Contacts of the strand formed by residues 563 - 570 (chain D) in PDB entry 2HDX
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 GLU 563 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D GLN* 4.1 0.3 - - - -
557D SER* 3.0 33.0 + - - -
560D ARG* 3.3 41.4 + - + +
561D ARG 3.2 2.4 - - - +
562D GLY* 1.3 81.2 - - - +
564D CYS* 1.3 79.9 + - - +
565D VAL* 4.1 11.4 - - - +
578D ARG* 2.5 46.6 + - + +
579D LEU 3.4 8.3 - - - +
580D SER* 5.4 1.3 - - - -
581D LEU* 5.4 0.4 - - - -
624F TYR* 4.1 4.7 + - - -
813J PTR 4.2 1.4 - - - +
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Residues in contact with CYS 564 (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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522D LEU* 4.7 2.9 - - - -
528D PHE* 4.5 8.5 - - - -
554D VAL* 4.5 2.9 - - + -
555D ARG 3.2 14.4 - - - +
556D GLN* 4.0 20.0 - - - -
557D SER 4.2 0.9 - - - +
563D GLU* 1.3 80.0 - - - +
565D VAL* 1.3 64.8 + - - +
578D ARG 3.7 0.2 - - - -
579D LEU* 2.7 53.0 + - + +
581D LEU* 3.9 22.4 - - + +
597D ILE* 4.3 12.3 - - + -
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Residues in contact with VAL 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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554D VAL* 3.4 4.5 - - - +
555D ARG* 2.7 84.7 + - + +
557D SER* 4.9 5.8 - - - -
563D GLU* 4.1 12.3 - - + +
564D CYS* 1.3 81.4 - - - +
566D LEU* 1.3 62.8 + - - +
567D THR* 3.7 4.9 + - - +
576D HIS* 3.9 18.8 - - + -
577D LEU 3.5 11.2 - - - +
578D ARG* 5.0 1.1 - - - -
579D LEU* 4.0 4.5 - - - -
813J PTR 4.1 21.3 - - + +
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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
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552D PHE* 3.7 35.4 - - + -
553D LEU 3.6 6.1 - - - +
554D VAL* 4.2 4.3 - - + +
565D VAL* 1.3 70.3 - - - +
567D THR* 1.3 59.7 + - - +
568D PHE* 3.6 20.6 - - + -
577D LEU* 2.8 59.3 + - + +
579D LEU* 3.9 16.7 - - + +
600D MET* 4.3 15.9 - - + -
601D LEU* 3.9 16.6 - - + -
604D PHE* 4.6 1.3 - - + -
609D ILE* 4.4 7.9 - - + -
621D LEU* 4.3 12.1 - - + -
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Residues in contact with THR 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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537D ALA* 3.8 24.0 - - + +
538D ALA* 4.1 0.7 - - - +
541D VAL* 3.7 12.2 - - + +
552D PHE* 3.0 4.0 - - - +
553D LEU* 2.9 45.9 + - - -
555D ARG* 2.8 31.2 + - - -
565D VAL* 3.7 1.0 + - - +
566D LEU* 1.3 72.7 - - - +
568D PHE* 1.3 63.2 + - - +
574D ALA* 5.1 0.7 - - + -
575D LYS 3.4 6.1 - - - +
576D HIS* 3.2 30.6 + - + -
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Residues in contact with PHE 568 (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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541D VAL* 3.9 7.9 - - - -
550D GLY* 5.3 1.3 - - - -
551D VAL 3.1 13.7 - - - +
552D PHE* 3.6 11.9 - - + -
566D LEU* 3.6 26.0 - - + -
567D THR* 1.3 76.0 - - - +
569D ASN* 1.3 70.9 + - - +
570D PHE* 3.7 9.8 + - + -
573D LYS 3.5 1.4 - - - +
574D ALA* 3.6 2.1 - - - -
575D LYS* 2.8 70.3 + - + -
577D LEU* 4.2 16.8 - - + -
609D ILE* 3.9 29.2 - - + -
611D LEU* 4.1 20.0 - - + -
619D VAL* 4.3 16.2 - - + -
621D LEU* 4.6 4.9 - - + -
814J GLU* 4.8 1.3 - - + -
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Residues in contact with ASN 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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541D VAL* 3.0 31.9 + - - +
542D LEU* 3.7 17.1 - - - +
545D GLY 3.1 23.7 + - - +
548D SER* 3.3 22.4 - - - +
549D HIS* 3.2 12.0 + - - -
550D GLY* 2.8 28.9 + - - -
551D VAL 2.7 11.7 + - - +
568D PHE* 1.3 74.3 - - - +
570D PHE* 1.3 59.7 + - - +
572D GLY* 3.1 21.1 + - - -
573D LYS 3.4 4.7 - - - -
619D VAL* 4.4 1.2 - - - +
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Residues in contact with PHE 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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549D HIS* 3.7 9.4 - + - -
568D PHE* 3.7 4.9 + - + -
569D ASN* 1.3 72.7 + - - +
571D GLN* 1.3 69.6 + - + +
572D GLY 3.0 0.9 - - - -
573D LYS* 2.7 38.3 + - + +
575D LYS* 3.5 43.1 - - + -
611D LEU* 4.0 14.6 - - + -
613D SER 4.9 8.7 - - - -
617D SER* 3.4 36.1 - - - -
619D VAL* 3.6 36.1 - - + -
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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