Contacts of the strand formed by residues 748 - 750 (chain L) in PDB entry 6KW5
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 SER 748 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H THR 3.0 24.0 + - - -
263H CYS* 3.7 7.6 - - - -
746L ALA* 3.1 4.1 + - - +
747L SER* 1.3 75.3 - - - +
749L PHE* 1.3 71.3 + - - +
790L LEU* 5.1 4.5 - - - -
791L TRP 3.6 8.5 - - - -
792L PHE* 3.9 15.9 - - - +
36M PRO* 3.8 0.5 - - - +
37M ILE* 3.4 44.9 + - - +
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Residues in contact with PHE 749 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 3.6 39.0 - - + -
204A LEU* 3.6 26.2 - - + -
746L ALA* 4.6 8.3 - - + -
747L SER* 4.4 8.5 - - - -
748L SER* 1.3 89.8 - - - +
750L VAL* 1.3 67.4 + - - +
790L LEU* 3.9 0.5 - - - +
791L TRP* 2.7 43.0 + - - +
793L ARG* 4.4 7.9 - - + -
34M ALA* 3.7 26.0 - - + -
35M ASN 3.4 16.2 - - - -
36M PRO* 3.6 28.7 - - + -
37M ILE* 5.2 0.2 - - - -
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Residues in contact with VAL 750 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749L PHE* 1.3 79.8 - - - +
751L LEU* 1.4 74.9 + - - +
752L PRO* 5.5 0.2 - - + -
765L THR* 4.3 3.6 - - + -
788L GLU* 2.5 46.2 - - + +
789L ILE 3.7 14.1 - - - +
790L LEU* 4.1 8.7 - - + -
791L TRP* 4.4 0.2 - - - -
34M ALA* 4.1 1.1 - - - -
35M ASN* 3.2 41.5 + - + +
37M ILE* 3.8 25.8 - - + -
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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
------------------------------------------------------------
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