Contacts of the strand formed by residues 481 - 485 (chain B) in PDB entry 5FS9
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 MET 481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B HIS* 3.9 14.5 - - - +
456B ASP* 3.1 36.0 + - + +
479B GLN 3.8 0.6 + - - -
480B SER* 1.3 74.0 - - - +
482B PHE* 1.3 79.1 + - - +
483B TRP* 4.0 12.9 - - + -
493B GLU* 3.8 28.7 - - + +
494B ALA 3.3 11.0 - - - +
495B ILE* 4.6 1.3 - - + -
529B ARG* 4.2 9.9 - - + +
530B SER* 3.8 17.5 - - - +
585B MET* 3.9 28.3 - - + -
589B ARG* 4.3 0.7 - - - +
1000B FAD 4.5 0.5 - - - +
1001B GOL 3.1 31.6 - - - +
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Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.6 53.8 - + + -
314B GLU* 5.4 0.4 - - - -
453B GLU 5.5 0.7 - - - -
454B HIS* 3.5 37.7 - + + -
481B MET* 1.3 80.9 - - - +
483B TRP* 1.3 85.3 + - - +
484B SER* 3.9 5.6 - - - -
492B TYR* 5.2 1.6 - - + -
493B GLU* 3.3 4.9 - - - -
494B ALA* 2.8 49.9 + - + +
1000B FAD 3.4 31.2 - + - -
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Residues in contact with TRP 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO* 3.8 23.6 - - + -
177B LYS* 4.2 7.9 - - - +
178B GLU* 5.7 1.0 + - - -
455B HIS* 3.9 15.9 - + + -
456B ASP 4.7 1.1 - - - -
481B MET* 4.0 10.1 - - + -
482B PHE* 1.3 87.5 - - - +
484B SER* 1.3 71.0 + - - +
485B ASP* 4.0 10.0 + - - -
492B TYR 3.2 13.9 - - - +
493B GLU* 4.1 0.2 - - + -
527B GLY 3.8 9.3 + - - -
528B ILE* 3.8 42.2 - - + -
529B ARG* 3.7 39.5 - - + +
530B SER 3.7 30.7 - - - -
1000B FAD 2.9 49.3 + - - +
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Residues in contact with SER 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.3 36.5 - - - +
314B GLU* 2.5 32.5 + - - +
482B PHE* 3.9 6.9 - - - -
483B TRP* 1.3 78.8 - - - +
485B ASP* 1.3 68.7 + - - +
486B LEU* 4.4 4.0 - - - +
491B GLY* 3.4 0.3 - - - -
492B TYR* 2.8 35.8 + - - +
1000B FAD 4.5 0.9 - - - -
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 3.6 17.1 - - + +
178B GLU* 4.7 2.3 - - - +
196B TRP* 2.8 34.1 + - + +
314B GLU* 3.5 22.0 + - - +
483B TRP* 4.1 11.0 + - - -
484B SER* 1.3 74.4 + - - +
486B LEU* 1.3 61.2 + - - +
487B GLY 3.5 15.5 + - - +
490B VAL 3.3 3.8 - - - +
517B PRO* 3.5 10.9 - - - +
527B GLY 4.5 3.8 - - - +
529B ARG* 2.5 46.5 + - - -
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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