Contacts of the strand formed by residues 675 - 680 (chain W) in PDB entry 5IY6
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 GLY 675 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488W VAL 3.3 2.2 + - - -
489W CYS* 3.4 5.5 - - - +
490W LEU 3.3 15.1 + - - +
613W HIS* 4.7 0.7 - - - -
616W ARG 3.9 10.1 - - - -
667W ALA 6.4 0.2 - - - -
668W ILE* 3.6 17.5 - - - +
674W TYR* 1.3 79.2 - - - +
676W LEU* 1.4 61.4 + - - -
677W MET* 4.3 1.0 - - - +
719W TYR* 2.8 26.3 + - - -
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Residues in contact with LEU 676 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490W LEU* 3.0 32.8 - - + +
492W PRO* 4.4 0.9 - - + -
527W MET* 6.3 0.2 - - + -
616W ARG 3.4 8.5 + - - +
617W ALA* 3.5 34.2 - - + -
618W VAL* 3.5 19.9 + - - +
619W ILE* 4.8 1.8 - - + -
667W ALA* 5.7 2.1 - - - +
675W GLY* 1.4 73.9 - - - +
677W MET* 1.3 70.0 + - - +
678W VAL* 3.7 24.7 - - + -
716W VAL* 3.7 27.4 - - + -
719W TYR* 3.9 16.2 - - + -
720W PHE* 4.0 17.7 - - + -
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Residues in contact with MET 677 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489W CYS* 4.9 2.7 - - + -
490W LEU 3.2 4.6 + - - +
491W CYS* 3.2 33.0 - - + +
492W PRO 3.1 18.9 - - - +
618W VAL* 3.5 21.1 - - + -
664W VAL* 3.5 37.5 - - + +
668W ILE* 4.0 37.5 - - + -
675W GLY 4.3 2.0 - - - +
676W LEU* 1.3 89.6 - - - +
678W VAL* 1.3 64.1 + - - +
679W PHE* 4.3 11.3 - - + -
694W PRO* 5.0 9.9 - - - -
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Residues in contact with VAL 678 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492W PRO* 3.1 37.0 - - + +
494W ILE* 3.9 42.4 - - + -
527W MET* 4.3 11.0 - - + -
618W VAL 2.9 6.2 + - - +
619W ILE* 4.0 23.8 - - + -
620W MET* 2.9 31.6 + - - +
676W LEU* 3.7 17.3 - - + -
677W MET* 1.3 76.3 - - - +
679W PHE* 1.3 65.9 + - - +
716W VAL* 5.2 0.7 - - + -
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Residues in contact with PHE 679 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491W CYS* 5.2 7.4 - - + -
492W PRO 2.9 17.9 + - - +
493W MET* 3.3 5.4 - - - +
494W ILE* 3.0 26.3 + - - -
620W MET* 3.9 36.1 - - + -
623W VAL* 4.1 16.4 - - + -
624W PRO* 5.0 0.2 - - + -
660W ALA* 4.0 14.8 - - + -
661W ALA* 6.1 0.2 - - - -
664W VAL* 4.4 19.1 - - + -
677W MET* 4.3 18.8 - - + -
678W VAL* 1.3 74.8 - - - +
680W ALA* 1.3 59.9 + - - +
681W ASP 3.8 2.4 + - - -
684W PHE* 3.7 37.9 - + + +
693W LEU* 3.8 32.1 - - + -
694W PRO* 5.6 2.0 - - + -
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Residues in contact with ALA 680 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494W ILE* 3.6 30.7 - - + +
504W ILE* 5.5 2.9 - - + -
520W TYR* 3.4 11.2 + - + -
619W ILE* 5.5 0.2 - - + -
620W MET 3.0 18.7 + - - +
621W PHE* 3.6 22.4 - - + -
622W GLY* 3.1 27.2 + - - +
623W VAL* 4.6 1.0 - - - +
679W PHE* 1.3 68.9 - - - +
681W ASP* 1.3 59.9 + - - +
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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