Contacts of the helix formed by residues 7 - 29 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASN* 5.8 1.6 + - - -
170A ASP* 6.0 4.0 - - - +
8C VAL* 1.3 66.6 + - - +
9C HIS* 3.4 6.9 - - - +
10C GLN* 3.5 10.0 + - - +
11C PHE* 3.0 26.7 + - - +
68C THR* 4.0 20.6 - - + -
71C LYS* 4.7 22.0 - - - -
72C LEU* 3.5 26.9 - - + -
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.2 28.7 - - + +
170A ASP* 5.0 12.6 - - + +
7C MET* 1.3 81.0 - - - +
9C HIS* 1.3 81.1 + - + +
11C PHE* 3.3 1.7 + - - +
12C PHE* 3.1 49.0 + - + -
72C LEU* 4.0 20.4 - - + +
77C THR* 6.1 0.4 - - - +
83C ILE* 4.5 16.8 - - + -
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Residues in contact with HIS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASN* 3.0 47.2 + - - +
123A GLU* 3.4 20.8 + - + +
124A GLU* 2.8 38.1 + - + -
167A ARG* 3.9 20.0 + - + +
170A ASP* 5.9 2.5 - - + -
171A VAL* 3.5 20.7 - - + +
7C MET 3.4 4.2 - - - +
8C VAL* 1.3 91.4 - - + +
10C GLN* 1.3 62.1 + - - +
12C PHE* 3.3 8.1 + - - +
13C ARG* 3.1 29.7 + - - +
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Residues in contact with GLN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.9 5.1 - - - +
42A GLN* 4.1 12.6 + - - +
116A GLN* 3.3 39.5 - - - +
120A ASN* 5.4 0.2 + - - -
7C MET* 3.5 11.6 + - - +
8C VAL 3.4 0.2 - - - -
9C HIS* 1.3 77.0 - - - +
11C PHE* 1.3 60.4 + - - +
13C ARG* 2.8 44.4 + - - +
14C ASP* 2.8 66.6 + - - +
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C MET 3.0 18.2 + - - +
8C VAL* 3.5 7.6 - - + +
10C GLN* 1.3 76.4 - - - +
12C PHE* 1.3 87.1 + + - +
14C ASP* 3.3 6.4 + - + +
15C MET* 2.9 46.0 + - + +
65C VAL* 3.4 35.9 - - + -
68C THR* 3.7 25.1 - - + -
69C GLY* 3.5 18.2 - - - -
72C LEU* 3.6 17.5 - - + -
83C ILE* 3.9 23.8 - - + -
87C LEU* 4.2 8.1 - - + -
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.9 21.3 - - - -
8C VAL* 3.1 43.5 + - + +
9C HIS* 3.9 5.8 - - - +
10C GLN 3.3 0.2 - - - -
11C PHE* 1.3 85.7 - + - +
13C ARG* 1.3 57.7 + - + +
15C MET* 3.6 30.4 - - + +
16C ASP* 2.9 39.4 + - - +
82C GLU* 3.6 19.7 - - - -
83C ILE* 4.0 24.5 - - + -
86C ARG* 3.7 26.7 - - + -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.5 24.1 - - - +
116A GLN* 4.1 10.1 + - - +
119A ALA* 4.2 7.1 - - - +
120A ASN* 2.9 34.7 + - - +
123A GLU* 2.9 35.1 + - - +
9C HIS* 3.1 17.0 + - - +
10C GLN* 2.8 49.2 - - - +
12C PHE* 1.3 77.9 - - + +
14C ASP* 1.3 63.5 + - - +
16C ASP* 3.3 6.7 + - - +
17C ASP* 3.0 33.4 + - - +
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Residues in contact with ASP 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN* 5.3 0.9 - - - +
10C GLN* 2.8 49.3 + - - +
11C PHE* 3.9 5.6 - - - +
13C ARG* 1.3 76.3 - - - +
15C MET* 1.3 58.7 + - - +
17C ASP* 3.3 9.4 + - - +
18C GLU* 2.9 35.6 + - + +
65C VAL* 4.3 15.7 - - + -
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Residues in contact with MET 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 2.9 33.4 + - + +
12C PHE* 3.6 21.3 - - + +
14C ASP* 1.3 77.1 - - - +
16C ASP* 1.3 57.9 + - - +
18C GLU* 3.4 4.3 + - - +
19C GLU* 2.9 45.3 + - - +
65C VAL* 4.2 15.4 - - + +
86C ARG* 3.1 70.0 - - + +
87C LEU* 4.2 2.2 - - - -
90C PHE* 3.9 19.9 - - + -
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 2.9 25.7 + - - +
13C ARG* 3.7 6.8 - - - +
14C ASP 3.3 0.2 - - - -
15C MET* 1.3 75.7 - - - +
17C ASP* 1.3 66.5 + - - +
19C GLU* 3.2 7.0 + - - +
20C SER* 3.0 23.9 + - - -
86C ARG* 2.9 30.8 + - - -
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Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 3.0 25.4 + - - +
14C ASP* 3.7 9.1 - - - +
16C ASP* 1.3 79.2 - - - +
18C GLU* 1.3 64.8 + - + +
20C SER* 3.0 21.1 + - - -
21C TRP* 3.1 10.4 + - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASP* 2.9 22.1 + - + +
15C MET 3.9 0.2 - - - +
17C ASP* 1.3 78.4 - - + +
19C GLU* 1.3 57.6 + - - +
21C TRP* 3.3 7.2 - - - +
22C ILE* 2.8 34.5 + - - +
58C HIS* 2.7 38.0 + - - -
61C ALA* 3.5 14.8 - - - +
62C ILE* 3.5 15.9 - - + +
65C VAL* 4.3 16.2 - - + -
90C PHE* 3.8 21.3 - - + -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C MET* 2.9 26.1 + - - +
16C ASP* 3.5 8.3 - - - +
17C ASP 3.2 0.2 - - - -
18C GLU* 1.3 75.3 - - - +
20C SER* 1.3 59.5 + - - +
22C ILE* 3.4 7.3 + - - +
23C LYS* 2.9 27.9 + - - +
86C ARG* 4.2 7.1 + - - +
89C GLN* 3.9 13.3 - - - +
90C PHE* 3.1 35.7 - - - +
93C HIS* 2.5 43.3 + - + +
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ASP 3.0 13.1 + - - -
17C ASP* 3.0 19.4 + - - -
19C GLU* 1.3 74.0 - - - +
21C TRP* 1.3 65.1 + - - +
23C LYS* 3.3 9.6 + - - +
24C GLU* 3.1 20.6 + - - +
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Residues in contact with TRP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASP 3.1 9.1 + - - +
18C GLU* 3.3 14.6 - - - +
20C SER* 1.3 81.0 + - - +
22C ILE* 1.3 93.4 + - + +
24C GLU* 2.8 22.1 + - - +
25C LYS* 3.1 27.4 + - + +
54C GLU* 3.6 28.6 + - + -
55C LEU* 3.5 22.4 - - + -
58C HIS* 3.2 56.7 + + + -
62C ILE* 4.7 0.7 - - + -
94C TRP* 3.7 24.7 - + - -
97C LEU* 4.1 6.5 - - + -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLU 2.8 21.3 + - - +
19C GLU* 3.6 6.7 - - - +
21C TRP* 1.3 98.0 - - + +
23C LYS* 1.3 57.7 + - - +
25C LYS* 3.5 1.6 + - - +
26C LYS* 2.8 31.4 + - + +
62C ILE* 4.6 5.6 - - + -
90C PHE* 3.9 26.2 - - + -
93C HIS* 3.6 32.5 - - + +
94C TRP* 3.9 34.5 - - + +
97C LEU* 4.1 13.9 - - + +
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLU 2.9 15.1 + - - +
20C SER* 3.5 12.6 - - - +
21C TRP 3.1 0.4 - - - -
22C ILE* 1.3 74.3 - - - +
24C GLU* 1.3 66.2 + - - +
26C LYS* 3.5 13.7 - - + +
27C LEU* 3.1 28.4 + - + +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER 3.1 10.2 + - - +
21C TRP* 2.8 20.6 + - - +
23C LYS* 1.3 71.4 - - - +
25C LYS* 1.3 84.6 + - + +
27C LEU* 2.9 17.1 + - + +
28C LEU* 2.9 32.4 + - + +
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Residues in contact with LYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TRP* 3.1 35.4 + - + +
22C ILE* 3.8 5.6 - - - +
24C GLU* 1.3 94.8 + - + +
26C LYS* 1.3 67.8 + - - +
28C LEU* 3.6 25.3 - - + +
29C VAL* 2.9 27.5 + - - +
51C LEU* 5.0 11.8 - - + +
54C GLU* 3.1 32.1 - - - +
55C LEU* 4.5 7.4 - - + -
97C LEU* 3.7 20.4 - - + -
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 2.8 21.7 + - + +
23C LYS* 3.5 16.2 - - + +
24C GLU 3.2 0.2 - - - -
25C LYS* 1.3 74.9 - - - +
27C LEU* 1.3 63.1 + - - +
29C VAL* 3.1 14.7 - - - +
30C SER* 2.9 23.0 + - - +
93C HIS* 6.3 0.4 - - + -
96C GLU* 3.5 37.7 + - + +
97C LEU* 3.5 18.6 - - + +
100C LEU* 3.9 21.3 - - + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 3.1 15.6 + - + +
24C GLU* 2.9 18.8 + - + +
26C LYS* 1.3 80.4 - - + +
28C LEU* 1.3 77.9 + - + +
30C SER* 3.2 17.6 + - - -
31C SER* 4.2 1.6 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU* 2.9 17.6 + - + +
25C LYS* 3.2 37.0 + - + +
27C LEU* 1.3 84.7 - - + +
29C VAL* 1.3 54.5 + - - +
30C SER 2.8 10.6 + - - -
31C SER* 2.9 24.6 + - - -
47C LYS* 5.9 9.2 - - - +
51C LEU* 4.7 15.3 - - + -
104C ARG* 5.3 0.2 + - - -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS 2.9 12.9 + - - +
26C LYS* 3.1 21.5 - - - +
28C LEU* 1.3 75.2 - - - +
30C SER* 1.3 58.4 + - - +
31C SER 3.1 3.9 + - - +
48C HIS* 4.1 15.7 - - + -
51C LEU* 4.6 14.9 - - + +
97C LEU* 4.4 5.2 - - + -
100C LEU* 3.6 31.2 - - + +
101C ALA* 3.3 35.2 - - + +
104C ARG* 3.5 24.0 - - - +
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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) + - + + + + + -
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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