Contacts of the helix formed by residues 11 - 25 (chain P) in PDB entry 6CNC
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 LEU 11 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10P GLN* 1.3 74.9 - - + +
12P SER* 1.3 54.1 + - - +
15P ALA* 2.4 38.9 + - + +
51P ILE* 3.4 21.9 - - + +
54P GLU* 3.3 47.1 - - + +
55P LEU* 4.4 10.5 - - + -
58P LYS* 3.9 12.8 - - + +
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Residues in contact with SER 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLN* 3.4 12.2 - - - +
11P LEU* 1.3 80.6 - - - +
13P ASP* 1.3 61.5 + - - +
15P ALA* 3.3 4.4 - - - +
16P LYS* 2.9 47.5 + - - +
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Residues in contact with ASP 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLN* 3.4 33.8 + - + +
12P SER* 1.3 78.7 - - - +
14P ASN* 1.3 60.0 + - - +
16P LYS* 3.1 6.2 + - - +
17P THR* 2.9 36.6 + - - +
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Residues in contact with ASN 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLN 2.7 30.8 + - - +
13P ASP* 1.3 71.5 - - - +
15P ALA* 1.3 54.3 + - - -
17P THR* 3.6 12.7 - - + +
18P LEU* 2.7 52.2 + - - +
40P MET* 5.3 6.5 - - - +
43P GLY* 6.1 2.4 - - - -
47P ASP* 6.3 1.2 - - - -
48P LEU* 5.0 8.9 - - - +
51P ILE* 3.5 25.7 - - + +
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Residues in contact with ALA 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 2.4 32.9 + - + +
12P SER* 3.3 9.6 - - - +
14P ASN* 1.3 78.3 - - - +
16P LYS* 1.3 60.0 + - + +
18P LEU* 4.3 0.5 - - - +
19P HIS* 2.9 28.6 + - - +
51P ILE* 3.5 0.6 - - - +
55P LEU* 3.5 35.2 - - + +
60P LEU* 4.2 14.5 - - + +
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Residues in contact with LYS 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P SER* 2.9 34.9 + - - +
13P ASP* 3.1 3.8 + - - +
15P ALA* 1.3 75.9 - - + +
17P THR* 1.3 62.4 + - - +
19P HIS* 3.5 11.2 - - + +
20P SER* 2.9 24.5 + - - -
23P MET* 5.6 0.9 - - - +
60P LEU* 6.3 1.8 - - + -
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Residues in contact with THR 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P ASP* 2.9 29.8 + - - +
14P ASN* 3.6 16.6 - - - +
16P LYS* 1.3 75.2 - - - +
18P LEU* 1.3 64.5 + - - +
19P HIS 3.2 0.4 - - - -
20P SER* 3.0 21.3 + - - -
21P GLN* 3.1 15.4 + - - +
40P MET* 3.8 29.1 - - + +
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Residues in contact with LEU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASN* 2.7 40.2 + - - +
15P ALA 4.3 0.4 - - - +
17P THR* 1.3 77.9 - - - +
19P HIS* 1.3 57.5 + - - +
20P SER 3.2 0.4 - - - -
21P GLN* 3.1 44.2 - - - +
22P MET* 3.1 23.8 - - + +
36P LEU* 4.5 20.4 - - + -
40P MET* 5.8 3.1 - - - -
48P LEU* 5.5 1.8 - - + +
51P ILE* 5.1 4.5 - - + -
52P VAL* 4.6 11.0 - - + -
55P LEU* 4.3 9.6 - - + -
61P ILE* 3.7 32.5 - - + -
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Residues in contact with HIS 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ALA 2.9 22.0 + - - +
16P LYS* 3.5 10.3 - - + +
18P LEU* 1.3 75.7 - - - +
20P SER* 1.3 58.8 + - - +
22P MET* 3.7 4.7 - - - -
23P MET* 2.9 47.5 + - + +
60P LEU* 3.8 27.3 + - + +
61P ILE* 5.7 1.1 - - + -
74P GLY* 4.4 7.2 - - - -
75P VAL 3.7 28.6 + - - -
76P LEU* 3.9 25.1 - - + +
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Residues in contact with SER 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LYS 2.9 14.1 + - - -
17P THR* 3.0 18.1 + - - -
19P HIS* 1.3 75.9 - - - +
21P GLN* 1.3 59.7 + - - +
22P MET 3.1 1.1 - - - -
23P MET* 3.3 16.4 - - - +
24P SER* 2.9 32.7 + - - -
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Residues in contact with GLN 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P THR 3.1 7.2 + - - +
18P LEU* 3.1 47.6 + - - +
20P SER* 1.3 76.1 - - - +
22P MET* 1.3 63.5 + - + +
24P SER* 4.6 3.6 - - - -
25P LYS* 3.2 10.8 + - + +
26P GLY* 2.5 33.0 + - - -
31P PHE* 4.6 12.9 - - - -
36P LEU* 5.3 10.3 - - - +
39P GLN* 2.9 52.7 + - - +
40P MET* 4.5 14.8 + - + +
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Residues in contact with MET 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P LEU* 3.1 27.8 - - + +
19P HIS* 3.6 10.5 - - - +
20P SER 3.1 0.8 - - - -
21P GLN* 1.3 88.8 - - - +
23P MET* 1.3 65.3 + - - +
25P LYS 3.3 19.2 - - - +
26P GLY* 3.6 20.8 - - - +
31P PHE* 3.6 34.3 - - + -
61P ILE* 4.9 5.6 - - + -
72P PHE* 4.1 11.7 - - + -
73P GLN* 3.8 10.8 - - - +
74P GLY* 3.5 38.8 + - - +
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Residues in contact with MET 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LYS 5.6 0.4 - - - +
19P HIS* 2.9 46.3 + - + +
20P SER* 3.3 19.1 - - - +
22P MET* 1.3 73.9 - - - +
24P SER* 1.3 65.9 - - - +
76P LEU* 5.9 3.1 - - + -
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Residues in contact with SER 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P SER* 2.9 21.0 + - - -
21P GLN* 4.3 3.8 - - - -
23P MET* 1.3 83.2 - - - +
25P LYS* 1.3 68.5 + - - +
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Residues in contact with LYS 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P GLN* 3.2 7.3 + - + +
22P MET 3.3 9.6 - - - +
24P SER* 1.3 86.9 - - - +
26P GLY* 1.3 71.9 + - - +
27P ILE* 3.2 31.5 + - + +
28P GLY* 3.7 10.6 + - - +
39P GLN* 5.4 6.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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