Contacts of the strand formed by residues 774 - 777 (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 TRP 774 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730C MET* 3.0 44.9 - - + -
731C LEU 3.3 15.9 - - - +
732C LYS* 4.1 16.2 - - + -
733C TRP* 3.5 10.7 - - - -
768C VAL* 5.4 0.7 - - - +
772C LYS* 4.2 17.0 - - + +
773C TYR* 1.3 119.5 + + + +
775C HIS* 1.3 76.9 + - - +
776C SER* 4.6 4.0 - - - -
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Residues in contact with HIS 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730C MET* 3.3 8.4 - - - +
731C LEU* 2.9 40.0 + - + +
733C TRP* 3.6 19.4 - - + -
750C ILE* 4.5 9.0 - - + -
766C ASP* 3.0 31.0 + - + +
767C MET 5.3 1.6 - - - -
768C VAL* 3.4 26.7 - - + +
774C TRP* 1.3 82.8 + - - +
776C SER* 1.3 85.7 + - - +
777C ILE* 3.9 15.3 - - + -
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Residues in contact with SER 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C VAL* 4.8 0.2 - - - +
728C THR* 2.7 35.5 - - - +
729C ILE 3.4 5.3 + - - -
730C MET* 3.6 21.2 - - - +
766C ASP* 4.7 0.2 - - - +
774C TRP* 4.5 5.4 - - - -
775C HIS* 1.3 94.6 + - - +
777C ILE* 1.3 60.6 + - - +
778C SER* 3.6 9.6 + - - -
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Residues in contact with ILE 777 (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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728C THR* 3.2 4.7 - - - +
729C ILE* 2.7 39.0 + - + +
731C LEU* 3.9 13.2 - - + -
750C ILE* 3.7 24.0 - - + -
752C TYR* 3.5 51.6 - - + +
766C ASP* 4.4 2.5 - - - +
775C HIS* 3.9 20.2 - - + +
776C SER* 1.3 69.1 - - - +
778C SER* 1.3 61.8 + - - +
780C LEU* 3.7 21.3 - - + +
788C ILE* 4.1 23.6 - - + -
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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
------------------------------------------------------------
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