Contacts of the helix formed by residues 7 - 29 (chain A) in PDB entry 1CUN
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 MET 7 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 1.3 66.2 + - + +
9A HIS* 3.2 13.1 - - - +
10A GLN* 3.8 16.7 - - - +
11A PHE* 3.0 25.5 + - - +
68A THR* 4.2 22.8 - - + +
71A LYS* 4.5 28.3 - - + +
72A LEU* 4.2 21.5 - - + -
116B GLN* 6.3 0.6 - - - -
120B ASN* 4.8 6.3 + - - -
170B ASP* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 1.3 82.6 - - + +
9A HIS* 1.3 66.8 + - + +
11A PHE* 3.5 6.2 + - - +
12A PHE* 3.1 49.4 + - + -
72A LEU* 3.4 35.9 - - + -
77A THR* 4.1 17.7 - - + -
83A ILE* 4.5 6.5 - - + -
167B ARG* 4.1 22.4 - - + +
170B ASP* 4.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET 3.2 4.7 - - - +
8A VAL* 1.3 80.3 - - + +
10A GLN* 1.3 64.4 + - - +
12A PHE* 3.4 5.8 + - - +
13A ARG* 3.1 29.9 + - - +
120B ASN* 3.1 46.1 + - + +
123B GLU* 3.2 22.4 + - + +
124B GLU* 2.7 37.1 + - + -
167B ARG* 3.8 24.0 + - + +
170B ASP* 5.8 4.3 - - + -
171B VAL* 3.5 20.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
7A MET* 3.5 17.2 + - - +
8A VAL 3.4 0.2 - - - -
9A HIS* 1.3 76.6 - - - +
11A PHE* 1.3 60.3 + - - +
13A ARG* 2.8 46.1 + - - +
14A ASP* 2.8 67.0 + - - +
38B LEU* 4.0 6.3 - - - +
42B GLN* 4.0 14.5 + - - +
116B GLN* 3.2 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET 3.0 18.6 + - - +
8A VAL* 3.5 5.8 - - - +
10A GLN* 1.3 77.1 - - - +
12A PHE* 1.3 94.0 + + - +
14A ASP* 3.4 6.4 + - - +
15A MET* 2.9 39.7 + - + +
65A VAL* 3.2 40.0 - - + +
68A THR* 3.7 26.5 - - + -
69A GLY* 3.6 17.3 - - - -
72A LEU* 3.7 16.4 - - + -
83A ILE* 4.3 11.2 - - + -
87A LEU* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.1 41.8 + - + +
9A HIS* 4.0 4.9 - - - +
10A GLN 3.3 0.2 - - - -
11A PHE* 1.3 82.4 - + - +
13A ARG* 1.3 66.2 + - - +
15A MET* 3.2 30.8 - - + +
16A ASP* 2.9 33.9 + - - +
82A GLU* 4.2 14.1 - - + -
83A ILE* 3.8 22.0 - - + -
86A ARG* 3.7 26.9 - - + -
167B ARG* 3.1 35.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET 5.8 0.2 - - - +
9A HIS* 3.1 17.0 + - - +
10A GLN* 2.8 49.9 + - - +
12A PHE* 1.3 77.6 - - + +
14A ASP* 1.3 60.5 + - - +
16A ASP* 3.9 4.9 - - - +
17A ASP* 3.0 39.7 + - - +
38B LEU* 3.7 23.3 - - - +
116B GLN* 4.3 8.3 + - - +
119B ALA* 4.4 6.1 - - - +
120B ASN* 2.8 35.3 + - - +
123B GLU* 2.8 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 2.8 49.1 + - - +
11A PHE* 3.8 5.6 + - - +
13A ARG* 1.3 74.8 - - - +
15A MET* 1.3 66.7 + - - +
17A ASP* 3.3 9.2 + - - +
18A GLU* 2.9 30.4 + - + +
65A VAL* 4.0 17.8 - - + +
42B GLN* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 2.9 31.7 + - + +
12A PHE* 3.2 33.7 - - + +
14A ASP* 1.3 79.3 - - - +
16A ASP* 1.3 57.1 + - - +
18A GLU* 3.3 3.6 + - - +
19A GLU* 2.9 34.0 + - - +
65A VAL* 3.9 16.5 - - + +
86A ARG* 3.2 66.9 - - + +
87A LEU* 4.6 1.1 - - - -
90A PHE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.9 25.2 + - - +
13A ARG* 3.9 5.8 - - - +
15A MET* 1.3 76.7 - - - +
17A ASP* 1.3 66.6 + - - +
19A GLU* 3.3 7.4 + - - +
20A SER* 3.0 27.2 + - - -
86A ARG* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.0 26.0 + - - +
14A ASP* 3.7 9.0 - - - +
16A ASP* 1.3 79.8 - - - +
18A GLU* 1.3 66.6 + - + +
20A SER* 3.3 8.7 + - - -
21A TRP* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 2.9 21.8 + - + +
17A ASP* 1.3 78.9 - - + +
19A GLU* 1.3 59.2 + - - +
21A TRP* 3.1 10.2 + - - +
22A ILE* 2.8 32.7 + - - +
58A HIS* 2.9 32.7 + - - -
61A ALA* 3.5 32.6 - - + +
62A ILE* 3.7 18.9 - - + +
65A VAL* 4.7 2.7 - - + -
90A PHE* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 2.9 20.2 + - - +
16A ASP* 3.8 6.3 - - - +
18A GLU* 1.3 76.9 - - - +
20A SER* 1.3 63.1 + - - +
22A ILE* 3.6 9.8 - - + +
23A LYS* 3.0 23.9 + - - +
86A ARG* 3.1 28.6 + - - +
89A GLN* 4.1 6.0 - - - +
90A PHE* 3.3 41.5 + - + +
93A HIS* 3.1 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.0 16.3 + - - +
17A ASP* 3.6 11.1 - - - -
18A GLU 3.2 0.2 - - - -
19A GLU* 1.3 76.0 - - - +
21A TRP* 1.3 63.5 + - - +
23A LYS* 3.3 9.3 + - - +
24A GLU* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.2 9.4 + - - +
18A GLU* 3.1 15.1 + - - +
20A SER* 1.3 79.5 - - - +
22A ILE* 1.3 86.8 + - + +
24A GLU* 3.0 14.2 + - + +
25A LYS* 2.9 46.6 + - + +
54A GLU* 3.0 32.0 + - + -
55A LEU* 3.4 28.3 - - + -
58A HIS* 3.5 63.0 + + + -
62A ILE* 4.7 1.3 - - + -
94A TRP* 3.8 19.5 - + - -
97A LEU* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU 2.8 21.2 + - - +
19A GLU* 3.6 7.9 - - - +
20A SER 3.3 0.2 - - - -
21A TRP* 1.3 97.6 - - + +
23A LYS* 1.3 59.2 + - - +
25A LYS* 3.1 2.8 + - - +
26A LYS* 2.8 33.0 + - + +
62A ILE* 4.2 4.7 - - + -
90A PHE* 4.0 25.8 - - + -
93A HIS* 3.7 34.1 - - + +
94A TRP* 4.1 28.7 - - + +
97A LEU* 4.2 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 3.0 17.7 + - - +
20A SER* 3.6 8.5 - - - +
22A ILE* 1.3 78.1 - - - +
24A GLU* 1.3 59.8 + - - +
26A LYS* 3.4 11.5 + - + +
27A LEU* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 3.1 11.6 + - - +
21A TRP* 3.0 15.7 + - + +
23A LYS* 1.3 75.0 - - - +
25A LYS* 1.3 81.2 + - + +
27A LEU* 3.5 7.8 + - - +
28A LEU* 3.3 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 2.9 51.9 + - + +
22A ILE* 3.7 7.2 - - - +
24A GLU* 1.3 89.7 + - - +
26A LYS* 1.3 66.2 + - - +
28A LEU* 3.1 30.2 + - - +
29A VAL* 2.9 27.0 + - - +
51A LEU* 4.3 12.6 - - + -
54A GLU* 3.1 24.7 + - - +
55A LEU* 4.0 11.2 - - + -
97A LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.8 21.4 + - + +
23A LYS* 3.5 12.3 - - + +
24A GLU 3.2 0.2 - - - -
25A LYS* 1.3 78.4 - - - +
27A LEU* 1.3 67.7 + - + +
29A VAL* 3.4 4.6 + - - +
30A SER* 2.5 37.3 + - - +
93A HIS* 6.0 2.9 - - + +
96A GLU* 3.1 38.8 - - - +
97A LEU* 3.7 15.4 - - + +
100A LEU* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 2.9 42.1 + - + +
24A GLU* 3.9 8.3 - - - +
25A LYS 3.2 0.4 - - - -
26A LYS* 1.3 93.6 - - + +
28A LEU* 1.3 63.2 + - + +
30A SER* 3.1 23.9 + - - +
31A SER* 3.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.3 11.1 + - + +
25A LYS* 3.1 41.5 + - - +
27A LEU* 1.3 80.6 - - + +
29A VAL* 1.3 59.6 + - - +
30A SER 3.1 1.1 + - - -
31A SER* 3.6 17.5 + - - -
47A LYS* 5.9 7.9 - - - +
51A LEU* 4.3 16.2 - - + -
104A ARG* 4.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS 2.9 19.5 + - - +
26A LYS 3.4 5.8 + - - +
27A LEU 3.3 0.2 - - - -
28A LEU* 1.3 73.2 - - - +
30A SER* 1.3 56.9 + - - +
31A SER 3.2 6.9 + - - +
48A HIS* 4.7 2.9 - - + +
51A LEU* 3.6 36.3 - - + -
97A LEU* 4.5 8.7 - - + -
100A LEU* 3.2 38.9 - - + +
101A ALA* 3.2 19.3 - - + +
104A ARG* 3.6 26.6 - - + +
----------------------------------------------------------
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