Contacts of the strand formed by residues 663 - 668 (chain A) in PDB entry 5HQG
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 663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659A SER* 3.0 29.4 + - - -
661A ASN* 2.9 34.3 + - - -
662A ASN* 1.3 76.8 + - - +
664A LEU* 1.3 60.0 + - - +
665A TYR* 4.0 2.2 - - - -
677A THR* 3.8 18.3 - - - +
678A PHE 3.1 13.2 - - - -
679A LYS* 3.6 15.6 - - - +
680A PHE 4.4 0.2 - - - +
700A VAL* 3.1 13.7 - - - +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ALA* 4.3 2.7 - - + -
657A CYS 3.3 32.3 - - - +
658A GLY* 4.0 4.5 - - - +
663A SER* 1.3 74.6 - - - +
665A TYR* 1.3 65.4 + - - +
666A LEU* 6.1 2.0 - - + -
676A LEU* 5.6 0.3 - - - +
677A THR* 3.3 8.3 - - - +
678A PHE* 2.7 44.2 + - + +
680A PHE* 4.7 6.7 - - + -
700A VAL* 3.9 11.4 - - + +
703A VAL* 4.1 22.7 - - + -
716A LEU* 3.9 31.4 - - + -
718A ALA* 4.0 12.8 - - + -
728A LEU* 4.1 9.4 - - + -
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Residues in contact with TYR 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A GLY* 3.5 26.2 + - - -
639A HIS* 3.7 14.8 - - + -
640A ILE* 4.3 2.8 - - - +
655A ILE 3.9 0.3 - - - +
656A ALA* 3.2 6.1 - - - +
657A CYS* 2.9 36.5 + - - +
659A SER* 3.3 36.8 - - - -
661A ASN* 3.0 25.8 + - - -
663A SER* 4.0 7.9 - - - -
664A LEU* 1.3 81.1 - - - +
666A LEU* 1.3 59.6 + - - +
667A TYR* 4.1 18.2 - - + -
674A THR* 3.5 22.4 - - + -
676A LEU 3.8 1.6 - - - -
677A THR* 3.4 27.3 - - + +
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 4.7 5.4 - - + -
654A TYR* 4.1 9.0 - - + -
655A ILE 3.4 15.7 - - - +
656A ALA* 4.1 5.6 - - + -
664A LEU* 6.1 1.6 - - + -
665A TYR* 1.3 73.7 - - - +
667A TYR* 1.3 67.9 + - - +
674A THR* 3.8 2.1 - - - +
675A LEU* 2.8 43.5 + - + +
676A LEU* 3.1 45.0 + - + +
705A TRP* 3.6 32.1 - - + -
716A LEU* 5.0 2.2 - - + -
730A LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A LEU* 3.9 29.6 - - + -
636A PHE* 3.9 26.9 - + + -
637A LYS 3.1 31.6 + - - -
638A GLY* 3.5 1.9 - - - -
639A HIS* 3.1 32.8 + - - +
654A TYR* 3.3 12.0 - - - +
655A ILE* 2.6 46.3 + - + +
657A CYS* 4.2 2.9 - - - -
665A TYR* 4.1 18.9 - - + -
666A LEU* 1.3 75.0 - - - +
668A TYR* 1.3 59.7 + - - +
672A SER 3.6 10.8 - - - -
673A LYS 3.5 16.6 - - - +
674A THR* 3.5 20.2 + - - -
675A LEU* 4.3 4.7 - - - +
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Residues in contact with TYR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU* 4.6 2.3 + - - +
395A CYS* 3.8 35.1 + - - +
398A LYS* 3.3 32.2 - - + +
399A PHE* 4.3 13.7 - - + -
636A PHE* 3.5 1.7 - - - -
653A ASP* 3.7 35.9 + - + -
654A TYR* 4.1 17.3 - + + -
667A TYR* 1.3 72.7 - - - +
669A LYS* 1.3 62.1 + - + +
670A GLY* 2.9 44.0 + - - -
671A LEU* 2.9 36.6 + - + +
673A LYS 4.9 2.0 + - - -
675A LEU* 4.3 12.5 - - + +
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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