Contacts of the helix formed by residues 23 - 34 (chain V) in PDB entry 4UJ3
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 GLY 23 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V GLY 3.2 0.6 - - - -
22V VAL* 1.3 81.5 - - - +
24V LYS* 1.3 67.1 + - - +
25V SER 3.3 2.5 - - - -
26V ASN* 3.1 3.3 + - - +
27V LEU* 3.0 28.5 + - - +
90V VAL* 5.2 0.2 - - - -
124V ASN* 3.8 9.4 + - - -
200V GNP 3.0 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V LEU* 3.6 31.1 - - + +
17V ILE* 3.5 31.9 - - - +
18V GLY 2.8 11.5 + - - +
19V ASP 2.6 30.5 + - - -
22V VAL* 3.7 11.8 - - + +
23V GLY* 1.3 77.7 - - - +
25V SER* 1.3 64.1 + - - +
27V LEU* 3.1 12.6 + - - +
28V LEU 3.1 16.6 + - - -
66V ASP* 4.1 7.6 - - - +
67V THR* 3.4 24.9 - - - -
69V GLY* 3.9 4.1 - - - +
90V VAL* 4.3 10.1 - - + -
200V GNP 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V LYS* 1.3 74.0 - - - +
26V ASN* 1.3 58.4 + - - +
28V LEU* 3.4 6.4 - - - +
29V SER* 3.1 25.1 + - - -
40V SER* 5.7 1.3 - - - -
43V THR* 2.6 11.0 + - - +
66V ASP* 2.7 25.3 + - - -
200V GNP 2.7 17.2 + - - -
201V MG 1.8 30.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V GLY 3.1 3.7 + - - +
25V SER* 1.3 75.1 - - - +
27V LEU* 1.3 66.8 + - - +
28V LEU 3.1 0.9 - - - -
29V SER* 3.0 7.6 + - - -
30V ARG* 3.0 26.2 + - - +
35V GLU 4.4 0.3 - - - +
36V PHE* 3.2 18.3 - - + -
37V ASN* 3.0 32.3 + - - +
40V SER* 3.1 22.5 + - - -
155V ALA* 3.7 19.8 - - + +
200V GNP 2.5 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V LEU* 5.1 7.0 - - + -
23V GLY 3.0 17.6 + - - +
24V LYS* 3.1 8.5 + - - +
26V ASN* 1.3 76.6 - - - +
28V LEU* 1.3 62.7 + - - +
30V ARG* 3.9 3.1 - - - +
31V PHE* 3.2 25.8 + - - +
88V LEU* 5.8 3.1 - - + -
90V VAL* 3.9 36.6 - - + -
122V VAL* 4.4 7.9 - - + -
124V ASN* 3.4 17.3 - - - +
153V THR* 3.4 30.7 - - + +
155V ALA* 4.0 9.8 - - + +
161V VAL* 4.1 16.2 - - + +
165V PHE* 3.9 16.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V LEU* 4.1 10.2 - - + +
24V LYS 3.1 11.4 + - - +
25V SER* 3.4 9.9 - - - +
27V LEU* 1.3 74.0 - - - +
29V SER* 1.3 65.8 + - - +
31V PHE* 3.3 2.6 + - - +
32V THR* 2.9 57.4 + - + +
33V ARG* 5.2 5.4 - - - +
47V GLU* 4.7 9.9 - - + +
48V PHE* 5.2 2.5 - - - -
49V ALA* 3.7 18.8 - - + +
64V ILE* 3.6 35.2 - - + +
66V ASP* 3.6 31.6 - - + +
165V PHE* 5.1 1.1 - - - -
755X VAL* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V SER 3.1 8.2 + - - -
26V ASN* 3.0 22.9 + - - -
28V LEU* 1.3 79.7 - - - +
30V ARG* 1.3 61.7 + - - +
32V THR* 3.9 5.6 - - - -
33V ARG* 3.1 48.7 + - - +
34V ASN 3.1 6.2 + - - -
35V GLU* 2.6 31.5 + - - -
36V PHE* 4.3 0.2 - - - -
37V ASN 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V ASN 3.0 18.4 + - - +
27V LEU* 3.9 3.6 - - - +
29V SER* 1.3 77.9 + - - +
31V PHE* 1.3 59.3 + - - +
34V ASN* 2.9 59.1 + - - +
35V GLU 3.6 7.6 - - - +
36V PHE* 3.3 21.8 - - - +
51V ARG* 5.2 0.9 + - - -
155V ALA* 3.1 19.3 + - - +
156V LEU 2.9 28.1 + - - -
157V ASP 4.6 0.2 - - - -
158V SER* 2.8 29.2 + - - -
161V VAL* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27V LEU 3.2 16.5 + - - +
28V LEU 3.8 2.0 - - - +
30V ARG* 1.3 82.8 - - - +
32V THR* 1.3 72.6 + - + +
34V ASN 4.7 0.3 + - - -
51V ARG* 3.0 75.2 + - + +
53V ILE* 4.6 10.3 - - + -
62V ALA* 4.6 5.6 - - + -
64V ILE* 4.1 15.3 - - + -
161V VAL* 4.3 8.7 - - + -
162V GLU* 4.3 13.5 - - - -
165V PHE* 3.3 64.6 - + + -
169V LEU* 4.6 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V LEU* 2.9 40.4 + - + +
31V PHE* 1.3 91.8 - - + +
33V ARG* 1.3 86.4 + - - +
34V ASN 3.7 0.2 - - - -
49V ALA* 3.6 21.5 - - + +
50V THR 4.3 18.5 - - - +
51V ARG* 4.5 11.7 - - - +
64V ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V LEU* 5.2 5.5 - - - +
29V SER* 3.1 29.8 + - - +
32V THR* 1.3 94.0 + - - +
34V ASN* 1.3 70.0 + - - +
35V GLU* 3.1 40.6 + - + +
49V ALA* 5.1 5.1 - - - +
755X VAL* 3.9 29.8 - - - +
756X LYS* 6.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V SER 3.1 2.8 + - - -
30V ARG* 2.9 54.0 + - - +
31V PHE 4.6 0.6 + - - -
32V THR 3.7 1.2 - - - -
33V ARG* 1.3 78.0 - - - +
35V GLU* 1.3 61.1 + - - +
158V SER* 4.3 1.2 + - - -
----------------------------------------------------------
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