Contacts of the helix formed by residues 258 - 263 (chain 5) 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 PRO 258 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1855 LEU* 5.1 1.1 - - + -
2175 CYS* 4.1 2.9 - - + -
2185 TYR 3.2 22.4 - - - +
2195 VAL* 3.3 25.8 - - + -
2235 PHE* 4.1 2.9 - - - -
2545 ARG 3.7 8.1 - - - +
2555 PHE 3.6 3.1 - - - +
2575 CYS* 1.3 89.6 - - + +
2595 GLU* 1.4 59.2 + - - +
2605 THR 2.9 5.6 - - - -
2615 LEU* 2.9 26.0 + - + +
2625 PHE* 3.8 7.1 - - - -
3065 TYR* 3.6 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2235 PHE* 3.1 60.1 - - + +
2245 GLU* 5.2 0.9 - - - -
2275 MET* 3.9 23.0 - - - +
2555 PHE* 3.1 24.8 + - - +
2565 ARG* 3.9 2.1 - - - +
2575 CYS 3.3 0.6 - - - -
2585 PRO* 1.4 73.4 - - - +
2605 THR* 1.4 60.3 + - - +
2625 PHE* 3.2 2.2 + - - -
2635 GLN* 2.7 59.7 + - - +
2665 PHE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805 LEU* 4.4 3.1 - - + +
1855 LEU* 4.3 15.0 - - + -
1885 TYR* 3.2 25.4 - - + -
2565 ARG 3.4 1.7 + - - -
2575 CYS 2.6 20.6 + - - -
2585 PRO 2.9 0.8 - - - -
2595 GLU* 1.4 77.0 - - - +
2615 LEU* 1.3 58.3 + - - +
2635 GLN 2.7 33.0 - - - +
2645 PRO* 3.4 5.5 - - - +
2665 PHE* 3.9 6.2 - - + -
2675 ILE* 3.6 46.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1555 SER* 4.8 3.8 - - - +
1785 LEU* 5.1 0.9 - - - +
1805 LEU* 3.5 30.9 - - + +
1855 LEU* 4.0 16.2 - - + -
2195 VAL* 5.6 0.7 - - + -
2585 PRO* 2.9 14.2 + - + +
2605 THR* 1.3 78.1 - - - +
2625 PHE* 1.4 65.5 + - + +
2645 PRO* 4.7 2.2 - - - +
2735 GLY* 3.8 3.1 - - - -
2745 ILE* 3.2 52.3 + - + +
3035 THR* 4.1 18.2 - - + +
3045 THR* 6.5 0.2 - - + -
3065 TYR* 4.0 30.7 - - + -
3095 ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2195 VAL* 3.5 28.5 - - + -
2235 PHE* 3.9 3.8 - + - -
2585 PRO 3.8 14.6 - - - -
2595 GLU* 3.2 2.2 + - - -
2615 LEU* 1.4 78.6 - - + +
2635 GLN* 1.3 75.0 + - - +
2645 PRO* 3.6 7.5 - - - +
2735 GLY* 4.0 4.5 + - - -
2745 ILE* 3.6 27.4 - - + -
2755 HIS* 3.4 40.7 - - + +
3095 ILE* 4.6 10.3 - - + -
3125 ARG* 3.3 51.6 - - + +
3135 MET* 4.2 17.5 - - + -
3165 GLU* 4.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2595 GLU* 2.7 65.1 + - - +
2605 THR* 2.7 23.9 - - - +
2625 PHE* 1.3 92.4 - - - +
2645 PRO* 1.3 59.8 - - - +
2655 SER* 3.1 21.2 + - - +
2665 PHE* 3.5 25.8 + - + +
3125 ARG* 3.4 10.3 + - - +
----------------------------------------------------------
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