Contacts of the strand formed by residues 704 - 708 (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 GLY 704 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A CYS* 3.2 5.1 - - - +
659A ALA 2.8 38.7 + - - -
660A GLY* 4.6 0.4 - - - -
668A PRO* 6.0 3.6 - - - -
702A ARG 3.8 0.2 + - - -
703A PRO* 1.3 73.0 - - - +
705A ILE* 1.3 61.4 + - - -
706A PHE* 3.1 13.8 - - - -
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Residues in contact with ILE 705 (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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646A HIS* 4.4 21.8 - - + +
650A VAL* 5.8 7.4 - - + -
652A LEU* 3.6 21.5 - - + -
656A GLU* 3.1 47.3 - - + +
657A ILE 3.3 7.4 - - - +
658A CYS* 4.1 5.8 - - - -
692A VAL* 4.3 13.8 + - + +
693A PRO 5.5 0.7 - - - +
694A GLY* 6.5 1.3 - - - -
695A ARG* 6.2 2.9 - - - -
704A GLY* 1.3 73.0 - - - -
706A PHE* 1.3 74.3 + - - +
191B ARG* 3.9 18.6 - - - +
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Residues in contact with PHE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A VAL* 3.2 35.2 - - + -
634A LEU* 3.7 13.7 - - + -
656A GLU* 3.3 5.7 - - - -
657A ILE* 2.6 45.9 + - + +
659A ALA* 3.7 19.7 - - + -
668A PRO* 4.2 14.4 - - + -
677A LEU* 3.5 23.3 - - + -
689A GLY* 4.0 7.9 - - - -
690A VAL 3.9 7.4 - - - +
691A ILE* 4.0 24.0 - - + -
692A VAL* 5.2 1.8 - - - +
704A GLY* 3.1 31.0 - - - -
705A ILE* 1.3 83.1 - - - +
707A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 707 (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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577A SER* 5.1 2.7 - - - -
578A ASP 5.4 5.2 - - - +
579A LEU* 3.9 17.0 - - + -
655A SER 3.7 7.0 - - - +
656A GLU* 4.5 4.0 - - + +
657A ILE* 3.9 1.3 - - - -
689A GLY* 3.0 21.7 - - - -
690A VAL* 3.1 42.0 + - + +
692A VAL* 3.7 18.3 - - + +
706A PHE* 1.3 74.5 - - - +
708A ARG* 1.3 75.1 + - - +
709A VAL* 3.0 2.4 + - - +
712A TYR* 3.8 25.4 - - + -
191B ARG* 6.0 2.9 - - - +
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Residues in contact with ARG 708 (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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602A TYR 5.0 1.6 + - - -
603A GLY 3.9 9.7 + - - -
604A SER 2.9 29.9 + - - -
605A THR* 4.2 14.6 - - - +
606A ILE* 4.7 12.1 - - - +
639A ASN* 5.6 1.8 - - - +
654A GLU* 3.2 22.9 + - - +
655A SER 2.8 22.7 + - - +
656A GLU 3.9 12.6 - - - -
657A ILE* 3.7 28.2 - - + +
688A LEU 3.8 2.2 - - - +
706A PHE 3.7 0.4 + - - -
707A VAL* 1.3 68.5 - - - +
709A VAL* 1.3 64.9 + - - +
710A ALA* 3.5 16.9 - - + +
711A TYR* 3.5 20.9 + - + +
712A TYR* 3.5 21.7 - - - -
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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