Contacts of the strand formed by residues 677 - 681 (chain C) in PDB entry 6T8G
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 ASP 677 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 5.6 1.1 - - + +
470C SER* 3.6 6.6 + - - -
652C PHE* 3.2 22.3 - - - -
653C GLN 3.7 5.1 + - - +
672C LEU* 3.4 16.9 - - + +
673C LEU* 3.6 11.0 + - + +
674C GLY* 3.9 22.7 - - - +
676C GLY* 1.3 77.1 - - - +
678C MET* 1.3 68.0 + - - +
690C ARG* 3.0 39.4 + - - +
691C VAL 3.5 9.3 - - - +
692C HIS* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 678 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C LEU* 4.0 40.2 - - + -
475C GLY* 5.1 8.7 - - - -
479C MET* 6.5 0.4 - - + -
650C ILE* 3.7 24.5 - - + -
651C ALA 3.3 8.3 - - - +
652C PHE* 3.6 36.3 - - + -
672C LEU* 4.5 0.9 - - - -
676C GLY 4.1 0.4 + - - -
677C ASP* 1.3 79.3 + - - +
679C LEU* 1.3 65.9 + - - +
680C TYR* 5.3 1.1 - - - -
690C ARG* 3.8 2.1 - - - -
691C VAL* 2.9 56.0 + - + +
693C GLY* 4.2 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 679 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ARG* 4.5 25.4 - - - +
649C ARG 3.7 1.0 - - - +
650C ILE* 3.5 5.4 - - - +
651C ALA* 2.6 34.7 + - + +
664C LEU* 4.4 25.1 - - + +
668C GLY 4.8 0.7 - - - +
669C ALA* 3.7 35.9 - - + +
672C LEU* 3.7 19.9 - - + +
678C MET* 1.3 74.5 - - - +
680C TYR* 1.3 63.0 + - - +
681C LEU* 3.8 0.6 + - - -
688C PRO* 4.9 6.3 - - + +
689C ILE 3.4 4.0 - - - +
690C ARG* 3.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 680 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C LEU* 3.9 17.3 - - + -
452C ILE* 5.3 4.3 - - + -
454C THR* 3.3 32.7 - - + +
459C MET* 3.3 35.4 - - + +
648C THR* 4.2 7.6 - - + -
649C ARG 3.9 0.9 - - - -
650C ILE* 3.8 21.1 - - + -
678C MET* 3.9 3.3 + - - -
679C LEU* 1.3 72.4 - - - +
681C LEU* 1.3 59.2 + - - +
682C PRO* 3.6 27.0 - - + +
683C PRO* 3.8 12.7 - - + +
688C PRO* 3.5 2.5 - - - -
689C ILE* 2.5 61.5 + - + +
691C VAL* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 681 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C PRO 4.5 4.9 - - - +
648C THR* 3.3 8.1 - - - +
649C ARG* 2.8 59.3 + - + +
664C LEU* 4.0 22.0 - - + -
665C ASP* 3.7 22.2 - - - +
666C GLN* 3.5 21.8 - - - +
679C LEU 3.8 0.4 + - - -
680C TYR* 1.3 75.5 - - - +
682C PRO* 1.3 80.4 - - + +
685C THR 4.6 3.1 - - - +
686C GLY* 4.9 0.4 - - - -
687C LEU 4.5 4.3 - - - +
688C PRO* 4.0 18.8 - - + -
----------------------------------------------------------
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