Contacts of the strand formed by residues 698 - 704 (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 698 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664G ILE* 5.8 3.1 - - - +
697G GLY* 1.3 73.6 - - - +
699G LEU* 1.3 60.0 + - - +
740G TYR* 5.6 4.9 - - + +
795G ARG* 4.4 4.0 + - - +
78H LYS* 3.1 5.0 - - - -
79H THR* 2.8 53.8 + - + +
80H ILE* 4.6 8.3 - - - +
82H LYS* 3.5 28.9 + - - +
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Residues in contact with LEU 699 (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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694G GLY* 3.5 27.4 - - - +
696G ASP 4.0 2.5 - - - +
697G GLY 3.7 0.8 + - - -
698G ASP* 1.3 76.3 - - - +
700G ILE* 1.3 66.6 + - - +
740G TYR* 4.4 5.2 + - - -
784G LEU* 3.5 32.5 - - + -
795G ARG* 3.7 31.2 - - - +
796G GLU 5.8 0.4 - - - +
797G LEU* 3.5 26.5 - - + +
799G ASP* 4.8 1.9 + - - +
76H SER* 4.7 9.9 - - - -
77H LEU 3.3 6.3 - - - +
78H LYS* 3.6 29.2 - - + +
88H THR* 4.8 2.5 - - + -
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Residues in contact with ILE 700 (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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699G LEU* 1.3 78.3 - - - +
701G LEU* 1.3 65.8 + - - +
721G ILE* 4.2 7.6 - - + -
740G TYR* 3.5 43.3 - - + +
764G PHE* 4.6 6.7 - - + -
797G LEU* 3.9 2.0 - - - -
799G ASP* 3.6 13.2 - - + +
801G PHE* 4.0 24.7 - - + -
76H SER* 3.4 5.2 - - - -
77H LEU* 2.9 57.4 + - + +
79H THR* 5.5 0.7 - - + -
85H PHE* 3.6 29.4 - - + -
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Residues in contact with LEU 701 (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* 1.3 80.5 - - - +
702G ALA* 1.3 54.6 + - - +
778G MET* 3.9 34.1 - - + -
797G LEU* 3.5 36.3 - - + +
799G ASP 3.1 7.7 + - - +
800G ILE* 3.2 20.2 - - + -
801G PHE* 2.7 36.8 + - - +
17H ILE* 4.2 12.3 - - + -
74H MET* 3.9 18.6 - - + -
75H GLU 3.3 4.0 - - - +
76H SER* 3.6 20.4 - - - -
91H ILE* 4.1 9.9 - - + -
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Residues in contact with ALA 702 (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* 5.6 0.4 - - + -
701G LEU* 1.3 75.7 - - - +
703G GLU* 1.3 61.0 + - - +
704G TYR* 3.9 9.7 - - + -
764G PHE* 3.8 31.0 - - + -
801G PHE* 3.3 6.7 - - + +
803G VAL* 3.9 9.9 - - + -
74H MET* 3.1 5.8 - - - -
75H GLU* 2.8 37.3 + - + -
77H LEU* 3.9 15.5 - - + +
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Residues in contact with GLU 703 (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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701G LEU 4.3 0.2 - - - -
702G ALA* 1.3 71.5 - - - +
704G TYR* 1.3 61.1 + - - +
705G SER 3.5 1.0 + - - -
800G ILE* 4.3 7.6 - - + +
801G PHE 2.7 14.4 + - - +
802G VAL* 3.6 5.1 - - - +
803G VAL 2.8 24.4 + - - -
70H LEU* 5.6 1.4 - - - +
71H PRO* 5.9 0.3 - - - +
72H CYS* 3.7 18.2 - - + +
73H VAL 3.8 3.4 - - - +
74H MET* 3.1 27.9 - - + +
135H GLY* 3.3 6.9 - - - -
136H ILE* 2.7 25.0 + - - -
137H THR* 2.7 40.9 + - + +
140H LEU* 3.4 19.5 - - + +
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Residues in contact with TYR 704 (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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702G ALA* 3.9 11.4 - - + -
703G GLU* 1.3 70.3 - - - +
705G SER* 1.3 65.0 + - - +
706G GLU* 3.4 20.7 + - + +
709G GLY* 6.3 0.2 - - - -
712G MET* 3.8 34.3 - - + -
713G MET* 3.8 5.9 + - - +
764G PHE* 3.9 7.6 - - - -
769G PHE* 3.7 26.1 - + - -
803G VAL* 3.7 35.9 - - + -
804G GLY 5.4 1.1 - - - -
806G GLN* 4.4 9.2 - - + -
72H CYS* 3.4 23.5 - - - +
73H VAL* 2.9 29.0 + - + +
75H GLU* 2.7 42.8 + - + -
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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