Contacts of the strand formed by residues 656 - 660 (chain A) in PDB entry 1SHY
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 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639A ASN* 3.2 21.3 + - - -
650A VAL* 5.4 6.4 - - - +
651A THR 4.3 3.1 - - - +
652A LEU* 3.6 16.5 - - + +
653A ASN* 3.0 32.5 + - - +
654A GLU 4.3 0.3 - - - -
655A SER* 1.3 87.9 + - - +
657A ILE* 1.3 63.1 + - - +
705A ILE* 3.1 31.9 - - + +
706A PHE 3.3 4.9 - - - +
707A VAL* 5.2 2.2 - - + -
708A ARG* 3.9 7.7 - - - -
191B ARG* 2.9 31.1 + - - +
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Residues in contact with ILE 657 (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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606A ILE* 3.8 33.7 - - + -
636A ILE* 4.0 20.6 - - + -
637A MET 5.5 0.2 - - - +
639A ASN* 4.1 7.6 - - - +
656A GLU* 1.3 75.6 - - - +
658A CYS* 1.3 70.6 + - - +
677A LEU* 4.3 5.8 - - + -
688A LEU* 4.1 19.5 - - + +
689A GLY* 4.2 1.3 - - - -
705A ILE* 3.3 1.9 - - - -
706A PHE* 2.6 62.9 + - + +
707A VAL 3.9 1.6 - - - -
708A ARG* 3.7 32.1 - - + +
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Residues in contact with CYS 658 (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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636A ILE* 3.3 16.1 - - - +
637A MET* 3.0 37.4 + - + +
638A GLY 4.5 0.2 - - - +
639A ASN* 4.0 5.7 + - - +
642A CYS* 2.0 51.1 - - + -
652A LEU* 3.5 15.9 - - - -
657A ILE* 1.3 80.4 - - - +
659A ALA* 1.3 63.0 + - - +
703A PRO* 4.6 1.6 - - + -
704A GLY 3.2 9.0 - - - +
705A ILE* 4.1 7.4 - - - -
706A PHE* 4.6 1.1 - - - -
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Residues in contact with ALA 659 (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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612A CYS* 5.1 0.2 - - + -
634A LEU* 3.6 22.0 - - + +
635A TYR 3.1 16.6 - - - +
636A ILE* 4.1 6.3 - - + -
637A MET 4.2 0.9 - - - +
658A CYS* 1.3 77.5 - - - +
660A GLY* 1.3 59.6 + - - +
677A LEU* 3.8 25.1 - - + -
703A PRO* 4.0 2.7 - - - -
704A GLY* 2.8 31.5 + - - +
706A PHE* 3.7 8.7 - - + -
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Residues in contact with GLY 660 (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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634A LEU* 3.7 12.1 - - - -
635A TYR* 2.7 35.0 + - - +
637A MET* 4.1 11.4 - - - +
659A ALA* 1.3 74.9 - - - +
661A ALA* 1.3 60.9 + - - -
703A PRO* 4.0 20.2 - - - +
704A GLY 4.6 0.2 - - - -
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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