Contacts of the strand formed by residues 743 - 748 (chain H) in PDB entry 6X34
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 VAL 743 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665H GLU* 3.8 23.1 - - + -
666H VAL 3.4 16.2 - - - +
667H MET* 4.6 12.1 - - + -
741H GLU 4.4 7.6 - - - +
742H ASP* 1.3 77.6 - - - +
744H VAL* 1.3 63.2 + - - +
745H SER* 5.9 0.2 - - - -
758H ARG 4.5 0.3 - - - +
760H ASN* 3.6 21.8 + - - +
761H GLY 4.8 1.2 + - - -
801H LYS* 4.8 11.2 - - + -
802H PHE* 3.7 38.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 744 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665H GLU* 4.8 0.4 - - - -
666H VAL* 3.4 36.7 + - + +
684H VAL* 5.2 11.6 - - + +
716H PHE* 5.6 9.9 - - + +
717H ASP* 5.9 4.0 - - - -
718H GLY 6.0 1.8 - - - +
742H ASP* 3.9 13.1 + - + +
743H VAL* 1.3 81.1 - - - +
745H SER* 1.3 68.1 + - - +
757H PHE* 5.4 4.7 - - + -
758H ARG 3.6 11.2 - - - +
759H ILE* 4.4 11.7 - - + -
760H ASN* 4.7 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 745 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663H TYR* 3.1 39.8 - - - -
664H PHE 2.3 30.4 + - - -
665H GLU* 3.8 10.8 - - - -
684H VAL* 6.3 1.8 - - - -
743H VAL 5.9 0.2 - - - -
744H VAL* 1.3 77.8 - - - +
746H CYS* 1.3 61.4 + - - +
757H PHE* 3.2 6.2 - - - +
758H ARG* 2.5 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 746 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662H TRP 4.5 0.7 - - - +
663H TYR* 3.8 10.4 - - - -
664H PHE* 3.5 35.1 + - - +
684H VAL* 5.7 11.4 - - + +
685H GLY* 5.5 5.2 - - - -
686H TRP* 3.0 37.5 - - + +
745H SER* 1.3 84.8 + - - +
747H CYS* 1.3 66.2 + - - +
748H LEU 4.3 0.3 + - - -
755H ILE* 6.3 0.4 - - + -
756H SER 3.8 6.1 - - - +
757H PHE* 3.6 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 747 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662H TRP 4.6 4.7 - - - +
663H TYR* 4.3 18.2 - - + -
746H CYS* 1.3 80.3 - - - +
748H LEU* 1.3 60.6 + - - +
754H SER 4.1 1.8 - - - +
755H ILE* 3.5 5.0 - - - +
756H SER* 2.7 52.3 + - - +
757H PHE* 4.4 2.7 - - - -
758H ARG* 4.1 19.7 - - - -
763H PRO* 6.4 2.5 - - - -
805H PRO* 5.2 3.1 - - - -
808H TYR* 4.4 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660H SER 3.2 14.1 - - - +
661H LYS* 4.7 0.9 - - - -
662H TRP* 4.0 18.5 + - + +
686H TRP* 3.5 45.9 - - + +
746H CYS 4.2 0.8 - - - -
747H CYS* 1.3 73.1 - - - +
749H ASP* 1.3 61.1 + - - +
750H LEU* 6.1 2.2 - - + -
754H SER 4.3 0.4 - - - -
755H ILE* 3.7 15.9 - - + -
808H TYR* 5.9 2.8 - - - -
----------------------------------------------------------
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