Contacts of the strand formed by residues 773 - 777 (chain A) in PDB entry 1NST
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 ILE 773 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A VAL* 3.1 25.4 - - + +
701A THR* 5.3 4.3 - - + -
761A ILE* 5.4 2.9 - - + +
764A TRP* 4.0 9.6 - - + +
765A LEU* 4.0 26.9 - - + +
768A TYR* 3.9 23.6 - - + +
769A HIS 3.7 14.6 - - - +
770A ALA 3.0 9.6 + - - +
771A ASN* 3.4 1.1 - - - -
772A GLN* 1.3 85.8 - - - +
774A LEU* 1.3 71.7 + - - +
775A VAL* 4.4 5.6 - - + -
795A PHE* 3.6 7.6 - - - -
866A MET* 3.6 23.6 - - + -
868A GLN* 3.0 17.6 + - - -
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Residues in contact with LEU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A VAL 2.8 8.5 + - - -
700A LEU* 3.5 25.1 - - + +
701A THR* 3.0 28.1 + - - +
773A ILE* 1.3 76.8 - - - +
775A VAL* 1.3 66.0 + - - +
776A LEU* 3.5 29.7 + - + -
791A MET* 4.8 7.4 - - + +
792A VAL* 4.1 10.5 - - + +
795A PHE* 3.6 46.4 - - + -
868A GLN* 3.6 8.7 - - - +
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Residues in contact with VAL 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A THR* 3.6 18.4 - - + -
703A LEU* 3.5 38.1 - - + -
761A ILE* 4.5 5.8 - - + -
773A ILE* 4.4 3.1 - - + -
774A LEU* 1.3 74.2 - - - +
776A LEU* 1.3 66.5 + - - +
777A ASP 4.1 0.3 + - - -
863A LEU* 3.8 33.7 - - + -
866A MET* 4.3 11.9 - - + -
868A GLN* 2.8 31.0 + - + +
869A THR 4.7 9.8 + - - +
871A PRO* 5.2 3.0 - - + +
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Residues in contact with LEU 776 (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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620A LEU* 3.9 14.4 - - + -
700A LEU* 3.6 27.1 - - + -
701A THR 2.8 15.8 + - - +
702A ILE* 4.2 13.7 - - + -
703A LEU* 3.1 29.3 + - - +
774A LEU* 3.5 26.2 - - + -
775A VAL* 1.3 77.8 - - - +
777A ASP* 1.3 61.4 + - - +
781A LEU* 5.3 3.4 - - + -
788A VAL* 3.7 34.5 - - + +
791A MET* 4.9 11.2 - - + -
792A VAL* 3.8 16.8 - - + -
871A PRO* 4.8 2.4 - - - +
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Residues in contact with ASP 777 (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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702A ILE* 4.5 0.9 - - - -
703A LEU 4.0 1.6 - - - -
775A VAL 4.1 0.4 + - - -
776A LEU* 1.3 74.8 - - - +
778A GLY* 1.3 62.3 + - - +
779A LYS* 2.9 21.0 + - - +
780A LEU* 3.7 26.1 - - + +
781A LEU* 3.0 21.7 + - - +
788A VAL* 4.7 3.3 - - - +
791A MET* 6.4 0.4 - - - -
871A PRO* 3.5 21.6 - - + +
872A THR* 2.9 38.4 + - - +
873A TRP* 3.6 8.3 - - - -
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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