Contacts of the strand formed by residues 563 - 567 (chain C) in PDB entry 1M7X
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 563 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C PHE 2.5 31.9 + - - -
241C ALA 3.0 18.0 + - - -
243C ILE* 3.4 30.5 - - + +
479C TYR* 3.9 26.5 - - + -
519C PHE 3.3 8.1 + - - +
520C VAL* 4.1 13.0 - - + -
521C LEU* 2.5 36.0 + - - +
562C GLY* 1.3 74.7 - - - -
564C LYS* 1.3 58.5 + - - +
610C TYR* 3.8 10.0 + - - +
617C HIS 3.2 9.5 + - - -
620C ASP* 2.9 23.5 + - - +
621C PHE* 3.6 14.6 - - + -
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Residues in contact with LYS 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE 2.8 14.3 + - - +
244C SER* 4.1 14.6 - - - +
245C ILE* 2.7 34.1 + - - +
520C VAL* 4.1 1.6 - - - -
521C LEU* 3.7 6.0 - - + +
557C MET* 3.0 36.6 + - + +
558C TRP* 3.1 49.6 + - + +
560C PHE 3.1 11.5 + - - -
562C GLY 2.7 21.5 + - - -
563C LYS* 1.3 74.2 - - - +
565C LEU* 1.3 59.8 + - - +
610C TYR* 3.4 37.7 - - + -
620C ASP* 5.6 0.2 + - - -
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Residues in contact with LEU 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 3.2 28.9 - - + +
247C GLU* 4.1 15.0 - - + +
285C GLU* 3.3 32.5 - - + +
481C TRP* 3.6 21.8 - - + +
520C VAL* 3.8 13.0 - - + -
521C LEU 3.2 8.9 + - - +
522C PRO* 4.2 5.8 - - + -
523C LEU* 3.1 30.6 + - - +
524C SER* 4.1 22.2 - - - +
557C MET* 4.1 2.9 - - - +
564C LYS* 1.3 79.4 - - - +
566C LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE 2.7 11.3 + - - +
246C TYR* 3.5 12.4 - - - -
247C GLU* 3.0 19.7 + - - -
281C PHE* 4.3 11.4 - - + -
523C LEU* 3.6 34.5 - - + -
554C TYR* 4.1 8.1 - - + +
557C MET* 4.6 0.7 - - + -
558C TRP* 3.9 27.4 - - + -
565C LEU* 1.3 73.7 - - - +
567C PHE* 1.3 63.4 + - - +
570C ASN* 3.6 25.4 - - + +
571C GLU* 4.0 24.7 - - + +
603C VAL* 4.0 23.6 - - + -
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Residues in contact with PHE 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C TYR* 4.5 0.7 - - - -
247C GLU* 3.2 39.8 + - + +
249C HIS 4.2 1.3 - - - -
287C LEU* 4.2 15.9 - - + -
523C LEU 3.1 23.1 + - - +
524C SER 3.6 2.9 - - - -
525C HIS* 3.5 31.9 - - + -
528C VAL* 4.1 9.9 - - + -
565C LEU 4.2 0.2 - - - -
566C LEU* 1.3 73.1 - - - +
568C MET* 1.3 111.4 + - + +
570C ASN* 3.1 26.2 + - - +
571C GLU* 3.9 2.1 - - - +
578C TRP* 3.5 46.7 - + + -
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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