Contacts of the helix formed by residues 258 - 263 (chain 4) 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 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1854 LEU* 5.1 1.1 - - + -
2174 CYS* 4.1 3.1 - - + -
2184 TYR 3.2 22.2 - - - +
2194 VAL* 3.3 26.2 - - + -
2234 PHE* 4.1 2.7 - - - -
2544 ARG 3.7 7.4 - - - +
2554 PHE 3.6 3.6 - - - +
2574 CYS* 1.3 88.6 - - + +
2594 GLU* 1.4 58.8 + - - +
2604 THR 2.9 5.2 - - - -
2614 LEU* 2.9 26.8 + - + +
2624 PHE* 3.8 7.5 - - - -
3064 TYR* 3.6 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2234 PHE* 3.1 59.6 - - + +
2244 GLU* 5.2 0.3 - - - -
2274 MET* 3.9 23.7 - - - +
2554 PHE* 3.1 24.4 + - - +
2564 ARG* 3.9 1.8 - - - +
2574 CYS 3.3 0.6 - - - -
2584 PRO* 1.4 73.8 - - - +
2604 THR* 1.4 60.1 + - - +
2624 PHE* 3.2 2.2 + - - -
2634 GLN* 2.7 59.6 + - - +
2664 PHE* 3.6 28.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804 LEU* 4.4 3.5 - - + +
1854 LEU* 4.3 15.9 - - + -
1884 TYR* 3.2 25.2 - - + -
2564 ARG 3.4 1.9 + - - -
2574 CYS 2.6 21.8 + - - -
2584 PRO 2.9 1.0 - - - -
2594 GLU* 1.4 76.4 - - - +
2614 LEU* 1.3 57.8 + - - +
2634 GLN 2.7 32.0 - - - +
2644 PRO* 3.4 5.4 - - - +
2664 PHE* 3.9 6.4 - - + -
2674 ILE* 3.6 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554 SER* 4.8 4.3 - - - +
1784 LEU* 5.1 0.7 - - - +
1804 LEU* 3.5 31.9 - - + +
1854 LEU* 4.0 16.4 - - + -
2194 VAL* 5.6 0.7 - - + -
2584 PRO* 2.9 14.9 + - + +
2604 THR* 1.3 77.5 - - - +
2624 PHE* 1.3 63.7 + - + +
2634 GLN 4.9 0.2 - - - -
2644 PRO* 4.7 2.0 - - - +
2734 GLY* 3.8 3.3 - - - -
2744 ILE* 3.2 51.7 + - + +
3034 THR* 4.1 17.5 - - + +
3044 THR* 6.5 0.2 - - + -
3064 TYR* 4.0 30.3 - - + -
3094 ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2194 VAL* 3.5 29.4 - - + -
2234 PHE* 3.9 4.3 - + - -
2584 PRO 3.8 13.9 - - - -
2594 GLU* 3.2 2.5 + - - -
2614 LEU* 1.3 78.6 - - + +
2634 GLN* 1.3 75.4 + - - +
2644 PRO* 3.6 7.4 - - - +
2734 GLY* 4.0 4.7 + - - -
2744 ILE* 3.6 26.5 - - + -
2754 HIS* 3.4 41.1 - - + +
3094 ILE* 4.6 10.8 - - + -
3124 ARG* 3.3 49.6 - - + +
3134 MET* 4.2 16.8 - - + -
3164 GLU* 4.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2594 GLU* 2.7 63.8 + - - +
2604 THR* 2.7 24.9 - - - +
2624 PHE* 1.3 93.7 - - - +
2644 PRO* 1.3 58.6 - - - +
2654 SER* 3.1 20.1 + - - +
2664 PHE* 3.5 26.3 + - + +
3124 ARG* 3.4 10.7 + - - +
----------------------------------------------------------
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