Contacts of the strand formed by residues 799 - 803 (chain G) in PDB entry 5FUR
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 ASP 799 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699G LEU 5.2 1.3 - - - +
700G ILE* 3.6 11.3 - - + -
701G LEU 3.1 21.9 + - - -
739G LYS* 2.7 25.6 + - - +
740G TYR* 2.6 45.3 + - + +
775G LEU* 3.9 18.7 - - + +
776G HIS 4.0 3.6 - - - +
797G LEU* 3.7 6.2 - - - +
798G VAL* 1.3 88.7 - - - +
800G ILE* 1.3 60.3 + - - +
801G PHE* 5.2 0.9 - - + -
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Residues in contact with ILE 800 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701G LEU* 3.2 26.7 - - + +
703G GLU* 4.3 6.5 - - + -
775G LEU* 4.1 0.4 - - - +
776G HIS* 2.7 43.0 + - - +
777G LYS 3.8 4.5 - - - +
778G MET* 3.6 38.6 - - - +
779G PRO* 5.4 0.2 - - + -
799G ASP* 1.3 75.2 - - - +
801G PHE* 1.3 66.4 + - - +
74H MET* 4.2 12.8 - - - -
136H ILE* 3.9 24.0 - - + -
137H THR* 3.6 31.9 - - + -
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Residues in contact with PHE 801 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700G ILE* 4.0 31.0 - - + -
701G LEU 2.7 14.5 + - - +
702G ALA* 3.3 8.5 - - + -
703G GLU* 2.7 34.0 + - - +
721G ILE* 4.1 8.5 - - + -
740G TYR* 3.8 35.0 - + + -
762G GLN* 3.4 26.2 - - - -
764G PHE* 5.4 1.1 - + + -
773G ILE* 3.5 44.2 - - + -
774G TYR 3.4 2.0 - - - -
775G LEU* 3.6 35.9 - - + -
799G ASP* 5.2 0.2 - - + -
800G ILE* 1.3 78.8 - - - +
802G VAL* 1.3 56.7 + - - +
803G VAL* 5.1 0.2 - - + -
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Residues in contact with VAL 802 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703G GLU* 3.6 6.3 - - - +
705G SER* 4.6 5.6 - - - -
773G ILE* 3.2 5.5 - - - -
774G TYR* 2.9 41.0 + - + +
776G HIS* 3.8 16.4 - - + +
800G ILE 4.0 0.2 + - - -
801G PHE* 1.3 74.2 - - - +
803G VAL* 1.3 72.2 + - - +
1098G LEU* 4.1 32.3 - - + +
137H THR* 3.1 38.1 - - + +
139H PRO* 4.3 6.7 - - + -
140H LEU* 4.6 8.1 - - + -
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Residues in contact with VAL 803 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702G ALA* 3.9 27.6 - - + -
703G GLU 2.8 18.6 + - - +
704G TYR* 3.7 35.4 - - + -
705G SER* 2.8 32.7 + - - -
764G PHE* 3.9 16.2 - - + -
771G ALA* 3.8 20.6 - - + -
772G PRO 3.8 4.0 - - - +
773G ILE* 4.2 7.6 - - + -
801G PHE* 4.4 0.9 - - + +
802G VAL* 1.3 77.5 - - - +
804G GLY* 1.3 71.0 + - - +
806G GLN* 5.7 0.7 - - + -
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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