Contacts of the strand formed by residues 488 - 490 (chain W) in PDB entry 6G0L
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 LEU 488 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428W HIS 3.6 6.8 + - - +
429W ILE* 4.1 15.5 - - + -
430W ILE* 3.0 30.4 + - - +
454W ILE* 3.2 24.7 - - + +
455W CYS 3.9 11.0 - - - +
456W TYR* 3.6 16.6 - - + +
466W ILE* 5.3 9.0 - - + -
470W GLU* 6.2 0.7 - - + -
485W PHE* 5.3 20.4 - - + -
486W ASN 5.5 0.4 - - - +
487W VAL* 1.4 75.7 - - - +
489W LEU* 1.3 81.7 + - - +
490W THR* 2.9 36.8 - - + -
502W LEU* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430W ILE* 3.2 24.5 - - + +
432W VAL* 4.1 11.9 - - + -
437W MET* 4.2 24.5 - - + +
440W TRP* 4.1 27.6 - - + -
441W LEU* 4.6 11.9 - - + +
444W PHE* 6.4 1.6 - - + -
453W CYS* 6.2 4.5 - - + -
455W CYS* 2.8 44.0 - - + +
456W TYR 3.2 3.1 + - - +
487W VAL* 5.2 7.6 - - + -
488W LEU* 1.3 94.2 - - - +
490W THR* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 490 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429W ILE* 4.1 16.7 - - + +
430W ILE 3.1 9.8 + - - +
431W VAL* 3.1 35.9 + - - +
432W VAL* 3.1 12.9 + - - +
456W TYR* 4.5 8.7 - - + -
488W LEU* 2.9 29.6 - - + -
489W LEU* 1.3 72.7 - - - +
491W THR* 1.3 66.5 + - - +
494W TYR* 5.3 5.2 - - - -
495W ILE* 3.9 12.9 - - - +
502W LEU* 5.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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