Contacts of the strand formed by residues 495 - 499 (chain A) in PDB entry 5FZ9
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 SER 495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLN* 2.9 30.7 + - - +
90A LEU* 3.5 22.5 - - - +
410A PHE* 4.0 9.6 - - - -
425A TYR* 5.4 0.3 - - - -
493A PHE 3.7 6.1 - - - -
494A SER* 1.3 76.3 - - - +
496A PHE* 1.3 65.8 + - - +
497A CYS* 4.2 0.4 - - - -
555A ILE* 3.9 13.0 - - - +
589A GLY 3.2 15.7 - - - -
590A PHE* 3.8 7.4 - - - +
1757A DMS 3.3 10.6 - - - +
1768A NUK 4.5 6.2 - - - -
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Residues in contact with PHE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A SER 5.3 0.4 - - - -
495A SER* 1.3 77.0 - - - +
497A CYS* 1.3 66.7 + - - +
499A HIS* 4.8 9.0 - + + -
517A LYS* 3.9 21.1 - - + -
518A THR 4.1 2.9 - - - -
519A TRP* 3.9 43.7 - + - -
555A ILE* 5.9 0.6 - - - +
587A HIS* 4.5 8.3 - + - -
588A SER* 3.3 27.9 - - - -
589A GLY* 3.0 52.5 + - - +
590A PHE* 3.6 5.6 - - - -
591A ASN* 5.4 0.2 - - - -
1757A DMS 3.7 5.8 - - - +
1768A NUK 3.7 45.1 - - + -
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Residues in contact with CYS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 5.1 1.6 - - - -
96A GLN* 3.5 36.6 - - - -
495A SER 5.8 0.2 - - - -
496A PHE* 1.3 76.5 - - - +
498A TRP* 1.3 67.3 + - - +
499A HIS* 3.2 18.9 + - - +
553A VAL* 3.6 18.6 - - + +
554A THR* 3.4 36.6 - - - +
555A ILE* 3.9 9.2 - - - +
587A HIS 3.5 2.8 - - - +
588A SER* 3.8 1.7 - - - -
1757A DMS 3.2 20.6 + - - +
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Residues in contact with TRP 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TRP* 5.4 0.2 - - - -
497A CYS* 1.3 72.1 - - - +
499A HIS* 1.3 61.2 + - - +
520A TYR* 3.9 23.6 - + + -
522A VAL* 3.8 25.8 - - + -
530A LEU* 4.2 6.3 - - + -
534A MET* 4.9 18.6 - - + -
553A VAL* 3.6 17.7 - - - +
554A THR 3.2 15.4 + - - +
555A ILE* 4.7 0.4 - - - -
556A MET* 2.9 53.1 + - + +
558A PRO* 4.6 8.3 - - + -
561A LEU* 3.6 27.7 - - + +
568A VAL* 4.4 3.8 - - + -
586A TYR* 3.9 17.6 - - + -
587A HIS* 3.4 43.7 - - - -
588A SER* 3.2 22.4 + - - -
1760A EPE 4.6 6.2 + - - -
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Residues in contact with HIS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 4.2 28.0 + - - +
496A PHE* 4.8 11.9 - + + -
497A CYS 3.2 19.0 + - - +
498A TRP* 1.3 76.0 - - - +
500A ILE* 1.3 78.8 + - - +
501A GLU* 3.0 3.4 + - - -
553A VAL* 4.5 12.3 - - + -
586A TYR* 3.4 18.0 - - - -
587A HIS* 3.1 49.8 + + - -
1759A MN 2.1 36.9 + - - -
1760A EPE 6.6 0.4 - - - -
1768A NUK 5.6 8.1 - - - -
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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