Contacts of the strand formed by residues 679 - 686 (chain F) in PDB entry 6BAA
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 VAL 679 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678F CYS* 1.3 79.5 + - - +
680F GLN* 1.3 60.1 + - - +
681F ILE 4.3 0.2 - - - -
702F ARG* 3.5 6.2 - - - +
703F ILE* 3.3 46.8 + - + +
704F PRO* 4.3 0.9 - - - +
738F PHE 3.2 11.9 - - - +
739F TRP* 4.5 18.1 + - + +
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Residues in contact with GLN 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678F CYS 3.5 4.5 + - - +
679F VAL* 1.3 75.0 - - - +
681F ILE* 1.3 58.3 + - - +
682F ILE* 4.2 0.4 - - - -
702F ARG* 3.5 26.2 - - - +
736F ALA 4.1 0.3 - - - +
737F VAL* 3.3 1.9 - - - -
738F PHE* 2.4 65.7 + - + +
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Residues in contact with ILE 681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679F VAL 4.3 0.4 - - - -
680F GLN* 1.3 73.7 - - - +
682F ILE* 1.3 60.4 + - - +
683F GLY 4.3 0.2 - - - -
684F GLY* 6.0 2.2 - - - +
699F ILE 5.0 4.7 - - - +
700F THR* 3.7 2.7 - - - -
701F ILE 2.9 45.5 + - - +
702F ARG* 3.6 9.0 - - - +
736F ALA 3.4 5.6 - - - +
737F VAL* 4.2 7.2 - - + +
738F PHE 5.7 0.2 - - - +
739F TRP* 5.7 7.6 - - + +
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Residues in contact with ILE 682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F ILE* 1.3 73.9 - - - +
683F GLY* 1.3 63.7 + - - +
684F GLY 3.4 2.6 + - - +
700F THR* 4.2 4.9 - - - -
702F ARG* 3.5 23.3 - - - +
735F GLY* 3.3 1.6 - - - -
736F ALA* 2.6 55.7 + - + +
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Residues in contact with GLY 683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682F ILE* 1.3 69.6 - - - +
684F GLY* 1.3 59.7 + - - +
685F PHE* 4.9 0.3 - - - +
698F ASN* 3.5 27.8 + - - -
699F ILE 3.2 8.0 + - - -
700F THR* 3.4 10.1 - - - -
734F SER* 2.9 18.9 - - - +
735F GLY* 3.2 7.0 - - - -
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Residues in contact with GLY 684 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F ILE* 6.1 2.0 - - - -
682F ILE 3.4 4.4 - - - -
683F GLY* 1.3 74.4 - - - +
685F PHE* 1.3 59.0 + - - -
686F PHE* 4.3 1.4 + - - -
696F LEU* 4.4 0.7 - - - +
697F SER* 3.7 0.9 - - - -
698F ASN 3.1 2.2 + - - -
699F ILE* 2.4 53.9 + - - +
734F SER 3.7 4.5 - - - -
735F GLY* 4.7 1.8 - - - -
736F ALA 5.2 3.4 - - - -
737F VAL* 6.6 0.2 - - - -
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Residues in contact with PHE 685 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F GLY 4.9 0.2 - - - +
684F GLY* 1.3 74.1 - - - -
686F PHE* 1.3 60.0 + - - +
694F PRO* 4.3 3.8 - - + -
696F LEU 3.2 11.9 - - - +
697F SER* 4.2 3.6 - - - +
698F ASN 4.2 8.3 - - - +
725F ALA* 5.8 0.2 - - - +
730F MET* 5.0 0.7 - - - +
731F GLN 3.2 13.9 - - - +
732F LYS* 3.2 14.0 - - - +
733F VAL* 3.6 32.5 - - + +
734F SER* 3.5 12.1 + - - +
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Residues in contact with PHE 686 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684F GLY 5.7 0.4 - - - -
685F PHE* 1.3 74.6 - - - +
687F THR* 1.3 54.9 + - - +
694F PRO* 3.2 2.6 - - - +
695F THR* 2.6 30.2 + - - -
696F LEU* 2.7 38.9 + - + +
721F SER* 5.0 5.8 - - - +
722F LEU* 6.0 0.4 - - - -
725F ALA* 3.7 30.7 - - + -
730F MET* 3.8 8.5 - - + -
731F GLN 3.9 0.9 - - - -
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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