Contacts of the strand formed by residues 564 - 571 (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 PRO 564 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473X TYR* 3.8 11.4 - - + -
529X GLU* 3.1 25.8 - - + +
539X ARG* 3.5 23.3 - - - +
541X VAL* 3.7 26.1 - - + +
558X SER 3.4 12.3 - - - +
559X GLY* 4.1 0.7 - - - -
560X SER 3.0 12.3 - - - +
561X THR 3.5 3.8 - - - +
563X SER* 1.3 87.5 - - - +
565X TYR* 1.3 67.6 + - - +
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Residues in contact with TYR 565 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541X VAL* 3.7 9.4 - - - -
556X ASN 4.3 0.3 - - - +
558X SER* 2.8 43.2 + - - +
559X GLY* 4.1 14.6 - - - -
563X SER* 3.9 9.2 - - - -
564X PRO* 1.3 81.7 - - + +
566X GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 566 (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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541X VAL* 3.5 15.6 + - - +
542X ILE* 3.9 13.6 - - - +
556X ASN 2.8 14.6 - - - -
557X ILE* 3.9 5.2 - - - -
565X TYR* 1.3 76.2 - - - +
567X SER* 1.3 64.7 + - - -
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Residues in contact with SER 567 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542X ILE* 3.6 5.8 - - - +
554X ASN 3.0 5.5 - - - +
556X ASN* 2.7 46.9 + - - +
566X GLY* 1.3 76.3 - - - -
568X ILE* 1.3 67.3 + - - +
569X THR* 4.9 10.0 + - - +
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Residues in contact with ILE 568 (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* 4.2 10.1 - - + -
542X ILE* 3.8 15.9 - - + -
544X GLU* 3.6 42.2 - - + +
547X VAL* 4.2 9.4 - - + -
553X ILE* 3.5 31.0 - - + -
554X ASN 3.6 4.5 - - - +
555X VAL* 4.0 17.9 - - + -
567X SER* 1.3 74.3 - - - +
569X THR* 1.3 67.2 + - - +
570X TYR* 3.9 28.3 - - + +
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Residues in contact with THR 569 (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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552X GLU 3.6 0.9 - - - +
553X ILE* 3.7 2.1 - - - -
554X ASN* 2.8 50.0 + - - +
556X ASN* 6.1 0.3 - - - -
567X SER* 4.9 13.2 - - - +
568X ILE* 1.3 80.4 - - - +
570X TYR* 1.3 69.1 + - - +
571X LYS* 4.1 2.2 - - - +
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Residues in contact with TYR 570 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544X GLU* 4.2 13.9 + - - -
547X VAL* 3.6 31.2 - - + +
548X LYS* 3.5 38.9 + - + +
550X SER* 3.1 30.5 - - - +
552X GLU 3.2 4.9 - - - -
553X ILE* 4.1 6.7 - - + -
568X ILE* 3.9 28.8 - - + +
569X THR* 1.3 79.3 - - - +
571X LYS* 1.3 64.2 + - - +
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Residues in contact with LYS 571 (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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550X SER* 4.1 2.9 - - - -
551X LYS* 3.9 15.2 + - - +
552X GLU* 3.2 53.9 + - - +
554X ASN* 4.2 10.7 + - - +
569X THR* 4.1 3.2 + - - +
570X TYR* 1.3 76.9 - - - +
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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