* 4.6 13.0 - - + -
470B VAL* 6.0 3.8 - - + -
472B ILE* 5.7 5.2 - - + -
476B GLU* 5.7 0.4 - - - +
480B ARG* 3.9 14.4 - - + -
481B HIS* 1.3 72.1 - - - +
483B ILE* 1.3 63.0 + - - +
484B ILE* 3.7 28.6 + - + -
493B LEU 3.3 2.6 - - - +
495B LEU* 2.9 45.1 + - + +
497B VAL* 3.7 23.8 - - + -
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Residues in contact with ILE 483 (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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427B GLU 4.0 0.3 - - - +
428B VAL 3.8 0.2 - - - -
429B LEU* 2.9 48.4 + - + +
481B HIS* 4.4 15.7 - - + +
482B ILE* 1.3 79.0 - - - +
484B ILE* 1.3 60.4 + - - +
485B LYS* 3.6 13.8 + - + +
492B ALA* 4.0 25.4 - - + -
493B LEU 3.3 2.5 - - - +
494B GLU* 3.7 31.4 - - + -
495B LEU 4.8 0.7 - - - +
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Residues in contact with ILE 484 (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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66B ILE* 3.9 5.7 - - + +
83B LEU* 6.1 0.9 - - + -
85B VAL* 6.0 2.7 - - + -
426B LEU* 5.0 17.7 - - + -
427B GLU 3.5 10.3 - - - +
428B VAL* 3.8 24.7 - - + +
437B LEU* 5.4 4.0 - - + -
439B PHE* 5.8 5.2 - - + -
468B VAL* 4.9 21.8 - - + -
470B VAL* 5.8 3.1 - - + -
482B ILE* 3.7 21.3 - - + -
483B ILE* 1.3 69.8 - - - +
485B LYS* 1.3 61.6 + - - +
492B ALA 3.8 0.2 - - - -
493B LEU* 2.6 58.3 + - + +
495B LEU* 3.8 23.3 - - + -
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Residues in contact with LYS 485 (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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66B ILE* 5.3 0.2 - - - -
426B LEU* 4.7 3.8 - - - -
427B GLU* 2.9 54.4 + - + +
429B LEU* 3.9 25.5 - - + +
483B ILE* 4.5 8.7 - - + +
484B ILE* 1.3 75.0 - - - +
486B PRO* 1.3 79.3 - - + +
489B LEU 4.7 13.4 + - - -
490B GLY 5.2 5.5 + - - -
491B ASP 4.6 0.4 - - - +
492B ALA* 3.7 25.4 - - + +
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Residues in contact with PRO 486 (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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66B ILE* 4.1 19.7 - - + -
87B VAL* 5.1 1.6 - - + -
424B VAL* 4.2 12.3 - - + -
425B GLU 3.3 10.3 - - - +
426B LEU* 3.7 18.6 - - + -
427B GLU* 4.0 4.7 - - - +
485B LYS* 1.3 103.6 - - + +
487B VAL* 1.3 63.3 + - - +
488B GLY 4.0 1.6 + - - -
489B LEU* 3.7 42.2 + - + +
491B ASP 3.5 18.2 - - - +
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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