Contacts of the helix formed by residues 727 - 734 (chain S) in PDB entry 1I84
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 PHE 727 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726S VAL* 1.3 69.5 - - - +
728S GLN* 1.3 57.7 + - - -
730S PHE* 4.1 3.8 - - - +
731S ARG* 3.5 22.0 + - - +
749S GLY* 4.0 3.4 - - - +
750S LYS* 3.2 25.6 - - + -
753S CYS* 4.2 13.6 - - - +
769S ILE* 4.1 9.4 - - + -
770S GLY 3.8 14.1 - - - -
771S GLN 3.0 13.0 - - - -
772S SER 2.9 10.4 + - - -
773S LYS* 3.4 20.2 - - - -
774S ILE* 3.5 21.3 - - + -
370V GLU* 1.4 35.0 + - + +
372V ASN* 0.8 262.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 728 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726S VAL* 2.6 7.2 + - + -
727S PHE* 1.3 40.3 - - - +
729S GLU* 1.3 79.6 + - - +
730S PHE 3.0 1.6 - - - -
731S ARG* 3.4 12.4 + - - +
732S GLN* 3.0 27.4 + - - +
370V GLU* 1.3 63.0 + - + +
373V THR* 4.6 2.5 - - - +
375V GLN 4.0 12.1 - - - +
376V ALA 4.6 0.2 - - - +
377V SER* 0.7 80.5 + - - +
378V MET* 2.7 8.0 + - - +
379V PRO* 4.9 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 729 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725S ILE* 3.7 13.3 - - + +
726S VAL* 3.0 26.0 + - + +
728S GLN* 1.3 96.5 - - - +
730S PHE* 1.3 56.9 + - - +
732S GLN* 3.3 10.8 - - + +
733S ARG* 2.9 33.6 + - - +
375V GLN* 5.4 2.4 - - - +
377V SER* 4.7 1.4 + - - -
404V THR* 5.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 730 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725S ILE* 3.3 27.5 - - + +
726S VAL 3.2 11.0 + - - +
727S PHE* 4.2 4.9 - - - +
728S GLN 3.0 0.8 - - - -
729S GLU* 1.3 74.2 - - - +
731S ARG* 1.3 60.7 + - - +
732S GLN 2.8 8.9 + - - -
734S TYR* 3.3 52.4 + + + +
753S CYS* 4.2 12.1 - - - -
756S MET* 3.9 24.2 - - + -
757S ILE* 4.4 20.9 - - + -
760S LEU* 4.9 13.5 - - + -
762S LEU* 6.5 0.7 - - + -
774S ILE* 4.0 9.0 - - + -
776S PHE* 3.1 44.2 - + - -
781S LEU* 4.4 1.6 - - + -
784S LEU* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 731 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727S PHE 3.5 14.5 + - - +
728S GLN* 3.4 13.6 + - - +
730S PHE* 1.3 77.6 - - - +
732S GLN* 1.3 56.7 + - - +
735S GLU* 2.9 42.2 + - - +
742S ILE* 4.2 26.2 - - - +
746S PHE* 5.7 4.8 - - - +
747S MET 4.6 10.9 + - - +
749S GLY* 5.0 6.8 - - - +
752S ALA* 3.8 23.4 - - - +
753S CYS* 3.9 16.6 - - + -
756S MET* 3.8 22.4 - - - -
379V PRO* 3.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 732 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728S GLN* 3.0 27.4 + - - +
729S GLU* 3.3 13.9 - - + +
730S PHE 2.8 1.6 - - - -
731S ARG* 1.3 82.7 - - - +
733S ARG* 1.3 67.0 + - + +
735S GLU* 4.0 6.6 + - - +
736S ILE 5.3 0.2 + - - -
377V SER* 4.9 1.6 - - - +
378V MET* 3.3 29.0 + - - +
379V PRO* 4.9 2.1 - - - +
381V ASN* 4.5 13.6 + - - +
399V THR* 5.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 733 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166S GLN* 5.2 10.0 + - - +
725S ILE* 5.6 2.7 - - + -
729S GLU* 2.9 20.3 + - - +
732S GLN* 1.3 78.7 - - + +
734S TYR* 1.3 87.2 + - + +
735S GLU 3.7 2.1 + - - -
736S ILE* 4.3 6.1 + - - +
785S GLU* 2.9 29.6 + - - -
788S ARG* 3.1 47.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 734 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725S ILE* 4.7 7.9 - - + +
730S PHE* 3.3 45.5 + + + +
733S ARG* 1.3 99.0 - - + +
735S GLU* 1.3 62.7 + - - +
736S ILE* 3.3 2.2 - - - +
737S LEU* 3.5 20.9 + - + +
738S ALA* 4.1 2.3 + - - +
756S MET* 4.0 9.4 - - - +
760S LEU* 5.5 3.6 - - + +
781S LEU* 3.4 39.7 + - + +
784S LEU* 4.0 43.3 - - + -
785S GLU* 2.5 30.1 + - - -
788S ARG* 4.1 9.4 - - + -
----------------------------------------------------------
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