Contacts of the strand formed by residues 31 - 37 (chain H) in PDB entry 1FO0
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 THR 31 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H TYR* 3.3 3.1 - - - -
28H VAL* 2.8 40.2 + - - +
29H ASP* 3.6 6.1 + - - +
30H ASP* 1.3 72.3 - - - +
32H GLU* 1.3 73.9 + - - +
33H PHE* 3.4 4.8 + - + +
51H TRP* 6.2 0.7 - - - +
179H LEU* 4.5 18.5 - - + +
209H TYR* 3.3 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL* 3.6 13.6 - - + +
26H GLY 3.4 7.6 - - - -
27H TYR* 3.3 20.2 + - + -
30H ASP 4.0 0.4 + - - -
31H THR* 1.3 82.5 - - - +
33H PHE* 1.3 61.7 + - - +
34H VAL 4.0 0.9 - - - +
35H ARG* 2.6 47.7 + - - +
48H ARG* 3.0 44.7 + - + +
49H ALA* 4.5 2.8 - - - +
55L SER* 4.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 3.8 10.8 - - + -
7H TYR* 3.8 4.7 - - - -
26H GLY* 3.0 35.2 + - - -
27H TYR 3.6 3.6 - - - -
28H VAL* 3.5 23.1 - - + -
31H THR* 4.1 3.4 - - + +
32H GLU* 1.3 75.3 - - - +
34H VAL* 1.3 78.2 + - + +
48H ARG* 2.7 29.0 + - - -
49H ALA* 3.6 7.9 + - + -
51H TRP* 3.8 24.5 - + + -
52H MET* 3.5 34.9 - - + +
59H TYR* 4.4 0.2 - - - -
171H TYR* 3.6 47.6 - + - -
179H LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 4.1 5.4 - - + +
25H VAL* 3.7 6.6 - - - +
26H GLY* 3.2 31.6 + - - +
32H GLU* 4.0 0.3 - - - +
33H PHE* 1.3 118.2 - - + +
35H ARG* 1.3 66.6 + - - +
45H TYR* 3.6 24.7 - - + -
46H GLU 3.3 5.6 - - - -
48H ARG* 3.6 3.6 - - - +
52H MET* 4.1 6.5 - - + -
59H TYR* 4.1 7.0 - - - +
60H TRP* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H MET* 2.8 21.9 - - + +
24H GLU 3.4 11.2 - - - +
25H VAL* 3.3 17.4 - - + +
32H GLU* 2.6 40.0 + - - -
34H VAL* 1.3 79.1 - - - +
36H PHE* 1.3 69.9 + - - +
37H ASP* 4.9 3.6 - - + +
44H ARG 3.6 2.3 - - - +
45H TYR* 4.5 4.0 - - - -
46H GLU* 2.8 36.0 + - + +
48H ARG* 3.6 33.0 - - + +
53L ASP* 3.0 31.7 + - - +
54L MET 2.8 29.1 + - - -
55L SER* 3.2 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H TYR* 4.0 26.2 - + - -
23H MET* 3.1 7.8 - - - +
24H GLU* 2.8 42.9 + - + +
35H ARG* 1.3 76.3 - - - +
37H ASP* 1.3 63.4 + - - +
38H SER* 3.6 22.4 - - - -
43H PRO* 3.6 39.0 - - + -
44H ARG* 3.5 21.3 - - - -
45H TYR* 3.5 24.0 - + + -
64H THR* 4.2 9.9 - - + -
67H ALA* 3.8 23.1 - - + -
68H LYS* 4.5 11.4 - - + -
71H GLU* 4.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ARG* 3.0 35.0 + - - -
22H TYR 3.5 4.6 - - - +
23H MET* 3.4 20.5 - - + +
35H ARG* 4.9 5.6 - - + +
36H PHE* 1.3 81.5 - - - +
38H SER* 1.3 63.5 + - - +
39H ASP* 3.1 28.8 + - - +
40H ALA* 3.5 12.8 - - + +
43H PRO* 3.4 12.6 - - - +
44H ARG 4.8 2.5 + - - -
53L ASP* 5.1 4.9 - - - +
----------------------------------------------------------
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