Contacts of the strand formed by residues 538 - 547 (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 TRP 538 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474X VAL* 4.1 13.9 - - + -
476X GLN* 3.4 43.3 - - + -
505X SER* 4.8 0.9 - - - -
528X ARG* 3.3 59.1 - - + +
529X GLU* 3.5 8.1 - - - -
530X CYS* 3.3 45.8 - - + -
536X GLU* 3.8 15.3 - - - +
537X TRP* 1.3 100.0 - + + +
539X ARG* 1.3 59.4 + - - +
540X LYS 4.2 0.7 + - - -
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Residues in contact with ARG 539 (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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528X ARG* 4.0 3.6 - - - -
529X GLU* 3.0 35.1 + - - +
531X THR* 3.8 19.2 - - + +
533X LEU* 5.1 8.1 - - - +
535X TRP* 6.0 1.4 - - - +
536X GLU* 2.8 38.7 + - - +
538X TRP* 1.3 73.0 - - - +
540X LYS* 1.3 77.2 + - - +
541X VAL* 3.4 4.5 + - - +
561X THR 4.4 3.1 - - - -
562X LEU* 2.7 30.5 + - - +
563X SER* 4.0 3.2 + - - +
564X PRO* 3.5 26.2 - - + +
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Residues in contact with LYS 540 (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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526X MET* 3.9 24.8 - - + +
527X ALA 3.5 7.4 - - - +
528X ARG* 4.0 6.5 - - + +
538X TRP 4.2 1.2 + - - +
539X ARG* 1.3 87.4 - - - +
541X VAL* 1.3 60.4 + - - +
542X ILE 4.4 5.2 - - - +
543X ASP* 3.0 42.4 + - + +
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Residues in contact with VAL 541 (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* 4.7 3.8 - - + +
527X ALA* 2.6 12.4 + - + +
528X ARG* 4.5 0.9 - - - -
529X GLU* 3.4 36.3 - - + +
539X ARG 3.5 5.4 - - - +
540X LYS* 1.3 73.3 - - - +
542X ILE* 1.3 69.6 + - + +
557X ILE* 4.4 14.4 - - + -
564X PRO* 3.7 16.2 - - + +
565X TYR* 3.7 18.6 - - - +
566X GLY* 3.5 32.0 + - - +
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Residues in contact with ILE 542 (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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525X ILE* 3.9 16.4 - - + +
526X MET* 3.1 6.3 - - - +
527X ALA* 2.8 34.8 + - + +
540X LYS* 4.4 0.3 - - - +
541X VAL* 1.3 87.8 + - - +
543X ASP* 1.3 67.1 + - - +
544X GLU* 4.3 3.8 - - + +
555X VAL* 3.4 26.0 - - + -
556X ASN 4.2 0.9 - - - +
557X ILE* 3.6 20.9 - - + -
566X GLY 4.0 9.6 - - - +
567X SER* 3.6 26.2 - - - +
568X ILE* 3.8 26.9 - - + -
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Residues in contact with ASP 543 (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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525X ILE 3.7 2.0 - - - +
526X MET* 3.7 13.3 - - - +
540X LYS* 3.0 44.1 + - + +
542X ILE* 1.3 75.3 - - - +
544X GLU* 1.3 64.3 + - - +
545X ARG* 3.4 25.3 + - - +
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Residues in contact with GLU 544 (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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525X ILE* 2.9 33.0 + - - +
542X ILE* 4.3 4.0 - - + -
543X ASP* 1.3 75.1 + - - +
545X ARG* 1.3 99.5 + - - +
546X ASP 3.6 12.8 + - - +
547X VAL* 3.1 15.8 - - + +
568X ILE* 3.6 23.0 - - + +
570X TYR* 4.2 14.7 + - - -
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Residues in contact with ARG 545 (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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522X ASN* 5.3 1.7 + - - -
523X ILE 4.0 2.5 - - - -
524X ARG* 3.6 21.4 - - - +
525X ILE 3.5 10.3 + - - +
543X ASP* 3.4 21.1 + - - +
544X GLU* 1.3 102.7 + - - +
546X ASP* 1.3 76.5 + - - +
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Residues in contact with ASP 546 (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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522X ASN* 4.8 15.4 + - - +
523X ILE 3.4 7.2 + - - +
524X ARG* 5.3 0.4 - - - -
544X GLU* 3.6 9.8 + - - +
545X ARG* 1.3 98.2 - - - +
547X VAL* 1.3 62.4 + - - +
548X LYS* 3.8 1.4 + - - +
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Residues in contact with VAL 547 (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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522X ASN 5.5 0.3 + - - -
523X ILE* 2.7 44.7 + - + +
525X ILE* 3.9 17.3 - - + -
544X GLU* 3.1 32.3 - - + +
546X ASP* 1.3 74.4 - - - +
548X LYS* 1.3 68.7 + - - +
549X LEU 3.8 0.2 + - - -
553X ILE* 3.7 25.8 - - + -
568X ILE* 4.2 8.3 - - + -
570X TYR* 3.6 29.2 - - + +
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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