Contacts of the helix formed by residues 754 - 762 (chain C) in PDB entry 1IW1
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 754 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752C GLY 3.3 5.0 + - - +
753C VAL* 1.3 80.6 - - - +
755C PRO* 1.3 74.5 - - - +
756C GLU* 2.8 54.8 + - + +
757C ALA* 2.9 27.0 + - + +
758C LEU* 3.8 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 755 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748C GLN* 3.2 24.7 - - - +
753C VAL 3.9 4.3 - - - +
754C ASP* 1.3 94.7 - - - +
756C GLU* 1.3 55.5 + - - +
757C ALA 3.0 0.7 - - - -
758C LEU* 3.0 35.9 + - + +
759C GLY* 3.8 1.4 + - - -
762C HIS* 4.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 756 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686C ASP* 3.5 8.0 - - - +
689C LYS* 2.9 56.6 + - + +
754C ASP* 2.8 41.3 + - + +
755C PRO* 1.3 72.0 - - - +
757C ALA* 1.3 58.6 - - + +
758C LEU 3.3 1.1 - - - -
759C GLY* 4.3 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 757 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C PHE* 4.4 1.9 - - - -
646C GLN* 5.6 0.3 - - - +
686C ASP* 3.3 26.1 - - - +
689C LYS* 4.1 15.9 - - + -
690C LEU* 3.6 38.9 - - + +
753C VAL* 3.9 4.0 - - + -
754C ASP* 2.9 15.5 + - + +
756C GLU* 1.3 78.3 - - + +
758C LEU* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C PHE* 3.5 37.7 - - + -
686C ASP* 3.9 1.6 - - - -
744C ALA* 3.6 14.4 - - + +
747C MET* 4.1 9.2 - - + -
748C GLN* 3.4 40.4 - - + +
753C VAL* 3.9 10.5 - - + -
754C ASP 3.8 12.3 - - - +
755C PRO* 3.0 9.7 + - + +
757C ALA* 1.3 79.8 - - - +
759C GLY* 1.3 64.0 + - - +
760C PHE 3.1 2.7 - - - -
761C TYR* 3.1 28.1 + - + +
762C HIS* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 759 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C ARG* 3.4 2.8 + - - -
682C VAL* 3.2 14.9 - - - +
686C ASP* 2.8 13.5 + - - -
755C PRO 3.8 3.0 + - - -
756C GLU 4.3 2.3 + - - -
758C LEU* 1.3 76.5 - - - +
760C PHE* 1.3 63.0 + - - +
762C HIS* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 760 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646C GLN* 3.9 10.8 - - - +
649C ALA* 5.5 2.5 - - + -
653C TYR* 3.5 34.8 - + - -
679C ARG* 2.8 57.5 + - + +
682C VAL* 3.3 9.3 - - - +
683C LEU* 3.4 35.2 - - + -
686C ASP* 2.8 17.9 + - - +
732C ARG* 4.2 5.6 - - - -
736C ASP* 3.6 19.5 - - - -
758C LEU 3.1 0.4 - - - -
759C GLY* 1.3 77.0 - - - +
761C TYR* 1.3 98.2 + + + +
762C HIS 3.3 0.2 - - - -
763C PHE* 4.1 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 761 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C PHE* 3.6 23.3 - + - -
645C LEU* 4.7 5.5 - - - +
646C GLN* 3.6 27.3 + - - -
736C ASP* 5.2 3.7 - - + +
740C GLY* 3.2 40.1 - - - +
741C GLN* 4.7 10.7 + - - +
743C ILE* 3.5 35.3 - - + +
744C ALA* 3.8 21.3 - - + -
758C LEU* 3.1 21.7 + - + +
760C PHE* 1.3 104.4 - + + +
762C HIS* 1.3 67.3 + - + +
763C PHE* 4.1 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 762 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C ARG* 3.0 9.5 + - - -
682C VAL* 5.7 0.7 - - - +
741C GLN* 6.2 3.8 - - + +
744C ALA* 4.9 8.0 - - + +
748C GLN* 5.4 5.8 + - - -
755C PRO* 4.4 13.8 + - + +
758C LEU* 3.0 41.1 + - - +
759C GLY* 2.9 21.6 + - - +
760C PHE 3.3 0.4 - - - -
761C TYR* 1.3 87.7 + - + +
763C PHE* 1.3 64.0 + - - +
764C GLU* 3.6 3.8 + - - +
----------------------------------------------------------
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