Contacts of the strand formed by residues 563 - 570 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C TYR* 4.0 5.8 + - - -
556E GLN* 3.9 1.0 - - - +
557E SER* 3.0 25.5 + - - -
560E ARG* 3.0 31.7 + - + +
561E ARG 3.3 12.2 - - - +
562E GLY* 1.3 83.2 - - - +
564E CYS* 1.3 71.6 + - - +
565E VAL* 6.1 0.3 - - - +
578E ARG* 2.8 51.8 + - - +
579E LEU 3.1 13.0 - - - +
580E SER* 4.7 11.6 + - - +
588E ARG* 5.8 1.2 + - - -
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Residues in contact with CYS 564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E LEU* 4.6 2.5 - - - -
528E PHE* 4.4 12.1 - - - -
554E VAL* 4.1 12.8 - - + -
555E ARG 3.0 14.8 - - - +
556E GLN* 4.0 19.3 - - - -
557E SER 4.0 0.9 - - - +
563E GLU* 1.3 81.7 - - - +
565E VAL* 1.3 72.4 + - - +
578E ARG* 3.8 0.9 - - - -
579E LEU* 2.9 39.7 + - + +
581E LEU* 3.7 27.1 - - + +
597E ILE* 5.1 0.2 - - + -
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Residues in contact with VAL 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554E VAL* 3.4 4.7 - - - -
555E ARG* 2.6 81.3 + - + +
557E SER* 5.0 9.9 - - - -
560E ARG* 6.2 0.4 - - - +
563E GLU* 6.0 0.7 - - + +
564E CYS* 1.3 80.9 - - - +
566E LEU* 1.3 66.2 + - - +
567E THR* 3.4 11.2 + - - +
576E HIS* 4.0 4.9 - - + -
577E LEU 3.4 20.4 - - - +
578E ARG* 4.6 5.4 - - + -
579E LEU* 4.3 4.0 - - - -
813K PTR 4.1 20.2 - - + +
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Residues in contact with LEU 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E PHE* 3.7 34.8 - - + -
553E LEU 3.6 7.0 - - - +
554E VAL* 3.9 6.3 - - + +
565E VAL* 1.3 71.5 - - - +
567E THR* 1.3 59.2 + - - +
568E PHE* 3.7 19.5 - - + -
577E LEU* 2.8 55.6 + - + +
579E LEU* 3.9 17.9 - - + +
600E MET* 4.6 12.8 - - + -
601E LEU* 3.8 16.4 - - + -
604E PHE* 4.6 1.1 - - + -
609E ILE* 4.4 6.7 - - + -
621E LEU* 4.3 18.6 - - + -
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Residues in contact with THR 567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E ALA 3.9 13.2 - - - +
538E ALA* 4.5 0.4 - - - -
541E VAL* 3.6 27.4 - - + +
552E PHE* 3.2 2.8 - - - +
553E LEU* 3.0 45.3 + - - -
555E ARG* 3.1 19.9 + - - -
565E VAL* 3.4 2.9 + - - +
566E LEU* 1.3 72.5 - - - +
568E PHE* 1.3 62.2 + - - +
575E LYS 3.3 13.2 - - - +
576E HIS* 2.8 31.3 + - + -
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Residues in contact with PHE 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541E VAL* 4.1 7.3 - - - +
550E GLY 5.4 0.9 - - - -
551E VAL 3.1 13.2 - - - +
552E PHE* 3.8 11.9 - - + -
566E LEU* 3.7 25.4 - - + -
567E THR* 1.3 75.0 - - - +
569E ASN* 1.3 72.1 + - - +
570E PHE* 4.0 9.6 - - + -
573E LYS 3.6 0.3 - - - +
574E ALA* 3.6 2.3 - - - -
575E LYS* 2.8 64.0 + - + -
576E HIS 4.7 0.4 - - - -
577E LEU* 4.4 15.0 - - + -
609E ILE* 4.0 17.5 - - + -
611E LEU* 3.8 33.0 - - + -
619E VAL* 4.2 17.9 - - + -
621E LEU* 4.7 5.8 - - + -
814K GLU* 4.7 1.1 - - + -
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Residues in contact with ASN 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541E VAL* 2.7 31.2 + - - +
542E LEU* 3.7 18.2 - - - +
545E GLY 3.3 18.6 + - - +
548E SER* 3.2 23.8 - - - +
549E HIS* 3.6 10.0 + - - -
550E GLY* 2.9 26.2 + - - -
551E VAL* 2.8 12.6 + - + +
568E PHE* 1.3 77.1 - - - +
570E PHE* 1.3 59.5 + - - +
572E GLY* 3.0 24.6 + - - -
573E LYS 3.6 4.5 - - - -
619E VAL* 4.2 1.2 - - - +
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Residues in contact with PHE 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E HIS* 3.6 12.8 - + - -
568E PHE* 3.8 4.0 + - + -
569E ASN* 1.3 72.7 + - - +
571E GLN* 1.3 68.5 - - + +
572E GLY 3.0 0.2 - - - -
573E LYS* 2.7 39.2 + - + +
575E LYS* 3.5 39.7 - - + -
611E LEU* 4.1 11.0 - - + -
614E GLY* 3.7 22.2 - - - -
617E SER* 3.4 40.8 - - - -
618E ASP 4.2 0.7 - - - -
619E VAL* 3.5 34.3 - - + -
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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