Contacts of the helix formed by residues 289 - 295 (chain 7) in PDB entry 1O1F
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 ILE 289 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667 TYR* 3.7 39.5 - - + -
1717 LEU* 3.6 33.0 - - + -
2857 CYS* 4.0 8.1 - - + -
2867 ASP* 3.1 42.3 + - + +
2877 ILE 3.2 0.6 - - - -
2887 ASP* 1.4 76.9 - - + +
2907 ARG* 1.3 65.5 + - - +
2917 LYS* 3.3 5.8 - - - +
2927 ASP* 3.0 17.4 + - - +
2937 LEU* 3.3 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2827 ILE* 3.4 35.4 + - + +
2837 MET* 3.9 45.9 + - - +
2857 CYS* 2.4 33.2 + - + -
2867 ASP 3.3 9.0 + - - +
2877 ILE* 3.8 11.6 - - - +
2887 ASP 3.4 1.8 - - - -
2897 ILE* 1.3 78.6 - - - +
2917 LYS* 1.4 61.6 + - - +
2927 ASP 3.3 0.3 + - - -
2937 LEU* 4.1 7.6 - - - +
2947 TYR* 3.1 33.1 + - + -
3257 MET* 4.7 5.4 - - + -
201V VAL* 4.5 12.9 - - - +
202V THR* 2.2 40.3 + - - +
205V GLU* 5.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 ILE 4.7 2.5 + - - +
2887 ASP* 3.0 29.4 + - - +
2897 ILE 3.3 0.8 - - - -
2907 ARG* 1.4 75.1 - - - +
2927 ASP* 1.4 96.8 + - - +
2947 TYR* 3.4 2.8 + - - +
2957 ALA* 3.2 22.9 + - - +
3257 MET* 3.7 25.8 - - - +
3267 LYS* 4.5 2.4 - - - +
204V ALA* 5.6 4.0 - - + -
243V PRO* 6.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 THR* 3.9 22.4 - - + +
1667 TYR* 4.0 19.9 + - - -
2897 ILE* 3.0 9.5 + - - +
2917 LYS* 1.4 104.0 + - - +
2937 LEU* 1.3 67.8 + - - +
2957 ALA* 3.1 5.6 + - - -
2967 ASN* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 THR* 3.8 22.4 - - + -
1507 GLY* 3.8 19.7 - - - +
1517 ILE* 3.4 30.6 - - + +
1647 PRO* 4.4 6.7 - - + -
1657 ILE 4.3 5.4 - - - +
2827 ILE* 4.5 18.4 - - + -
2857 CYS* 4.0 22.0 - - + -
2897 ILE* 3.3 42.2 + - + +
2907 ARG* 4.1 7.0 - - - +
2927 ASP* 1.3 77.1 - - - +
2947 TYR* 1.3 63.0 + - - +
2967 ASN 3.0 20.8 + - - -
2977 ASN* 3.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2797 TYR* 3.4 19.9 - + - -
2827 ILE* 3.6 38.1 - - + +
2837 MET* 3.4 32.8 - - + +
2907 ARG* 3.1 28.9 + - + +
2917 LYS 3.7 3.4 - - - +
2927 ASP 3.2 1.0 - - - -
2937 LEU* 1.3 78.4 - - - +
2957 ALA* 1.3 59.7 + - - +
2967 ASN 3.1 0.9 + - - -
2977 ASN* 4.6 2.1 + - - +
3177 ILE* 4.0 19.0 - - + +
3217 ALA* 3.6 20.7 - - + +
3227 PRO* 4.7 0.2 - - + -
3257 MET* 3.4 32.8 - - + -
3267 LYS 3.2 15.7 - - - +
3277 ILE* 3.4 16.3 - - + -
3287 LYS 2.8 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 ARG* 4.6 0.2 + - - -
2917 LYS 3.2 11.0 + - - +
2927 ASP* 3.1 4.1 + - - -
2947 TYR* 1.3 77.5 - - - +
2967 ASN* 1.3 75.3 + - - +
3267 LYS* 3.8 32.3 - - + +
3287 LYS* 3.2 33.1 - - + +
3307 ILE* 3.8 1.0 - - - +
----------------------------------------------------------
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