Contacts of the strand formed by residues 608 - 614 (chain M) in PDB entry 2O93
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 LYS 608 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606M GLU* 3.2 22.0 - - - +
607M SER* 1.3 73.7 - - - +
609M VAL* 1.3 66.6 + - - +
610M VAL* 5.5 1.8 - - + -
625M GLU* 3.7 26.6 + - - +
628M VAL* 4.7 4.9 - - - -
660M VAL* 3.1 6.8 - - - +
661M ILE* 2.8 47.5 + - + +
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Residues in contact with VAL 609 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596M MET* 5.6 0.9 - - + -
598M LEU* 4.7 5.2 - - + -
608M LYS* 1.3 81.2 - - - +
610M VAL* 1.3 63.3 + - - +
611M PHE* 4.2 24.0 - - + -
625M GLU* 3.5 6.4 - - - +
626M ALA* 2.8 38.1 + - + +
628M VAL* 4.0 10.5 - - + +
638M LEU* 4.2 15.3 - - + -
640M VAL* 3.8 35.9 - - + -
658M PHE* 4.4 14.1 - - + -
659M TYR 3.4 9.4 - - - +
660M VAL* 4.2 4.0 - - + -
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Residues in contact with VAL 610 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608M LYS* 5.5 1.6 - - + -
609M VAL* 1.3 82.5 - - - +
611M PHE* 1.3 69.2 + - - +
612M THR* 3.7 22.2 - - + -
623M GLU* 3.8 19.1 - - + +
624M MET 3.7 6.5 - - - +
625M GLU* 4.6 11.7 - - + -
658M PHE* 2.9 22.6 - - - -
659M TYR* 3.0 47.9 + - + +
661M ILE* 4.8 9.2 - - + -
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Residues in contact with PHE 611 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596M MET* 4.2 16.8 - - + -
609M VAL* 4.2 8.3 - - + -
610M VAL* 1.3 75.5 - - - +
612M THR* 1.3 60.9 + - - +
622M TRP* 3.9 17.9 - + + +
623M GLU* 3.3 2.9 - - - -
624M MET* 2.7 40.7 + - - +
626M ALA* 3.9 18.6 - - + -
640M VAL* 5.1 1.3 - - + -
642M ILE* 4.4 9.2 - - + -
643M PRO* 3.6 27.4 - - + -
656M VAL* 4.4 10.5 - - + -
657M ASN 3.1 12.6 - - - -
658M PHE* 3.8 24.9 - + + -
673M PHE* 3.8 28.5 - + + -
675M TYR* 3.8 19.1 - - - -
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Residues in contact with THR 612 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581L GLU* 3.9 12.0 + - - -
610M VAL* 3.7 19.0 + - + -
611M PHE* 1.3 80.2 - - - +
613M GLU* 1.3 64.8 + - - +
614M LYS* 4.4 2.9 - - - +
620M GLN* 3.9 24.9 + - - +
622M TRP* 3.0 15.7 - - - +
623M GLU* 4.2 5.8 - - + +
656M VAL* 3.6 2.9 - - - +
657M ASN* 2.8 46.8 + - - +
659M TYR* 4.3 17.6 - - + +
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Residues in contact with GLU 613 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582L ARG* 5.8 4.2 + - - +
612M THR* 1.3 78.4 - - - +
614M LYS* 1.3 69.1 + - - +
620M GLN* 3.7 1.6 - - - +
621M ILE* 2.8 44.0 + - + +
622M TRP* 2.9 22.9 + - + +
645M TYR* 2.6 33.4 + - - -
646M ARG* 3.4 13.7 + - - -
654M VAL* 3.9 9.3 - - - +
655M LYS 4.5 7.6 - - - +
656M VAL* 4.0 13.5 - - + +
657M ASN* 5.0 3.1 - - - +
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Residues in contact with LYS 614 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581L GLU* 3.0 45.3 + - + +
582L ARG* 2.8 27.7 + - + -
599L THR* 4.8 9.4 - - + +
600L GLY 4.7 9.7 + - - -
601L GLN* 4.9 5.2 + - - +
636L ASN* 5.6 1.8 - - - +
612M THR* 4.4 7.4 - - - +
613M GLU* 1.3 82.7 - - - +
615M THR* 1.3 64.9 + - - +
618M GLY* 3.2 27.1 + - - +
619M GLN 3.1 18.4 - - - +
620M GLN* 3.5 24.0 - - - +
621M ILE* 4.0 3.8 - - - +
657M ASN* 5.5 1.7 + - - +
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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
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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