Contacts of the strand formed by residues 8 - 12 (chain 1) 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 LEU 8 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 ALA* 1.3 76.0 - - - +
91 VAL* 1.3 65.8 + - - +
101 CYS* 4.1 1.8 - - + +
201 GLY 3.6 4.0 - - - +
211 PHE* 3.5 36.1 - - + -
901 PHE* 4.0 25.6 - - + -
941 LEU* 4.2 13.9 - - + -
961 VAL* 4.0 18.8 - - + -
981 PRO* 5.3 3.1 - - + -
1011 HIS* 3.7 35.7 - - + +
1021 PRO 2.8 10.9 + - - +
1031 THR* 4.2 13.7 - - + +
1041 LEU* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 LEU* 1.3 78.8 - - - +
101 CYS* 1.3 64.8 + - - +
111 ASP 4.9 0.2 - - - +
191 ALA* 3.2 12.5 - - - +
201 GLY 3.0 10.7 + - - -
221 ALA* 4.2 15.0 - - + -
941 LEU* 6.4 0.2 - - - -
1041 LEU* 3.3 26.0 - - + +
1061 THR* 5.4 3.4 - - + -
3401 TRP* 2.8 58.8 + - + +
3431 GLY* 3.9 26.2 - - - +
3441 SER* 3.9 9.6 - - - +
3471 ALA* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 10 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 LEU* 5.9 1.1 - - + -
91 VAL* 1.3 76.3 - - - +
111 ASP* 1.3 59.2 + - - +
121 ASN* 3.5 25.5 + - - -
171 VAL* 4.1 16.8 - - - -
181 LYS 3.6 3.1 - - - -
191 ALA* 4.5 3.8 - - + +
861 TRP* 4.0 17.9 - - - -
891 THR* 4.7 11.9 - - + -
901 PHE* 5.8 5.6 - - + -
1031 THR* 4.9 6.3 - - + -
1041 LEU 2.9 7.7 + - - +
1051 LEU* 3.5 20.5 - - + +
1061 THR* 3.4 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 VAL* 4.0 1.4 - - + -
101 CYS* 1.3 72.8 - - - +
121 ASN* 1.3 66.5 + - - +
131 GLY* 5.3 0.3 - - - -
171 VAL* 3.5 5.4 - - - -
181 LYS* 2.8 59.2 + - + +
1061 THR* 2.9 27.0 + - + +
1371 GLN* 4.2 7.6 - - - +
3391 VAL* 3.4 34.4 - - + +
3401 TRP* 4.0 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 12 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 CYS* 3.5 19.9 + - - -
111 ASP* 1.3 78.4 + - - +
131 GLY* 1.3 58.5 + - - +
161 LEU 4.7 0.2 - - - -
171 VAL* 4.5 9.3 - - + +
711 ILE* 3.5 23.8 - - + +
741 GLY* 5.3 3.1 - - - +
761 ILE* 5.5 3.2 - - + +
821 MET* 3.5 11.7 - - + +
851 ILE* 5.6 0.2 - - - +
861 TRP* 2.9 39.0 + - - +
1051 LEU* 4.3 7.3 - - - +
1061 THR* 3.7 21.1 + - - +
1191 MET* 4.8 3.6 - - - +
1371 GLN* 4.1 15.6 + - - +
----------------------------------------------------------
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