Contacts of the strand formed by residues 831 - 835 (chain B) in PDB entry 3PT6
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 831 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B GLN* 3.7 8.1 - - - +
755B ILE* 6.0 4.5 - - + -
766B VAL* 3.6 30.1 - - + -
767B SER 3.8 5.8 - - - +
768B VAL* 4.4 1.6 - - + -
782B VAL* 5.3 3.8 - - + -
785B LEU* 6.1 1.1 - - + -
795B PHE* 3.7 41.5 - - + -
828B LEU* 2.9 29.8 + - + +
829B SER 3.3 9.0 - - - +
830B TYR* 1.3 81.2 - - - +
832B HIS* 1.3 62.9 + - - +
833B SER 4.1 10.8 - - - +
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Residues in contact with HIS 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B GLN* 3.5 19.7 + - + +
767B SER* 3.2 24.5 + - - +
768B VAL* 4.3 2.2 - - - -
769B ILE* 3.1 43.8 - - + +
830B TYR 4.6 1.1 - - - +
831B ILE* 1.3 79.3 - - - +
833B SER* 1.3 81.3 + - - +
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Residues in contact with SER 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B VAL* 3.3 6.6 - - - +
767B SER* 2.9 30.2 + - - -
831B ILE* 4.1 5.5 - - - +
832B HIS* 1.3 99.0 - - - +
834B LYS* 1.3 65.8 - - - +
835B VAL* 5.1 2.2 - - - -
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Residues in contact with LYS 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B GLU* 5.3 8.2 - - + +
759B MET* 2.8 37.0 + - - +
760B LEU* 4.6 10.3 - - + -
764B ASP* 4.0 17.7 + - + +
765B CYS 3.3 17.9 - - - +
766B VAL* 4.3 2.7 - - + +
831B ILE* 5.9 0.2 - - - -
833B SER* 1.3 78.8 - - - +
835B VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B CYS* 2.7 56.7 + - + +
766B VAL 3.9 6.5 - - - +
767B SER* 4.0 25.4 - - - +
777B LEU* 6.0 0.4 - - + -
779B LEU* 3.9 25.4 - - + -
780B ALA 5.0 0.4 - - - +
833B SER* 4.3 3.4 - - - +
834B LYS* 1.3 83.2 - - - +
836B LYS* 1.3 59.8 + - - +
837B VAL* 4.0 7.4 - - + -
867B TYR* 4.7 10.8 - - + -
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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