Contacts of the strand formed by residues 563 - 567 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D PHE 2.7 30.7 + - - -
241D ALA 2.6 24.5 + - - +
243D ILE* 3.4 39.3 - - + +
479D TYR* 3.9 22.9 - - + -
519D PHE 3.0 13.7 + - - +
520D VAL* 4.1 11.7 - - + -
521D LEU* 2.6 35.9 + - - +
562D GLY* 1.3 74.9 - - - +
564D LYS* 1.3 60.8 + - - +
610D TYR* 3.7 9.8 + - - +
617D HIS 3.3 7.5 + - - -
620D ASP* 3.1 21.5 + - - +
621D PHE* 4.1 9.6 - - + -
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Residues in contact with LYS 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ILE 2.8 13.9 + - - +
244D SER* 3.1 9.9 - - - +
245D ILE* 2.5 35.8 + - - +
520D VAL* 4.4 2.0 - - - -
521D LEU* 3.8 5.5 - - + +
557D MET* 3.1 31.9 + - + +
558D TRP* 3.4 50.8 - - + +
559D ALA 4.7 0.2 - - - -
560D PHE 2.7 22.8 + - - -
562D GLY 2.5 26.6 + - - +
563D LYS* 1.3 76.8 - - - +
565D LEU* 1.3 55.0 + - - +
610D TYR* 3.5 35.0 - - + -
616D MET 5.0 1.1 + - - -
620D ASP* 5.3 0.8 + - - -
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Residues in contact with LEU 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ILE* 3.2 22.0 - - + +
247D GLU* 4.1 21.8 - - + +
285D GLU* 3.5 29.4 - - - +
481D TRP* 3.5 29.2 - - + +
520D VAL* 3.8 13.5 - - + -
521D LEU 3.1 11.5 + - - +
522D PRO* 4.1 7.2 - - + -
523D LEU 3.0 42.9 + - - +
524D SER* 4.2 3.4 - - - -
557D MET* 3.6 6.5 - - - +
558D TRP* 5.7 0.4 - - - -
564D LYS* 1.3 76.4 - - - +
566D LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE 2.8 10.7 + - - +
246D TYR* 3.6 9.8 - - + -
247D GLU* 3.0 21.8 + - - -
281D PHE* 4.4 9.9 - - + -
523D LEU* 3.6 33.4 - - + -
554D TYR* 4.0 9.4 - - + +
557D MET* 4.8 0.4 - - + -
558D TRP* 3.8 29.4 - - + -
565D LEU* 1.3 75.1 - - - +
567D PHE* 1.3 63.9 + - - +
570D ASN* 3.5 23.6 - - + +
571D GLU* 3.9 32.8 - - + +
603D VAL* 4.1 15.3 - - + -
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Residues in contact with PHE 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D TYR* 4.6 0.4 - - - -
247D GLU* 3.1 41.2 - - - +
248D VAL 4.6 0.7 - - - -
249D HIS* 4.4 10.5 - - + -
287D LEU* 4.6 1.6 - - + -
523D LEU 2.8 18.2 + - - +
524D SER 3.6 6.1 - - - -
525D HIS* 3.3 24.2 - + + -
528D VAL* 3.7 11.2 - - + -
566D LEU* 1.3 73.9 - - - +
568D MET* 1.3 109.8 + - + +
570D ASN* 3.0 28.2 + - - +
571D GLU* 3.9 1.6 - - - +
578D TRP* 3.3 58.8 - + + -
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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