Contacts of the strand formed by residues 717 - 725 (chain C) in PDB entry 3N1G
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 TYR 717 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ARG* 5.0 5.2 + - - -
131B GLU 4.8 6.8 + - - -
132B ASP 3.6 15.3 + - - -
133B GLY* 4.6 4.9 - - - -
715C GLY 3.9 0.9 + - - +
716C PRO* 1.3 74.6 - - - +
718C ILE* 1.3 74.5 + - - +
719C THR* 3.4 23.3 + - + -
733C TRP* 3.2 3.6 - - - -
734C MET* 2.9 39.6 + - + +
803C ASN* 3.3 34.8 - - + -
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Residues in contact with ILE 718 (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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132B ASP 4.6 0.5 - - - +
717C TYR* 1.3 77.4 + - - +
719C THR* 1.3 62.0 + - - +
720C PHE 3.7 16.4 - - - +
721C THR* 3.8 5.8 - - + -
731C LEU* 4.2 15.5 - - + -
732C LYS 3.4 13.2 - - - +
733C TRP* 4.1 0.9 - - + -
788C ILE* 3.9 18.2 - - + +
789C LYS* 3.9 7.4 - - - -
790C MET* 3.8 26.5 - - + -
802C SER* 3.4 21.8 - - - +
803C ASN* 2.8 37.5 + - - +
805C MET* 3.6 27.0 - - + +
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Residues in contact with THR 719 (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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133B GLY 5.6 1.7 - - - +
717C TYR* 3.7 28.0 - - + +
718C ILE* 1.3 73.7 - - - +
720C PHE* 1.3 64.4 + - - +
732C LYS* 2.8 25.6 + - - +
733C TRP* 3.9 1.9 + - - -
734C MET* 3.6 35.8 - - + +
805C MET* 4.8 4.0 - - - +
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Residues in contact with PHE 720 (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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718C ILE* 3.5 3.0 - - - +
719C THR* 1.3 86.7 + - - +
721C THR* 1.3 71.4 + - - +
722C ASP* 3.2 43.5 - - + -
730C MET* 4.3 16.8 - - + -
731C LEU* 3.1 5.2 - - - +
732C LYS* 2.9 61.9 + - + -
805C MET* 4.5 2.7 - - - +
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Residues in contact with THR 721 (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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134B HIS* 4.6 1.9 - - - +
718C ILE* 3.8 7.2 - - + -
720C PHE* 1.3 86.5 - - - +
722C ASP* 1.3 65.1 + - - +
729C ILE* 4.6 2.0 - - - -
730C MET 3.3 7.4 - - - -
731C LEU* 3.9 11.2 - - + -
788C ILE* 4.7 10.3 - - + -
805C MET* 3.6 46.0 - - + +
806C ILE 4.3 3.5 + - - -
807C CYS* 3.7 25.3 - - - +
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Residues in contact with ASP 722 (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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720C PHE* 3.2 29.8 - - + -
721C THR* 1.3 77.0 - - - +
723C ALA* 1.3 79.2 + - - +
724C VAL* 3.5 0.3 + - - +
730C MET* 2.9 34.4 + - + +
807C CYS* 3.7 9.8 - - - -
810C LYS* 6.1 0.4 - - - -
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Residues in contact with ALA 723 (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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722C ASP* 1.3 93.4 + - - +
724C VAL* 1.3 61.1 + - - +
725C ASN 4.2 0.9 - - - +
728C THR 3.7 5.6 - - - -
729C ILE* 4.3 4.0 - - - +
807C CYS* 3.7 5.9 - - - -
808C GLU 3.1 25.6 - - - +
809C THR* 3.9 3.4 - - - -
810C LYS* 3.7 41.6 + - + +
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Residues in contact with VAL 724 (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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722C ASP* 3.9 0.9 - - + +
723C ALA* 1.3 77.3 - - - +
725C ASN* 1.3 75.5 + - - +
728C THR* 2.9 38.8 + - + -
729C ILE 4.3 0.2 - - - -
730C MET* 3.4 46.2 - - + +
776C SER* 4.8 0.2 - - - +
810C LYS* 3.9 14.5 + - - +
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Residues in contact with ASN 725 (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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723C ALA* 3.7 0.9 - - - +
724C VAL* 1.3 86.8 + - - +
726C GLU* 1.3 75.2 + - - +
727C THR* 3.0 20.1 + - - -
728C THR* 3.0 33.8 + - - +
809C THR* 3.8 1.6 - - - -
810C LYS* 3.1 32.2 + - - +
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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