Contacts of the helix formed by residues 39 - 49 (chain R) in PDB entry 1U8F
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 ASP 39 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193O GLY* 5.8 1.4 - - - +
196O TRP* 5.0 3.3 + - - -
36R PRO 5.3 0.2 + - - -
37R PHE 4.2 0.6 - - - -
38R ILE* 1.3 76.6 - - - +
40R LEU* 1.3 59.6 + - - +
41R ASN* 3.1 13.0 + - - +
42R TYR* 2.8 30.3 + - - +
43R MET* 2.9 26.3 + - - +
78R GLN* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R ASP* 1.3 73.6 - - - +
41R ASN* 1.3 68.2 + - - +
43R MET* 3.0 20.6 + - - +
44R VAL* 3.2 11.3 + - - +
62R ALA* 3.7 21.8 - - + -
65R GLY* 3.4 38.4 - - - +
66R LYS 3.7 4.0 - - - +
67R LEU* 3.6 40.4 - - + +
76R ILE* 3.9 17.4 - - + +
78R GLN* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196O TRP* 3.6 18.9 - - + -
39R ASP* 3.1 8.1 + - - +
40R LEU* 1.3 80.3 - - - +
42R TYR* 1.3 61.7 + - - +
44R VAL* 3.4 18.0 + - - +
45R TYR* 3.5 8.5 + - - +
62R ALA* 3.6 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190O GLY 3.7 6.2 + - - -
191O PRO* 3.6 7.4 - - + +
192O SER* 2.7 31.5 + - - -
193O GLY* 3.5 27.4 - - - -
196O TRP* 3.3 53.6 + + + +
37R PHE 4.3 6.1 - - - -
38R ILE* 3.8 21.1 - - + -
39R ASP* 2.8 27.4 + - - +
41R ASN* 1.3 74.6 - - - +
43R MET* 1.3 67.7 + - - +
45R TYR* 3.2 11.9 + + - -
46R MET* 2.9 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R PHE* 3.8 22.7 - - + -
33R ILE* 3.7 26.2 - - + -
35R ASP* 3.9 20.0 - - + +
38R ILE* 3.5 29.6 - - + +
39R ASP 2.9 18.4 + - - +
40R LEU* 3.0 10.0 + - - +
42R TYR* 1.3 76.8 - - - +
44R VAL* 1.3 63.4 + - - +
46R MET* 3.8 1.1 - - - +
47R PHE* 2.9 28.3 + - - +
67R LEU* 4.4 15.3 - - + -
76R ILE* 3.7 42.2 - - + -
78R GLN* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R LEU 3.2 12.5 + - - +
41R ASN* 3.5 10.1 - - - +
42R TYR 3.2 0.2 - - - -
43R MET* 1.3 78.6 - - - +
45R TYR* 1.3 57.8 + - - +
47R PHE* 3.8 1.2 - - - +
48R GLN* 2.9 44.9 + - - +
60R VAL* 3.8 32.0 - - + +
61R LYS* 3.8 3.4 - - - -
62R ALA* 3.6 32.8 - - + +
67R LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196O TRP* 3.5 57.4 + + + -
197O ARG* 4.3 0.2 - - - -
200O ARG* 3.0 40.5 + - - +
279P HIS* 5.6 1.1 - - + -
280P GLN* 2.6 41.3 + - + -
41R ASN 3.5 1.4 + - - +
42R TYR* 3.2 25.6 + + - +
44R VAL* 1.3 81.3 - - - +
46R MET* 1.3 68.8 + - + +
48R GLN* 3.4 14.5 - - - +
49R TYR* 3.2 49.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189O ASP* 5.6 1.1 - - + -
190O GLY* 3.5 37.9 - - - +
191O PRO* 3.7 6.7 - - + -
200O ARG* 6.6 0.2 - - - +
11R PHE* 5.0 0.4 - - + -
16R ARG* 3.3 53.3 + - - +
38R ILE* 3.5 35.2 - - + -
42R TYR* 2.9 42.1 + - + +
43R MET* 4.0 4.7 - - - +
45R TYR* 1.3 83.1 - - + +
47R PHE* 1.3 57.9 + - - +
49R TYR 3.1 18.8 - - - +
50R ASP* 5.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R PHE* 3.6 24.5 - + + -
16R ARG* 3.6 30.4 - - + +
19R THR* 3.6 18.4 - - + -
20R ARG* 3.1 49.4 + - + -
23R PHE* 5.0 0.4 - + - -
43R MET 2.9 18.2 + - - +
44R VAL 3.9 2.0 - - - +
46R MET* 1.3 79.0 - - - +
48R GLN* 1.3 59.5 + - - +
56R PHE* 3.5 41.2 - + + +
60R VAL* 4.1 15.7 - - + -
67R LEU* 5.5 1.1 - - + -
69R ILE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P HIS* 4.3 17.6 + - - -
44R VAL* 2.9 29.1 + - - +
45R TYR* 3.4 26.3 - - - +
47R PHE* 1.3 79.2 - - - +
49R TYR* 1.3 91.3 + - + +
55R LYS* 3.2 9.9 - - - +
56R PHE* 2.9 33.9 + - + +
60R VAL* 3.7 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189O ASP* 4.2 4.5 - - - +
200O ARG* 3.7 15.3 + - - +
277P THR* 4.8 1.6 + - - -
279P HIS* 2.8 40.1 - + + +
281P VAL* 4.3 8.1 - - + +
285P ASP* 3.4 36.3 - - + +
16R ARG* 5.8 0.2 + - - -
20R ARG* 4.6 0.2 - - - -
45R TYR* 3.2 29.8 + + + +
46R MET* 3.1 21.7 - - - +
48R GLN* 1.3 116.2 + - + +
50R ASP* 1.3 62.0 + - - +
55R LYS* 3.7 32.7 - - + +
----------------------------------------------------------
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