Contacts of the strand formed by residues 776 - 781 (chain U) in PDB entry 6FF7
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 THR 776 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731U HIS* 5.4 0.2 - - - -
732U ASN* 3.3 15.0 - - - -
734U LYS* 5.9 4.0 - - - -
750U THR 4.3 5.0 - - - +
751U PHE* 5.2 0.3 - - - -
752U PRO* 4.4 16.3 - - - +
773U GLU* 4.2 20.0 - - - -
774U ALA 3.2 3.9 + - - +
775U LYS* 1.3 78.3 - - - +
777U LEU* 1.3 61.8 + - - +
778U ILE 4.2 0.9 + - - -
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Residues in contact with LEU 777 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728U PHE* 6.0 2.7 - - + -
731U HIS* 4.9 12.1 - - + -
732U ASN 2.8 11.4 + - - +
733U VAL* 3.6 8.3 - - + +
734U LYS* 2.7 34.2 + - - +
749U ILE* 5.6 7.9 - - + -
750U THR 3.8 8.7 - - - +
751U PHE* 5.7 0.7 - - - +
775U LYS 3.9 1.2 + - - -
776U THR* 1.3 74.3 - - - +
778U ILE* 1.3 58.8 + - - +
779U VAL* 3.7 2.7 + - + +
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Residues in contact with ILE 778 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734U LYS* 3.3 11.4 - - + +
736U THR* 6.6 0.2 - - - -
748U ARG 3.6 0.7 - - - +
749U ILE* 3.5 4.6 - - - -
750U THR* 3.0 47.3 + - - +
776U THR 4.2 1.0 + - - -
777U LEU* 1.3 70.8 - - - +
779U VAL* 1.3 60.6 + - - +
780U GLU* 3.9 0.9 + - - +
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Residues in contact with VAL 779 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733U VAL* 5.7 6.3 - - + -
734U LYS 2.7 14.7 + - - +
735U VAL* 3.3 12.3 - - + +
736U THR* 3.0 25.7 + - - -
747U PHE* 5.4 7.4 - - + -
748U ARG 3.3 7.6 - - - +
749U ILE* 4.7 3.8 - - + +
777U LEU* 3.7 3.7 + - + +
778U ILE* 1.3 71.4 - - - +
780U GLU* 1.3 60.7 + - - +
781U PRO 4.0 1.7 - - - -
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Residues in contact with GLU 780 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736U THR* 4.4 16.4 - - - -
747U PHE* 4.4 2.0 - - - -
748U ARG* 2.8 49.2 + - + +
778U ILE 3.9 1.9 + - - +
779U VAL* 1.3 73.6 - - - +
781U PRO* 1.3 65.8 - - - +
782U HIS* 3.7 2.8 + - + +
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Residues in contact with PRO 781 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736U THR 5.8 0.2 - - - -
737U VAL* 5.8 7.7 - - + -
742U LEU* 3.2 28.3 - - + +
743U GLN* 4.5 4.3 - - - -
744U ILE 3.7 15.0 - - - +
746U PRO 3.4 8.1 - - - +
747U PHE* 4.4 3.1 - - + -
779U VAL 4.0 3.0 - - - -
780U GLU* 1.3 77.2 - - - +
782U HIS* 1.3 60.3 + - - +
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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
------------------------------------------------------------
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