Contacts of the strand formed by residues 610 - 615 (chain B) in PDB entry 3I8E
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 ALA 610 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B ALA* 3.8 2.3 - - - +
606B LEU* 3.0 32.4 + - + -
608B ASP* 3.3 24.8 + - - +
609B GLY* 1.3 81.9 - - - +
611B LEU* 1.3 61.9 + - - +
612B PHE* 5.4 0.2 - - + -
628B LYS* 4.1 18.6 - - + -
629B VAL 3.4 19.5 - - - +
630B THR* 4.1 11.3 + - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 4.5 15.3 - - + -
604B CYS 3.4 13.9 - - - +
605B ALA* 4.4 6.1 - - + +
609B GLY 4.8 2.2 - - - +
610B ALA* 1.3 77.4 - - - +
612B PHE* 1.3 88.6 + - - +
613B TYR* 4.2 4.3 - - + +
629B VAL* 3.3 48.0 + - + +
631B LEU* 4.5 20.6 - - + -
636B THR* 5.2 1.6 - - + +
638B LEU* 3.9 37.9 - - + -
659B ILE* 5.0 3.8 - - + -
668B PHE* 4.2 14.8 - - + -
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Residues in contact with PHE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LEU* 3.7 36.1 - - + -
583B GLY 5.6 4.5 - - - -
602B LEU 4.2 0.5 - - - +
603B LEU* 3.8 2.9 - - - -
604B CYS* 3.0 35.9 + - + +
606B LEU* 3.5 38.4 - - + -
610B ALA* 5.4 0.2 - - + -
611B LEU* 1.3 89.8 - - - +
613B TYR* 1.3 60.8 + - - +
614B PHE* 3.7 23.3 + + + -
626B ARG* 4.5 21.1 - - + -
627B LYS 3.5 16.4 - - - +
628B LYS* 3.4 41.3 - - + -
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Residues in contact with TYR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU 4.1 2.0 - - - -
603B LEU* 5.0 11.0 - - + +
611B LEU* 4.4 14.6 - - + -
612B PHE* 1.3 76.4 - - - +
614B PHE* 1.3 58.2 + - - +
625B ASP* 2.7 37.0 - - + +
626B ARG* 4.1 3.3 - - - -
627B LYS* 3.3 60.0 + - + +
629B VAL* 3.6 30.2 - - + +
666B LEU* 6.5 1.3 - - + -
668B PHE* 4.6 11.2 - + + -
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Residues in contact with PHE 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ALA* 5.8 3.4 - - + -
580B GLU* 3.5 35.9 - - + -
582B LEU* 4.4 6.5 - - + -
601B TYR* 3.8 9.7 - - - +
602B LEU* 3.0 56.6 + - + +
603B LEU* 5.6 0.4 - - - +
604B CYS* 5.5 7.0 - - + -
612B PHE* 3.7 26.7 - - + -
613B TYR* 1.3 75.0 - - - +
615B GLY* 1.3 59.0 - - - +
623B LEU* 3.6 20.0 - - + -
624B SER 4.2 0.4 - - - +
625B ASP* 2.9 29.2 - - - -
626B ARG* 3.5 35.0 - - + -
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Residues in contact with GLY 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B HIS 4.0 7.4 - - - -
601B TYR* 6.3 0.2 - - - -
614B PHE* 1.3 77.4 - - - +
616B LEU* 1.3 59.5 + - - -
617B ASN* 5.4 1.1 - - - -
622B LEU 3.0 14.0 - - - +
623B LEU* 3.5 1.2 - - - -
624B SER* 2.7 44.9 + - - +
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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