Contacts of the strand formed by residues 595 - 601 (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 GLN 595 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584M ASP* 4.7 3.3 - - - +
585M THR* 4.4 5.8 + - - -
594M GLN* 1.3 76.6 - - - +
596M MET* 1.3 63.5 + - - +
597M ILE* 3.7 17.1 + - - +
629M ASP* 5.0 4.6 + - + +
632M LYS* 4.4 13.9 - - - +
639M PHE* 3.3 32.4 - - + +
640M VAL 3.1 19.1 - - - +
641M GLU* 4.5 2.2 - - + +
642M ILE* 5.0 0.9 - - - -
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Residues in contact with MET 596 (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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583M GLN* 4.4 1.3 - - - +
584M ASP* 3.5 12.1 - - - +
585M THR* 3.7 33.2 - - - +
594M GLN 4.1 1.6 + - - -
595M GLN* 1.3 73.9 - - - +
597M ILE* 1.3 66.7 + - - +
598M LEU* 3.7 35.7 - - + -
609M VAL* 5.6 0.4 - - + -
611M PHE* 4.2 22.2 - - + -
638M LEU 3.4 2.3 - - - +
639M PHE* 3.6 1.4 - - - -
640M VAL* 2.8 46.3 + - + +
642M ILE* 3.9 15.5 - - + +
658M PHE* 3.8 22.9 - - + -
673M PHE* 4.1 10.1 - - - -
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Residues in contact with ILE 597 (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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582M ARG 4.0 0.2 - - - +
583M GLN* 3.7 1.7 - - - -
584M ASP* 2.8 52.2 + - + +
595M GLN* 3.7 16.6 - - - +
596M MET* 1.3 75.2 - - - +
598M LEU* 1.3 68.3 + - - +
599M THR* 4.6 3.1 + - - +
637M MET* 3.4 33.2 - - + -
638M LEU 3.1 7.6 - - - +
639M PHE* 3.3 37.2 - - + -
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Residues in contact with LEU 598 (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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580M VAL* 4.3 11.7 - - + -
582M ARG 3.4 2.9 - - - +
583M GLN* 3.9 16.8 - - + -
596M MET* 3.7 28.7 - - + -
597M ILE* 1.3 76.1 - - - +
599M THR* 1.3 61.8 + - - +
603M PHE* 4.1 6.7 - - + -
609M VAL* 4.7 4.9 - - + -
637M MET* 3.2 6.6 - - - +
638M LEU* 2.8 47.0 + - + +
640M VAL* 4.2 21.3 - - + -
658M PHE* 3.7 29.2 - - + -
660M VAL* 4.2 20.2 - - + -
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Residues in contact with THR 599 (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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580M VAL* 4.8 0.4 - - - -
581M GLU* 2.8 28.7 + - + +
582M ARG* 2.8 36.1 + - + +
597M ILE* 4.6 3.3 + - - +
598M LEU* 1.3 76.4 + - - +
600M GLY* 1.3 63.7 + - - +
603M PHE* 3.9 1.6 - - - -
636M ASN* 3.2 14.4 - - + +
637M MET* 4.2 19.7 - - + +
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Residues in contact with GLY 600 (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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579M MET 2.9 16.8 - - - -
581M GLU* 3.7 8.8 - - - +
599M THR* 1.3 75.8 - - - +
601M GLN* 1.3 71.6 + - - +
603M PHE* 3.2 12.4 - - - -
636M ASN* 2.8 32.1 + - - +
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Residues in contact with GLN 601 (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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578M PRO* 3.4 1.7 - - - +
579M MET* 3.1 50.6 + - + +
581M GLU* 3.4 18.2 + - - +
600M GLY* 1.3 78.3 - - - +
602M ASN* 1.3 82.6 + - - +
603M PHE* 3.3 8.1 + - - -
635M PRO 3.9 3.8 - - - -
636M ASN* 4.8 1.1 - - + +
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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