Contacts of the helix formed by residues 14 - 30 (chain B) in PDB entry 5D0Y
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 ARG 14 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 1.3 74.9 - - + +
15B GLU* 1.3 62.8 + - - +
16B LEU 3.0 4.5 - - - -
17B VAL* 2.8 62.9 + - - +
18B LEU* 3.5 9.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.3 44.9 - - - +
14B ARG* 1.3 82.7 + - - +
16B LEU* 1.3 71.5 + - + +
18B LEU* 3.1 14.6 - - + +
19B LEU* 2.9 22.9 + - - +
55B PHE* 3.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.0 34.8 - - + +
14B ARG 2.9 1.6 + - - -
15B GLU* 1.3 86.6 - - + +
17B VAL* 1.3 66.0 + - - +
18B LEU 3.2 0.2 - - - -
19B LEU* 3.8 28.2 - - + +
20B ALA* 3.4 18.2 + - - +
55B PHE* 5.8 0.9 - - + -
59B TRP* 5.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 4.2 7.2 - - - +
14B ARG* 2.8 48.5 + - - +
16B LEU* 1.3 77.8 - - - +
18B LEU* 1.3 66.9 + - + +
20B ALA* 3.4 5.3 + - - +
21B MET* 3.1 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.5 13.0 + - - +
15B GLU* 3.1 17.7 - - + +
17B VAL* 1.3 82.5 - - + +
19B LEU* 1.3 66.6 - - - +
21B MET* 2.9 28.6 + - + +
22B VAL* 3.0 15.4 + - + +
54B LEU* 5.0 13.7 - - + -
55B PHE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU 2.9 17.5 + - - +
16B LEU* 3.8 28.0 - - + +
17B VAL 3.4 0.2 - - - -
18B LEU* 1.3 71.7 - - - +
20B ALA* 1.3 64.4 + - - +
22B VAL* 3.0 6.0 - - - +
23B ILE* 2.9 48.4 + - + +
51B LEU* 4.2 10.5 - - + -
55B PHE* 3.5 27.1 - - + -
59B TRP* 4.6 24.5 - - + +
62B ALA* 6.2 1.6 - - + -
63B GLY* 4.3 9.6 - - - +
66B LEU* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 3.4 8.9 + - - +
17B VAL* 3.6 10.3 - - - +
18B LEU 3.1 0.6 - - - -
19B LEU* 1.3 77.8 - - - +
21B MET* 1.3 53.2 + - + +
23B ILE* 2.8 13.8 + - - +
24B ALA* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.1 34.5 - - + +
18B LEU* 2.9 21.2 + - + +
20B ALA* 1.3 73.6 - - + +
22B VAL* 1.3 51.1 + - - +
24B ALA* 3.3 9.6 - - - +
25B ILE* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.0 15.3 + - + +
19B LEU 3.0 19.3 - - - +
21B MET* 1.3 74.1 - - - +
23B ILE* 1.3 60.4 + - - +
24B ALA 3.2 0.2 - - - -
25B ILE* 3.6 9.3 - - + +
26B LYS* 2.9 27.9 + - - +
47B GLY 4.5 2.5 - - - +
50B MET* 3.6 46.4 - - + -
51B LEU* 3.6 28.6 - - + +
54B LEU* 5.1 3.6 - - + -
55B PHE* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.9 35.5 + - + +
20B ALA* 2.8 10.8 + - - +
22B VAL* 1.3 75.4 - - - +
24B ALA* 1.3 60.8 + - - +
26B LYS* 3.2 3.7 + - - +
27B VAL* 2.8 34.2 + - + +
51B LEU* 3.6 15.9 - - + -
63B GLY* 3.1 42.0 - - - +
66B LEU* 4.9 11.7 - - + -
67B SER* 3.4 25.8 - - - +
70B VAL* 5.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 2.7 11.5 + - - +
21B MET* 3.3 14.4 - - - +
23B ILE* 1.3 79.5 - - - +
25B ILE* 1.3 61.6 + - - +
27B VAL* 3.8 5.6 - - - +
28B VAL* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 2.7 24.7 + - + +
22B VAL* 3.6 15.3 - - + +
24B ALA* 1.3 76.7 - - - +
26B LYS* 1.3 58.1 + - - +
28B VAL* 2.9 7.4 + - - +
29B LEU* 2.8 56.7 + - + +
47B GLY* 4.7 1.8 - - - -
50B MET* 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL 2.9 21.6 + - - +
23B ILE* 3.2 8.0 + - - +
25B ILE* 1.3 73.5 - - - +
27B VAL* 1.3 61.9 + - - +
29B LEU* 4.5 1.9 - - - +
30B GLY* 3.1 18.9 + - - -
44B GLY* 3.9 15.6 + - - +
47B GLY* 3.4 33.2 - - - +
48B SER* 3.4 29.0 - - - +
51B LEU* 4.6 5.6 - - + -
64B GLY* 4.8 8.5 - - - -
67B SER* 3.3 25.0 + - - +
89B ALA* 4.4 11.6 - - - +
92B GLU* 3.7 14.6 + - - -
93B SER* 4.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 2.8 22.6 + - + +
24B ALA* 3.8 6.3 - - - +
26B LYS* 1.3 76.1 - - - +
28B VAL* 1.3 70.1 + - + +
30B GLY* 3.3 8.7 + - - -
31B GLN* 3.5 13.5 + - - +
67B SER* 3.2 35.0 - - - +
70B VAL* 4.1 16.6 - - + -
71B SER* 3.9 24.2 + - - +
74B ILE* 5.0 2.7 - - + -
75B PHE* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.0 22.6 + - + +
25B ILE* 2.9 7.3 + - - +
27B VAL* 1.3 76.4 - - + +
29B LEU* 1.3 65.1 + - + +
30B GLY 3.0 1.1 - - - -
31B GLN* 2.8 34.3 + - - +
32B PHE* 3.6 17.3 - - + -
75B PHE* 5.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 2.8 40.3 + - + +
26B LYS* 4.5 2.9 - - - +
28B VAL* 1.3 78.8 - - + +
30B GLY* 1.3 64.1 + - - +
32B PHE* 2.9 34.0 + - + +
43B LEU* 3.6 40.5 - - + +
46B ILE* 3.9 34.8 - - + -
47B GLY* 4.2 4.3 - - - +
50B MET* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS 3.1 18.9 + - - -
27B VAL 3.6 4.0 - - - -
28B VAL 3.0 1.8 - - - -
29B LEU* 1.3 78.8 - - - +
31B GLN* 1.3 63.9 + - - +
32B PHE 3.1 2.2 + - - +
33B LYS* 3.4 27.2 + - - +
42B GLY* 5.7 0.2 - - - -
43B LEU 5.4 0.2 + - - -
44B GLY* 3.9 17.1 + - - -
71B SER* 5.7 0.9 - - - -
----------------------------------------------------------
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