Contacts of the strand formed by residues 588 - 592 (chain C) in PDB entry 2HYE
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 588 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577C VAL* 4.4 15.9 - - + +
578C LEU 3.0 11.9 - - - +
579C LYS* 3.6 30.6 - - + +
586C LYS* 4.1 5.4 - - - +
587C LYS* 1.3 79.9 - - - +
589C PHE* 1.3 62.8 + - - +
665C PHE* 3.9 25.4 - - + -
666C ARG* 2.8 46.9 + - + +
667C ILE* 3.0 5.5 + - - +
25D LYS* 5.2 6.1 - - - +
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Residues in contact with PHE 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C ALA 3.6 0.7 - - - +
577C VAL* 3.1 11.0 - - - +
578C LEU* 2.7 42.0 + - + +
580C ALA* 3.5 31.9 - - + -
582C PHE* 4.4 4.9 - + - -
587C LYS* 4.9 1.1 - - + -
588C GLU* 1.3 75.5 - - - +
590C GLN* 1.3 61.5 + - - +
591C VAL* 3.6 11.4 + - + -
599C LEU* 5.4 3.6 - - + -
638C VAL* 4.1 22.4 - - + -
660C PHE* 3.4 30.5 - + - -
666C ARG* 5.4 0.9 - - - -
667C ILE* 3.5 35.2 - - + -
669C ILE* 3.2 34.1 - - + -
22D PHE* 4.7 7.9 - + - -
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Residues in contact with GLN 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C GLY* 4.9 11.1 - - - +
575C HIS* 5.1 13.4 - - + -
576C ALA 3.5 7.6 - - - +
577C VAL* 4.7 11.7 - - + -
589C PHE* 1.3 72.5 - - - +
591C VAL* 1.3 57.9 + - - +
666C ARG* 5.3 9.8 + - + +
667C ILE 2.8 17.5 + - - +
668C LYS* 3.4 38.3 - - + +
669C ILE 3.5 4.2 + - - -
670C ASN* 3.3 34.7 + - - +
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Residues in contact with VAL 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C HIS* 3.3 1.0 - - - +
576C ALA 2.6 40.8 + - - +
578C LEU* 3.1 44.0 - - + -
589C PHE* 4.1 8.1 - - + +
590C GLN* 1.3 73.7 - - - +
592C SER* 1.3 63.2 + - - +
595C GLN* 3.1 26.9 - - + +
596C THR* 3.6 4.9 + - - +
599C LEU* 4.7 7.6 - - + -
631C LEU* 5.4 0.2 - - + -
669C ILE* 3.5 31.0 - - + -
670C ASN* 3.1 7.2 - - - -
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Residues in contact with SER 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C GLY 3.7 7.2 - - - -
575C HIS* 3.8 0.4 - - - +
591C VAL* 1.3 74.1 - - - +
593C LEU* 1.3 60.7 + - - +
594C PHE* 3.5 9.0 + - - +
595C GLN* 3.1 32.5 + - - +
596C THR* 2.8 30.0 + - - -
627C THR* 4.7 0.7 - - - +
670C ASN* 2.8 9.2 + - - -
672C ILE* 6.1 0.8 - - - +
673C GLN* 3.1 38.6 - - - -
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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