Contacts of the strand formed by residues 568 - 573 (chain D) in PDB entry 3IYD
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 SER 568 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563D LEU 4.1 3.6 - - - +
564D VAL* 4.3 7.3 - - - +
565D ALA 2.8 28.5 + - - +
566D LYS* 3.2 8.2 + - - +
567D THR* 1.3 79.1 - - - +
569D LEU* 1.3 62.5 + - - +
570D LYS* 3.2 26.4 + - - +
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Residues in contact with LEU 569 (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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544D LEU* 5.3 9.6 - - + -
547D ARG* 6.3 0.9 - - - +
562D GLU* 3.2 33.9 - - - +
563D LEU 5.0 1.1 - - - -
568D SER* 1.3 73.6 - - - +
570D LYS* 1.3 74.4 + - - +
571D ASP* 3.5 21.8 - - - +
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Residues in contact with LYS 570 (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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562D GLU* 4.0 18.7 - - - +
563D LEU* 3.9 16.9 + - + +
565D ALA* 2.9 38.8 + - - +
568D SER* 3.2 26.2 + - - +
569D LEU* 1.3 82.0 - - - +
571D ASP* 1.3 71.7 + - - +
572D THR* 3.8 17.4 + - + +
580D TRP* 3.4 39.7 - - + -
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Residues in contact with ASP 571 (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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537D TYR 4.7 8.7 - - - +
538D ARG 4.0 12.5 - - - +
539D SER* 3.3 34.7 + - - -
540D GLY 5.5 0.2 - - - +
543D SER* 3.7 37.8 + - - +
544D LEU* 3.7 11.1 - - - +
561D GLY 4.5 1.3 - - - -
562D GLU* 5.0 0.2 - - - +
569D LEU* 3.5 16.9 - - - +
570D LYS* 1.3 84.2 - - - +
572D THR* 1.3 66.7 + - - +
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Residues in contact with THR 572 (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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543D SER* 5.0 2.4 + - - -
560D ASN* 4.2 3.6 + - - +
561D GLY 2.9 23.8 + - - +
563D LEU* 3.7 14.3 - - - +
570D LYS* 3.8 16.5 + - + +
571D ASP* 1.3 83.7 + - - +
573D THR* 1.3 67.3 + - - +
576D ARG* 3.6 26.6 - - + +
577D ALA* 4.3 11.1 - - - +
580D TRP* 5.9 4.4 - - + -
593D ASN* 6.0 6.7 - - + -
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Residues in contact with THR 573 (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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513D MET 5.2 1.3 - - - +
515D ARG 4.9 2.9 - - - +
516D ASP* 4.2 11.0 - - - +
534D GLU* 2.8 33.0 + - + +
560D ASN* 3.2 30.9 + - - +
563D LEU* 4.6 5.0 - - - +
572D THR* 1.3 80.2 + - - +
574D VAL* 1.3 70.8 + - - +
575D GLY* 3.3 15.9 - - - +
576D ARG* 3.2 31.1 + - + +
577D ALA* 3.5 10.9 + - - +
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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