Contacts of the strand formed by residues 520 - 530 (chain X) in PDB entry 4HSC
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 520 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481X TRP* 3.4 27.4 + - - -
482X ASP 3.3 4.9 + - - -
483X GLU* 4.2 4.3 - - - +
484X ILE* 5.3 0.4 - - - +
516X LEU* 3.7 10.7 - - - -
517X GLY* 2.7 36.3 + - - -
518X ALA 3.1 4.8 - - - +
519X ASN* 1.3 78.3 - - - +
521X ARG* 1.3 60.2 + - - +
523X ILE* 4.9 3.8 - - - +
549X LEU* 3.8 22.8 - - - +
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Residues in contact with ARG 521 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481X TRP* 3.7 1.7 - - - +
482X ASP* 2.7 45.3 + - + +
484X ILE* 3.2 56.0 - - + +
486X TYR* 5.3 1.0 + - - -
492X GLU* 3.3 32.7 + - - -
494X ILE* 3.9 10.7 - - - +
519X ASN 3.9 0.4 + - - -
520X SER* 1.3 75.8 - - - +
522X ASN* 1.3 86.4 + - + +
523X ILE* 3.4 5.8 - - - -
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Residues in contact with ASN 522 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481X TRP* 3.4 2.1 - - - -
482X ASP* 2.8 25.0 - - - +
521X ARG* 1.3 92.9 - - + +
523X ILE* 1.3 61.1 + - - +
524X ARG* 3.0 49.5 + - - +
545X ARG 5.3 2.2 + - - -
546X ASP* 4.8 15.0 + - - +
547X VAL 5.5 0.4 + - - -
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Residues in contact with ILE 523 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465X ILE* 5.2 2.9 - - + -
479X ILE* 5.6 1.6 - - + -
480X LEU 3.4 8.1 - - - +
481X TRP* 3.9 12.1 - - + -
516X LEU* 3.7 32.3 - - + -
520X SER* 4.9 5.2 - - - +
521X ARG* 4.2 10.1 - - - +
522X ASN* 1.3 75.9 - - - +
524X ARG* 1.3 62.0 + - - +
525X ILE* 4.4 13.0 - - + -
546X ASP* 3.4 7.7 - - - +
547X VAL* 2.7 69.1 + - + +
548X LYS 4.3 0.7 - - - -
549X LEU* 3.9 30.7 - - + +
553X ILE* 4.5 2.7 - - + -
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Residues in contact with ARG 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478X GLU 3.7 2.0 - - - +
479X ILE* 3.3 4.2 - - - +
480X LEU* 2.7 73.9 + - + +
481X TRP* 3.5 24.2 + - - +
482X ASP* 3.9 7.3 + - - -
497X ARG 5.3 0.2 + - - -
522X ASN* 3.0 50.6 + - - +
523X ILE* 1.3 74.8 - - - +
525X ILE* 1.3 65.4 + - - +
545X ARG* 3.6 28.0 - - - +
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Residues in contact with ILE 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465X ILE* 4.0 14.6 - - + -
477X TYR* 5.4 2.2 - - + -
478X GLU 3.6 2.9 - - - -
479X ILE* 4.3 23.1 - - + -
523X ILE* 4.4 7.9 - - + -
524X ARG* 1.3 80.2 - - - +
526X MET* 1.3 66.0 + - - +
527X ALA 5.2 0.2 - - - +
542X ILE* 3.9 6.3 - - + +
543X ASP* 3.7 1.1 - - - +
544X GLU 2.9 42.2 + - - +
545X ARG 3.5 0.2 - - - +
547X VAL* 3.9 20.9 - - + -
553X ILE* 4.1 11.4 - - + -
555X VAL* 3.8 45.5 - - + -
568X ILE* 4.2 8.3 - - + -
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Residues in contact with MET 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477X TYR* 3.0 10.2 - - - +
478X GLU* 2.8 63.1 + - + +
503X TRP* 3.6 35.7 - - + -
525X ILE* 1.3 79.1 - - - +
527X ALA* 1.3 77.1 + - - +
528X ARG* 3.8 17.5 - - + +
540X LYS* 3.9 26.0 - - + +
542X ILE 3.1 11.7 - - - +
543X ASP* 3.7 17.9 - - - +
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Residues in contact with ALA 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476X GLN 3.4 5.6 - - - +
477X TYR* 3.5 28.7 - - + -
526X MET* 1.3 76.9 - - - +
528X ARG* 1.3 55.0 + - - +
540X LYS* 3.5 1.4 - - - -
541X VAL* 2.6 33.9 + - + -
542X ILE* 2.8 23.9 + - + +
555X VAL* 5.4 0.9 - - + -
557X ILE* 4.0 24.7 - - + -
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Residues in contact with ARG 528 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475X ALA* 3.2 5.9 - - - +
476X GLN* 2.7 69.4 + - + +
503X TRP* 3.4 27.2 - - - -
526X MET* 3.8 15.5 - - + -
527X ALA* 1.3 75.2 - - - +
529X GLU* 1.3 60.0 + - - +
538X TRP* 3.3 55.9 - - + +
539X ARG 3.2 15.5 - - - +
540X LYS* 4.0 8.7 - - + +
541X VAL* 4.2 1.8 - - - +
557X ILE* 6.2 0.4 - - - -
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Residues in contact with GLU 529 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473X TYR* 3.2 35.5 - - + +
474X VAL 3.2 4.9 - - - -
528X ARG* 1.3 74.3 - - - +
530X CYS* 1.3 75.5 + - - +
531X THR* 3.4 9.7 + - - +
538X TRP* 3.5 4.9 - - - -
539X ARG* 3.0 33.2 + - + +
541X VAL* 3.4 22.4 - - + -
561X THR* 2.5 42.5 - - - +
564X PRO* 3.1 18.4 - - + +
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Residues in contact with CYS 530 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473X TYR* 4.3 3.3 - - - +
474X VAL* 3.1 21.3 + - + +
529X GLU* 1.3 76.8 - - - +
531X THR* 1.3 61.6 + - - +
532X GLY* 3.5 10.4 + - - -
537X TRP* 3.3 46.4 - - - -
538X TRP* 3.3 26.3 - - + -
561X THR* 3.7 10.6 - - - +
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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