Contacts of the strand formed by residues 760 - 765 (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 LEU 760 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723G ASN* 3.9 19.1 - - + +
724G TYR 3.4 13.0 - - - +
725G TYR* 3.7 25.8 - - + -
735G ALA* 4.4 8.5 - - + -
736G PRO* 4.4 20.9 - - + +
738G CYS* 3.8 26.7 - - - -
743G THR* 5.5 0.2 - - - +
758G GLY 3.7 3.0 + - - +
759G GLN* 1.3 80.1 + - - +
761G LEU* 1.3 68.1 + - - +
762G GLN* 3.9 19.5 - - + +
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Residues in contact with LEU 761 (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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722G LYS 3.8 0.3 - - - +
724G TYR* 2.8 43.8 + - + +
751G PHE* 3.7 27.8 - - + -
755G LEU* 4.3 13.0 - - + -
759G GLN* 4.9 5.4 - - - +
760G LEU* 1.3 80.2 - - - +
762G GLN* 1.3 74.3 + - - +
772G PRO* 4.2 7.0 - - + -
773G ILE 4.5 1.6 - - - +
774G TYR* 3.9 20.2 - - + -
1091G PHE* 3.7 29.2 - - + -
1095G ASN* 3.9 24.7 - - + +
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Residues in contact with GLN 762 (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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721G ILE* 3.9 7.5 - - + +
722G LYS 3.5 4.0 - - - -
723G ASN* 2.9 27.0 + - - +
738G CYS* 3.6 15.3 - - - +
740G TYR* 3.1 25.5 + - - +
760G LEU* 3.9 16.3 - - + +
761G LEU* 1.3 78.7 - - - +
763G ALA* 1.3 65.4 + - - +
772G PRO* 3.4 4.5 - - - +
773G ILE* 2.9 41.8 + - + +
775G LEU* 4.2 13.2 + - - +
801G PHE* 3.4 22.1 - - - -
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Residues in contact with ALA 763 (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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721G ILE* 3.2 5.9 - - - +
722G LYS* 2.8 32.9 + - - +
724G TYR* 3.9 18.2 - - + -
751G PHE* 3.8 25.4 - - + -
762G GLN* 1.3 79.2 - - - +
764G PHE* 1.3 66.2 + - - +
770G ARG* 4.6 1.3 - - + -
771G ALA 3.1 14.8 - - - +
773G ILE* 3.7 9.5 - - - +
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Residues in contact with PHE 764 (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* 4.6 9.0 - - + -
702G ALA* 3.8 29.8 - - + -
704G TYR* 3.9 19.5 - - - -
713G MET* 5.3 0.4 - - + -
719G THR* 3.9 26.2 - - + +
720G LYS 3.4 12.1 - - - -
721G ILE* 3.6 27.1 - - + -
763G ALA* 1.3 73.7 - - - +
765G GLU* 1.3 60.3 + - - +
769G PHE* 4.1 19.1 - + + -
770G ARG* 3.2 8.5 - - - +
771G ALA* 2.8 32.7 + - + +
773G ILE* 3.8 20.7 - - + +
801G PHE* 5.4 1.6 - - + -
803G VAL* 3.9 14.1 - - + -
75H GLU* 4.9 0.7 - - - -
77H LEU* 4.3 15.3 - - + -
85H PHE* 5.3 1.1 - + - -
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Residues in contact with GLU 765 (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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610G ILE* 3.9 2.8 - - - +
719G THR* 3.6 0.4 + - - -
720G LYS* 2.9 37.2 + - + +
722G LYS* 3.9 34.5 - - + +
724G TYR* 2.5 29.1 + - - -
764G PHE* 1.3 74.2 - - - +
766G ASN* 1.3 64.9 + - - +
769G PHE 3.9 2.7 - - - -
770G ARG* 2.7 48.3 + - - +
809G LEU* 4.3 7.6 - - - +
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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