Contacts of the helix formed by residues 34 - 49 (chain V) in PDB entry 5GJQ
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 SER 34 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32V TYR 3.9 1.0 + - - -
33V ILE* 1.3 78.2 - - - +
35V SER* 1.3 66.0 + - - +
36V LEU* 3.8 5.4 - - - +
37V ALA* 3.2 11.6 + - - +
38V LEU* 3.1 16.8 + - - +
69V VAL 3.0 15.7 + - - -
70V ILE* 2.9 38.4 + - - -
208V ARG* 4.1 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U LEU* 3.5 19.0 - - - +
175U LEU* 4.0 24.0 - - - +
33V ILE 3.7 0.6 + - - -
34V SER* 1.3 73.5 - - - +
36V LEU* 1.3 72.0 + - - +
38V LEU* 2.8 13.9 + - - +
39V LEU* 2.9 19.0 + - - +
208V ARG 4.0 4.8 + - - -
213V GLU* 2.4 41.2 + - - -
217V LEU* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U LEU* 5.2 1.1 - - - +
17U LEU* 4.1 33.9 - - + +
18U SER* 4.5 5.4 - - - +
21U ASP* 4.6 10.3 - - + -
34V SER* 3.8 6.3 - - - +
35V SER* 1.3 81.9 + - - +
37V ALA* 1.3 68.0 + - - +
39V LEU* 4.1 3.7 - - - +
40V LYS* 3.0 38.0 + - + +
70V ILE* 3.5 22.0 - - + +
71V ASP* 5.3 0.7 - - - -
104V ARG* 4.6 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V ILE* 3.8 14.1 - - + -
34V SER* 3.2 22.4 + - - +
35V SER 3.1 0.6 - - - -
36V LEU* 1.3 84.6 - - - +
38V LEU* 1.3 58.1 + - - +
40V LYS* 3.3 4.1 + - - +
41V MET* 2.8 34.7 + - + +
69V VAL* 4.2 9.4 - - + +
70V ILE 4.5 4.9 - - - +
71V ASP 5.2 0.9 - - - -
72V VAL* 3.9 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171U GLY* 4.4 8.1 - - - +
174U HIS* 3.4 34.8 - - + -
175U LEU* 3.7 18.6 - - + -
33V ILE* 4.1 16.6 - - + +
34V SER 3.1 7.5 + - - +
35V SER 2.8 8.3 + - - +
37V ALA* 1.3 78.6 - - - +
39V LEU* 1.3 57.7 + - - +
41V MET* 3.0 16.0 - - + +
42V LEU* 3.0 45.4 + - + +
155V VAL* 4.1 11.9 - - + -
157V ILE* 4.5 22.0 - - + -
207V TYR* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U PRO* 4.4 23.3 - - + +
14U LEU* 3.9 10.7 - - + +
17U LEU* 3.8 25.6 - - + -
167U ALA 5.4 0.2 - - - -
168U GLU* 4.2 15.1 - - + +
171U GLY* 3.3 39.5 - - - +
172U VAL* 3.6 21.1 - - + +
175U LEU* 4.6 7.4 - - + -
35V SER 2.9 19.8 + - - +
36V LEU* 4.1 3.4 - - - +
38V LEU* 1.3 74.8 - - - +
40V LYS* 1.3 64.7 + - - +
42V LEU* 3.4 3.7 + - - +
43V LYS* 2.9 26.2 + - - +
217V LEU* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U LEU* 3.2 33.0 - - + +
18U SER* 5.5 7.7 - - - -
52U ASN* 3.7 23.2 + - - +
53U SER 5.1 3.6 + - - -
82U PHE* 5.8 4.4 - - - -
36V LEU* 3.0 35.8 + - + +
37V ALA* 3.6 3.4 - - - +
39V LEU* 1.3 75.4 - - - +
41V MET* 1.3 64.7 - - - +
43V LYS* 3.3 1.9 + - - +
44V HIS* 3.0 26.4 + - - +
71V ASP* 6.2 0.4 - - - -
72V VAL* 3.4 41.7 - - + +
73V PHE* 5.1 2.9 - - - +
104V ARG* 5.9 7.0 - - - +
112V TYR* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 41 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V ILE* 5.2 8.1 - - + -
37V ALA* 2.8 21.3 + - + +
38V LEU* 3.0 23.8 - - + +
40V LYS* 1.3 77.6 - - - +
42V LEU* 1.3 66.2 + - - +
44V HIS* 3.1 2.1 + - - +
45V GLY* 2.9 20.8 + - - -
57V MET* 4.6 9.2 - - + -
72V VAL* 4.2 22.1 - - + +
112V TYR* 3.2 59.3 - - + -
143V VAL* 4.5 11.4 - - + -
145V VAL* 3.4 28.1 - - + +
157V ILE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167U ALA* 2.8 30.1 - - + +
170U VAL* 3.5 14.8 - - + -
171U GLY* 3.0 42.6 - - - +
38V LEU* 3.0 25.5 + - + +
39V LEU* 4.0 2.0 - - - +
41V MET* 1.3 78.4 - - - +
43V LYS* 1.3 57.6 + - - +
45V GLY* 4.6 1.3 - - - +
46V ARG* 2.9 24.1 + - - +
145V VAL* 3.6 27.8 - - + -
147V PRO* 5.3 6.3 - - + +
150V SER* 4.7 5.8 - - - +
155V VAL* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U HIS* 4.7 7.6 - - - -
14U LEU* 3.7 16.6 - - + -
51U SER* 2.3 39.4 + - - +
52U ASN* 5.5 2.0 - - + +
86U ASN* 5.4 1.6 - - - +
89U GLU* 3.1 19.7 + - - +
165U GLU* 5.7 6.5 - - + -
167U ALA* 3.2 9.3 - - + +
168U GLU* 3.2 29.2 - - - +
39V LEU 2.9 13.5 + - - +
40V LYS 3.5 4.5 - - - +
41V MET 3.1 0.2 + - - -
42V LEU* 1.3 78.5 - - - +
44V HIS* 1.3 65.5 + - - +
46V ARG* 3.3 1.6 + - - +
47V ALA* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85U VAL* 5.7 4.6 + - + +
86U ASN* 6.4 2.9 - - + -
40V LYS 3.0 16.6 + - - +
41V MET 3.7 2.9 - - - +
43V LYS* 1.3 76.5 - - - +
45V GLY* 1.3 64.2 + - - +
47V ALA* 3.1 9.5 + - + +
48V GLY* 3.0 20.9 + - - -
53V VAL* 3.5 30.0 - - + +
54V MET 3.6 16.6 - - - -
74V ALA* 3.5 24.9 - - + +
75V MET 4.3 7.0 + - - -
77V GLN* 4.5 3.6 + - - -
112V TYR* 2.3 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V MET 2.9 14.7 + - - -
42V LEU* 3.9 2.0 - - - -
44V HIS* 1.3 74.9 - - - +
46V ARG* 1.3 62.1 + - - +
47V ALA 3.0 1.6 + - - -
48V GLY* 3.0 12.5 + - - -
49V VAL* 3.4 8.8 + - - +
53V VAL* 4.1 16.8 - - - +
112V TYR* 5.3 1.2 - - - -
114V SER* 4.7 4.5 + - - -
145V VAL* 6.0 3.1 - - - -
147V PRO* 3.6 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85K ILE* 6.1 2.6 - - - +
67L GLU* 3.1 36.7 + - - +
85L ARG* 3.5 25.3 + - - +
165U GLU* 5.6 6.9 + - + -
166U GLU* 4.1 39.9 + - + +
167U ALA* 3.6 14.8 - - + +
170U VAL* 6.5 0.2 - - + -
42V LEU 2.9 22.0 + - - +
43V LYS 3.9 0.9 - - - +
45V GLY* 1.3 72.3 - - - +
47V ALA* 1.3 57.6 + - - +
48V GLY 3.4 0.2 - - - -
49V VAL* 3.6 36.9 - - - +
147V PRO* 3.8 24.5 + - + +
148V ILE* 5.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85L ARG* 3.4 34.4 - - - +
86U ASN* 4.9 15.0 - - - +
43V LYS* 2.9 26.9 + - + +
44V HIS* 3.4 11.7 - - + +
45V GLY 3.0 0.4 - - - -
46V ARG* 1.3 80.6 - - - +
48V GLY* 1.3 60.8 + - - +
49V VAL 3.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L ARG* 5.2 0.3 - - - +
85L ARG* 5.3 0.2 - - - -
44V HIS* 3.0 13.8 + - - -
45V GLY 3.0 4.8 + - - -
47V ALA* 1.3 77.8 - - - +
49V VAL* 1.3 71.3 + - - +
50V PRO* 4.1 0.2 - - - +
51V MET* 3.1 21.1 + - - +
53V VAL* 3.9 20.0 - - - -
77V GLN* 5.0 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L GLY* 6.4 0.4 - - - -
83L CYS 4.2 14.4 - - - +
84L ARG* 3.4 28.6 - - - +
85L ARG* 4.2 3.8 - - - +
104L THR* 5.3 2.5 - - + -
106L THR* 5.2 4.5 - - + +
45V GLY 3.4 9.5 + - - +
46V ARG* 3.6 41.7 - - - +
47V ALA 3.3 1.8 - - - -
48V GLY* 1.3 90.5 - - - +
50V PRO* 1.3 76.7 - - + +
116V PRO* 5.1 2.9 - - + -
147V PRO* 4.7 4.9 - - + -
148V ILE* 4.0 25.8 - - + -
----------------------------------------------------------
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