Contacts of the helix formed by residues 676 - 685 (chain D) in PDB entry 2QY0
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 TYR 676 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526D HIS* 3.4 47.1 - + - -
528D ASP* 5.0 1.3 - - - -
538D GLU* 3.7 5.2 + - - -
539D GLY* 3.4 25.8 + - - -
541D ILE* 3.9 27.1 - - + -
619D ASN* 3.3 33.8 + - + +
671D THR* 3.4 26.0 - - + +
672D LYS 3.4 16.6 - - - -
673D VAL 2.7 16.5 + - - +
675D ASN* 1.3 77.4 - - - +
677D VAL* 1.3 57.0 + - - -
678D ASP 3.2 3.1 - - - -
679D TRP* 2.9 14.2 + - + +
680D ILE* 2.8 31.4 + - + +
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Residues in contact with VAL 677 (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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561D LEU* 4.4 13.0 - - + -
562D PRO* 3.4 36.8 - - + +
563D ASP* 6.1 0.2 - - - -
673D VAL* 3.5 12.3 - - + +
674D LEU* 3.5 24.8 + - + +
675D ASN 3.7 0.6 - - - -
676D TYR* 1.3 77.2 - - - +
678D ASP* 1.3 59.9 + - - +
680D ILE* 3.7 8.2 - - + +
681D LYS* 2.9 56.5 + - + +
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Residues in contact with ASP 678 (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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675D ASN 5.5 0.2 + - - -
676D TYR 3.2 0.6 - - - -
677D VAL* 1.3 76.8 - - - +
679D TRP* 1.3 62.4 + - - +
681D LYS* 3.3 14.0 + - - +
682D LYS* 2.9 30.9 + - - +
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Residues in contact with TRP 679 (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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524D SER* 3.8 27.8 - - - -
525D VAL 4.1 4.9 - - - -
526D HIS* 3.6 53.4 - + + +
527D PRO* 3.9 16.7 - - + +
541D ILE* 4.4 20.0 - - + -
542D ALA* 4.6 0.7 - - - -
543D LEU* 4.4 14.8 - - + -
676D TYR* 2.9 17.1 + - + +
678D ASP* 1.3 80.6 - - - +
680D ILE* 1.3 80.5 + - + +
682D LYS* 3.4 6.9 + - + +
683D GLU* 3.2 55.7 + - + +
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Residues in contact with ILE 680 (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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475D LEU* 4.0 9.4 - - + -
481D LEU* 4.1 13.0 - - + -
541D ILE* 4.1 17.5 - - + -
543D LEU* 4.0 10.9 - - + +
561D LEU* 3.9 38.6 - - + -
673D VAL* 4.1 10.8 - - + -
676D TYR* 2.8 29.5 + - + +
677D VAL* 3.7 5.6 - - - +
679D TRP* 1.3 90.5 - - + +
681D LYS* 1.4 63.4 + - - +
683D GLU* 3.1 4.9 + - - +
684D MET* 3.0 39.1 + - - +
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Residues in contact with LYS 681 (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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561D LEU* 4.6 16.7 - - + +
677D VAL* 2.9 43.0 + - + +
678D ASP* 3.3 12.3 + - - +
680D ILE* 1.4 76.9 - - - +
682D LYS* 1.3 57.5 + - - +
684D MET* 3.3 9.4 + - - +
685D GLU* 3.0 26.9 + - - +
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Residues in contact with LYS 682 (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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678D ASP 2.9 17.5 + - - +
679D TRP* 3.7 9.4 - - + +
681D LYS* 1.3 76.4 - - - +
683D GLU* 1.3 65.6 + - + +
685D GLU* 3.4 20.8 - - + +
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Residues in contact with GLU 683 (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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479D TRP* 3.3 19.4 - - + -
522D ARG* 3.1 25.3 + - - +
524D SER* 2.8 30.4 + - - +
543D LEU* 3.5 23.1 - - + -
679D TRP* 3.2 46.2 + - + +
680D ILE 3.1 2.1 + - - +
682D LYS* 1.3 82.3 - - - +
684D MET* 1.3 60.0 + - - +
685D GLU 3.2 3.7 + - - +
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Residues in contact with MET 684 (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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475D LEU* 4.2 22.4 - - + +
476D GLY* 4.7 0.9 - - - +
479D TRP* 3.5 58.3 + - + +
543D LEU* 4.3 4.3 - - + -
561D LEU* 5.4 3.8 - - - -
680D ILE* 3.0 32.7 + - - +
681D LYS* 3.3 9.4 + - - +
683D GLU* 1.3 76.4 - - - +
685D GLU* 1.3 64.2 + - - +
686D GLU* 3.2 12.5 + - - +
800D GOL 4.2 27.8 - - - -
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Residues in contact with GLU 685 (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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681D LYS 3.0 11.4 + - - +
682D LYS* 3.4 21.4 - - + +
683D GLU 3.2 5.2 - - - +
684D MET* 1.3 74.8 - - - +
686D GLU* 1.3 59.8 + - - +
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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