Contacts of the helix formed by residues 14 - 28 (chain J) in PDB entry 4ADV
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 14 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TRP* 4.1 20.2 - - + -
12J ALA* 3.4 3.2 - - - +
13J PHE* 1.3 98.2 - - - +
15J HIS* 1.3 61.1 + - - +
16J ARG* 3.3 16.8 - - + +
17J LEU* 3.3 29.0 - - - +
18J ILE* 3.1 29.4 + - - +
70J HIS* 3.3 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A A 3.0 53.2 + - + +
1153A G 5.5 0.6 - - - -
14J ASP* 1.3 69.8 - - - +
16J ARG* 1.3 55.4 + - - +
17J LEU 2.8 16.5 + - - -
18J ILE* 3.2 25.1 - - + -
19J ASP* 2.9 61.8 + - + +
22J THR* 5.5 1.6 - - - +
70J HIS* 4.2 6.7 + - + +
72J ARG* 3.4 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL 6.1 0.6 - - - +
16C PRO* 6.2 2.0 - - - +
14J ASP* 3.3 20.5 - - + +
15J HIS* 1.3 77.0 - - - +
17J LEU* 1.3 71.7 + - + +
19J ASP* 4.8 0.4 - - - -
20J GLN* 3.2 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C THR* 4.9 13.0 - - - +
12J ALA* 4.8 1.8 - - + -
14J ASP* 3.3 21.6 + - - +
16J ARG* 1.3 94.9 - - + +
18J ILE* 1.3 62.2 + - - +
19J ASP 2.9 6.1 + - - -
20J GLN* 3.5 13.2 + - - +
21J ALA* 3.0 26.9 + - - +
93J ALA* 5.5 4.0 - - + -
94J ALA* 5.4 9.9 - - + +
95J GLY* 4.5 11.7 - - - +
96J VAL* 4.0 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J LEU* 3.5 33.4 - - + +
12J ALA* 3.4 31.9 - - + +
14J ASP 3.1 15.8 + - - +
15J HIS* 3.2 29.2 - - + -
17J LEU* 1.3 77.8 - - - +
19J ASP* 1.3 65.6 + - - +
21J ALA* 4.1 3.6 - - - -
22J THR* 3.3 15.0 + - - +
70J HIS* 4.1 10.5 - - + +
72J ARG* 3.3 39.9 - - + +
96J VAL* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J HIS* 2.9 52.0 + - + +
16J ARG 5.0 0.2 - - - -
17J LEU 2.9 1.2 - - - -
18J ILE* 1.3 75.5 - - - +
20J GLN* 1.3 77.0 + - + +
22J THR* 2.8 30.0 + - - +
23J ALA* 2.9 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG 3.2 22.3 - - - +
17J LEU* 3.5 11.2 + - - +
19J ASP* 1.3 89.6 - - + +
21J ALA* 1.3 63.9 + - - +
23J ALA* 4.0 5.6 - - - +
24J GLU* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J LEU* 3.4 11.7 - - + +
17J LEU 3.0 21.0 + - - +
18J ILE 4.1 1.3 - - - +
20J GLN* 1.3 77.3 - - - +
22J THR* 1.3 60.3 + - - +
24J GLU* 3.7 19.3 - - - +
25J ILE* 4.1 7.8 + - - +
93J ALA* 4.8 7.9 - - + -
96J VAL* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J LEU* 3.6 15.3 - - - +
15J HIS* 5.5 0.9 - - - +
18J ILE* 3.3 17.4 + - - +
19J ASP* 2.8 23.4 + - - +
21J ALA* 1.3 77.8 - - - +
23J ALA* 1.3 81.1 + - + +
24J GLU 2.9 1.8 - - - -
25J ILE* 2.9 18.1 + - - +
26J VAL* 3.3 14.8 + - + +
39J PRO* 5.0 4.1 - - + +
72J ARG* 4.4 16.0 - - + +
74J VAL* 3.6 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ASP* 2.9 21.5 + - - +
20J GLN* 4.0 6.7 - - - +
22J THR* 1.3 81.0 - - + +
24J GLU* 1.3 63.2 + - - +
26J VAL* 3.5 9.6 + - - +
27J GLU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J GLN* 2.9 20.9 + - - +
21J ALA* 3.7 14.6 - - - +
23J ALA* 1.3 77.9 - - - +
25J ILE* 1.3 51.7 + - + +
27J GLU* 3.1 7.7 + - - +
28J THR* 2.5 49.5 + - + +
90J LEU* 3.0 44.9 - - + +
92J LEU* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 3.8 34.3 - - + -
10J LEU* 3.8 23.8 - - + -
21J ALA 4.1 6.5 - - - +
22J THR* 2.9 12.0 + - - +
24J GLU* 1.3 80.0 - - + +
26J VAL* 1.3 66.0 + - + +
27J GLU 2.9 0.2 + - - -
28J THR* 3.8 1.8 - - - -
29J ALA* 2.6 44.9 + - + -
30J LYS 2.9 5.5 + - - -
36J VAL* 5.2 1.6 - - + -
74J VAL* 4.4 20.2 - - + -
75J ASP 5.9 0.7 - - - +
76J ILE* 5.0 9.9 - - + -
87J LEU* 4.0 22.0 - - + -
90J LEU* 5.4 0.7 - - + -
98J VAL* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 3.3 18.1 + - + +
23J ALA* 3.8 8.7 - - - +
25J ILE* 1.3 76.6 - - - +
27J GLU* 1.3 56.7 - - - +
30J LYS* 2.9 59.1 - - - +
36J VAL* 5.0 3.1 - - + -
39J PRO* 4.5 21.5 - - + -
74J VAL* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ALA* 2.9 18.9 + - - +
24J GLU* 3.5 6.1 - - - +
25J ILE 2.9 0.6 + - - -
26J VAL* 1.3 76.9 - - - +
28J THR* 1.3 70.8 + - + +
30J LYS 3.1 16.3 - - - +
31J ARG* 3.6 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLU* 2.5 39.1 + - + +
25J ILE* 3.8 0.2 - - - -
27J GLU* 1.3 81.2 - - + +
29J ALA* 1.3 66.5 + - - -
30J LYS 2.8 10.3 + - - -
31J ARG* 3.2 44.6 + - - +
83J THR* 5.4 0.9 - - - +
86J ALA* 4.9 11.7 - - - +
90J LEU* 3.2 32.0 - - + +
----------------------------------------------------------
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