Contacts of the strand formed by residues 455 - 460 (chain C) in PDB entry 4QG0
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 LYS 455 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS* 5.0 0.2 - - - +
453C LEU* 3.8 11.4 - - + +
454C PHE* 1.3 72.8 - - - +
456C TYR* 1.3 66.4 + - - +
457C VAL* 4.1 0.7 - - - +
553C TYR* 3.1 5.3 - - - -
554C CYS 2.7 39.5 + - - +
557C VAL* 3.6 33.0 - - + +
562C LEU* 3.7 39.5 - - + -
702C DGT 2.7 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LYS* 3.9 45.8 - - + +
378C VAL* 5.8 1.1 - - + -
454C PHE 3.8 2.8 + - - -
455C LYS* 1.3 80.1 - - - +
457C VAL* 1.3 62.8 + - - +
458C GLY* 3.4 28.9 - - - -
459C GLU* 3.2 28.4 + - - +
551C ARG* 4.0 15.9 - - + -
552C VAL 4.1 2.2 - - - -
553C TYR* 3.6 32.7 - + + -
562C LEU* 5.6 3.6 - - - +
566C ARG* 5.2 6.8 + - - -
583C ASP* 5.7 4.7 - - - -
702C DGT 5.0 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LYS 4.1 0.7 - - - +
456C TYR* 1.3 79.4 - - - +
458C GLY* 1.3 60.1 + - - +
552C VAL* 2.9 23.9 + - + +
553C TYR* 3.6 21.8 - - - -
554C CYS* 3.8 12.1 - - + +
562C LEU* 5.4 5.6 - - + +
565C ALA* 3.8 29.2 - - + +
566C ARG* 3.9 27.0 + - + +
569C PHE* 3.9 18.3 - - + -
583C ASP* 4.8 6.1 - - - +
587C ILE* 4.2 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C TYR* 3.3 21.2 - - - -
457C VAL* 1.3 82.0 - - - +
459C GLU* 1.3 58.7 + - - -
550C ILE 3.8 0.2 - - - +
551C ARG* 3.3 4.2 - - - -
552C VAL* 2.9 34.1 + - - +
569C PHE* 3.6 19.7 - - - -
581C PRO* 5.9 0.7 - - - -
583C ASP* 5.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLN 5.7 0.7 - - - +
537A VAL 5.4 2.6 - - - +
456C TYR* 3.2 18.5 + - - +
458C GLY* 1.3 71.5 - - - +
460C THR* 1.3 72.0 + - - +
461C GLN* 5.9 0.2 - - + -
549C LEU* 3.8 23.4 - - + +
550C ILE 3.2 14.1 - - - +
551C ARG* 2.5 42.7 + - + +
569C PHE* 3.6 3.4 - - - -
581C PRO* 3.9 22.1 - - - +
582C GLN* 4.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C GLU* 1.3 78.8 - - - +
461C GLN* 1.3 70.1 + - - +
549C LEU* 3.9 0.7 - - - -
550C ILE* 2.9 50.8 + - + +
569C PHE* 4.3 6.5 - - + -
572C TRP* 4.6 1.3 - - + -
573C CYS* 3.6 27.7 - - - -
578C PHE* 3.3 27.5 - - + +
579C THR* 2.5 30.2 + - - -
581C PRO* 4.9 0.2 - - - -
----------------------------------------------------------
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