Contacts of the helix formed by residues 6 - 23 (chain A) in PDB entry 5A74
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 ASN 6 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 1.3 66.9 + - - +
8A HIS* 3.8 11.0 + - + +
9A ASP* 3.3 45.5 + - + +
10A GLN* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 1.3 78.1 - - - +
8A HIS* 1.3 58.0 + - - +
10A GLN* 3.9 6.8 - - + +
11A LEU* 3.1 34.6 + - + +
7B PHE* 4.1 40.2 - + + -
11B LEU* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 4.4 10.4 + - + +
7A PHE* 1.3 77.9 - - - +
9A ASP* 1.3 85.9 + - - +
11A LEU* 3.2 13.8 + - + +
12A LYS* 3.1 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 3.3 31.2 + - + +
8A HIS* 1.3 94.4 + - - +
10A GLN* 1.3 61.3 + - - +
12A LYS* 3.1 11.2 + - - +
13A PHE* 3.0 52.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN 3.1 21.2 + - - +
7A PHE* 3.9 8.1 - - + +
8A HIS 3.2 0.4 - - - -
9A ASP* 1.3 78.4 - - - +
11A LEU* 1.3 65.3 + - - +
13A PHE* 3.6 27.8 - - - -
14A ALA* 3.1 25.3 + - - +
94A LYS 4.8 1.4 - - - +
97A PRO* 5.5 2.3 - - - +
98A TYR* 2.6 40.6 + - - +
11B LEU* 3.7 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.1 19.2 + - + +
8A HIS* 3.2 15.9 + - + +
10A GLN* 1.3 75.1 - - - +
12A LYS* 1.3 66.5 + - + +
14A ALA* 4.6 0.2 - - - -
15A TRP* 3.2 22.5 + - - +
10B GLN* 3.7 29.4 - - + +
11B LEU* 3.6 22.7 - - + -
14B ALA* 3.6 15.4 - - + +
98B TYR* 3.6 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 3.1 42.1 + - + +
9A ASP* 3.3 12.8 - - - +
11A LEU* 1.3 76.5 - - + +
13A PHE* 1.3 59.5 + - + +
15A TRP* 3.1 14.9 + - + +
16A LEU* 2.8 27.9 + - - +
64A ILE* 4.1 43.4 - - + +
100B GLN* 5.8 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 3.0 32.2 + - + +
10A GLN* 3.6 33.0 - - - +
11A LEU 3.4 0.2 - - - -
12A LYS* 1.3 74.6 - - + +
14A ALA* 1.3 53.0 + - - +
16A LEU* 3.1 3.9 + - + +
17A ALA* 2.7 36.0 + - - +
64A ILE* 3.9 34.3 - - + -
65A LEU* 4.6 4.3 - - + -
94A LYS* 3.7 62.8 - - + +
95A LEU* 3.6 14.4 - - + +
98A TYR* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 3.1 19.9 + - - +
11A LEU 3.8 4.0 - - - +
12A LYS 3.3 0.2 - - - -
13A PHE* 1.3 78.3 - - - +
15A TRP* 1.3 61.4 + - - +
17A ALA 3.4 0.3 + - - -
18A GLY 3.2 12.3 + - - -
98A TYR* 3.7 30.2 - - + -
11B LEU* 3.7 30.1 - - + +
14B ALA* 4.2 2.7 - - + -
15B TRP* 3.1 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.2 11.3 + - - +
12A LYS* 3.1 17.4 + - + +
14A ALA* 1.3 76.1 - - - +
16A LEU* 1.3 99.2 + - + +
18A GLY 3.3 1.7 + - - -
19A PHE* 3.0 40.6 + + + +
57A ILE* 3.9 26.2 - - + -
60A ASP* 6.2 0.7 - - + -
61A ILE* 4.2 9.2 - - + -
64A ILE* 4.2 23.3 - - + -
14B ALA* 3.2 21.8 + - + +
17B ALA 4.0 0.9 - - - -
18B GLY* 3.3 30.4 - - - -
21B ASP* 3.0 21.0 + - + -
98B TYR* 3.4 23.1 + - + -
100B GLN* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS 2.8 13.6 + - - +
13A PHE* 3.1 8.7 + - + +
15A TRP* 1.3 86.1 - - + +
17A ALA* 1.3 55.1 + - - +
19A PHE* 3.1 5.0 + - + -
20A VAL* 2.7 50.4 + - + +
46A LEU* 6.1 1.1 - - + -
48A VAL* 4.8 1.3 - - + -
61A ILE* 3.8 49.6 - - + -
64A ILE* 4.6 13.7 - - + -
65A LEU* 4.0 30.1 - - + -
95A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE 2.7 20.0 + - - +
14A ALA 3.6 2.2 - - - +
15A TRP 3.3 0.2 - - - -
16A LEU* 1.3 71.8 - - - +
18A GLY* 1.3 53.8 + - - +
20A VAL* 3.5 2.6 - - - +
21A ASP* 2.6 40.0 + - - +
95A LEU* 4.2 9.8 - - + +
98A TYR* 3.6 39.7 - - + +
99A LEU* 3.8 18.2 - - + +
15B TRP* 3.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.2 7.7 + - - -
15A TRP 3.3 1.8 + - - -
16A LEU 3.2 0.2 - - - -
17A ALA* 1.3 78.8 - - - +
19A PHE* 1.3 60.2 + - - +
21A ASP 3.2 1.4 + - - -
22A ALA* 3.0 19.9 + - - +
15B TRP* 3.2 40.7 - - - -
19B PHE* 3.5 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.0 30.6 + + + +
16A LEU* 3.4 15.0 - - + +
18A GLY* 1.3 75.7 - - - +
20A VAL* 1.3 53.9 + - - +
22A ALA 3.2 0.3 + - - -
23A ASP* 2.6 42.9 + - + +
24A GLY 3.6 0.2 + - - -
48A VAL* 3.6 32.5 - - + -
49A PHE 4.4 0.2 - - - -
50A GLN* 3.5 30.7 - - + -
57A ILE* 4.7 7.0 - - + -
61A ILE* 4.2 11.9 - - + -
18B GLY 3.5 18.4 - - - -
21B ASP* 3.7 29.8 - - + -
22B ALA* 3.8 6.1 - - + -
101B LEU* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 2.7 35.7 + - + +
17A ALA* 3.7 3.4 - - - +
19A PHE* 1.3 68.1 - - - +
21A ASP* 1.3 67.2 + - - +
22A ALA 2.9 1.6 - - - -
24A GLY* 2.9 32.7 + - - +
25A CYS 4.7 0.7 - - - +
26A ILE* 4.2 23.3 - - + -
46A LEU* 4.2 18.8 - - + -
48A VAL* 3.9 25.1 - - + -
95A LEU* 4.4 3.6 - - + -
99A LEU* 4.1 17.5 - - + -
102A LYS* 3.4 11.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.6 19.5 + - - +
18A GLY 3.5 5.8 - - - +
20A VAL* 1.3 72.3 - - - +
22A ALA* 1.3 57.8 + - - +
99A LEU* 3.4 11.6 - - - +
100A GLN* 2.5 28.6 + - - +
101A LEU* 2.9 40.8 + - + +
102A LYS* 3.0 34.6 + - - +
15B TRP* 3.1 16.3 + - - +
19B PHE* 3.8 17.3 - - + -
50B GLN* 4.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.0 11.9 + - - +
20A VAL 2.9 1.6 + - - -
21A ASP* 1.3 79.4 - - - +
23A ASP* 1.3 55.9 + - - +
24A GLY 3.5 1.1 - - - -
102A LYS* 4.7 0.7 + - - -
19B PHE* 3.7 19.5 - - + -
22B ALA* 3.4 22.4 - - + -
23B ASP* 3.5 22.9 - - + +
515E G 2.7 13.2 + - - +
1525E MN 2.3 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.6 19.5 + - + +
22A ALA* 1.3 71.1 - - - +
24A GLY* 1.3 56.0 + - - +
48A VAL* 3.9 3.1 - - - +
49A PHE* 3.1 37.1 + - - +
50A GLN* 3.3 6.9 - - - +
22B ALA* 3.0 15.4 - - + +
23B ASP* 2.7 6.1 - - - +
514C C 3.0 15.1 + - - +
515E G 3.8 8.3 - - - -
615F G 3.5 0.2 - - - -
1625F MN 2.1 34.0 + - - -
1626F MN 2.1 33.4 + - - -
----------------------------------------------------------
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