Contacts of the helix formed by residues 9 - 21 (chain D) in PDB entry 6KNC
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 GLY 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.1 16.2 + - - -
8D ASP* 1.3 74.9 - - - +
10D ALA* 1.3 57.7 + - - +
11D LYS* 2.9 12.8 + - - -
12D GLU* 3.4 8.8 + - - +
85D ALA* 3.3 22.4 + - - -
87D ASP* 3.1 18.3 + - - -
234D ARG* 3.6 12.9 + - - -
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 4.3 9.2 - - - -
8D ASP* 3.7 0.6 - - - +
9D GLY* 1.3 72.3 - - - +
11D LYS* 1.3 50.2 + - - +
13D PHE* 4.0 2.8 - - - +
14D ALA* 2.7 37.2 + - - +
80D LEU* 4.1 10.5 - - + +
82D ARG 5.9 0.7 - - - +
83D GLY* 4.8 4.0 - - - +
84D LYS 4.5 0.2 - - - -
87D ASP* 3.1 23.8 + - - +
89D LEU* 3.7 37.4 - - + +
103D PHE* 4.2 4.0 - - + -
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY 2.9 1.6 + - - +
10D ALA* 1.3 75.9 - - - +
12D GLU* 1.3 61.9 + - - +
14D ALA* 3.3 5.6 - - + +
15D ASP* 2.8 38.2 + - - +
83D GLY 4.2 7.9 - - - +
84D LYS* 3.9 12.8 + - + +
85D ALA* 4.0 38.6 - - + +
11F G 3.8 28.7 + - - -
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 5.1 2.5 - - + -
9D GLY 3.4 8.4 + - - +
11D LYS* 1.3 79.0 - - - +
13D PHE* 1.3 58.0 + - - +
15D ASP* 2.8 16.1 - - - +
16D LEU* 2.7 26.9 + - + +
231D TYR* 5.6 2.8 - - - -
232D MET 4.7 1.6 - - - +
233D ILE* 3.3 41.0 - - + +
234D ARG* 3.8 31.4 + - - +
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Residues in contact with PHE 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.4 35.5 - + + -
9D GLY 3.9 2.8 + - - -
10D ALA* 4.3 4.9 - - - +
11D LYS 3.3 0.2 - - - -
12D GLU* 1.3 75.9 - - - +
14D ALA* 1.3 59.3 + - - +
16D LEU* 3.7 19.5 - - + -
17D ILE* 2.9 56.8 + - + +
29D PHE* 5.4 6.1 - + - -
36D ILE* 5.8 5.4 - - + -
51D LEU* 5.2 2.9 - - + -
53D LEU* 4.8 16.8 - - + -
58D PHE* 6.2 2.9 - + - -
76D PHE* 4.7 6.1 - + - -
80D LEU* 3.6 29.4 - - + -
89D LEU* 4.0 15.9 - - + -
91D LEU* 4.9 13.0 - - + -
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 2.7 23.8 + - - +
11D LYS* 3.1 10.5 + - + +
13D PHE* 1.3 78.0 - - - +
15D ASP* 1.3 58.2 + - - +
17D ILE* 3.9 2.5 - - - +
18D ALA* 2.9 27.8 + - - +
77D LYS* 5.3 4.0 - - - +
80D LEU* 3.2 36.1 - - + +
81D LYS* 4.6 7.9 - - + +
83D GLY 5.4 0.9 - - - +
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Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LYS* 2.8 29.7 + - + +
12D GLU* 2.8 22.8 - - - +
14D ALA* 1.3 71.1 - - - +
16D LEU* 1.3 55.3 + - - +
18D ALA* 3.7 9.8 - - + +
19D THR* 2.3 38.9 + - - +
210D GLY* 3.9 18.8 - - - +
212D GLY 5.7 1.9 + - - -
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 2.7 24.7 + - + +
13D PHE* 3.5 25.4 - - + +
14D ALA 3.1 0.2 - - - -
15D ASP* 1.3 76.2 - - - +
17D ILE* 1.3 63.2 + - + +
19D THR* 3.1 6.8 + - - -
20D ALA* 3.0 27.6 + - + +
51D LEU* 4.2 27.4 - - + -
53D LEU* 5.3 4.0 - - + -
231D TYR* 3.7 13.0 - - + +
233D ILE* 4.6 24.0 - - + -
239D LEU* 3.7 30.2 - - + +
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PHE* 2.9 54.2 + - + +
14D ALA* 4.0 3.4 - - - +
16D LEU* 1.3 78.9 - - + +
18D ALA* 1.3 57.2 + - - +
20D ALA* 3.3 6.2 + - + +
21D SER* 2.9 27.1 + - - -
29D PHE* 4.0 24.0 - - + -
38D MET* 6.1 1.3 - - + -
51D LEU* 5.4 7.4 - - + -
73D MET* 3.6 25.3 - - + +
76D PHE* 4.0 26.2 - - + -
77D LYS* 5.0 9.4 - - + -
80D LEU* 4.9 2.9 - - + -
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 2.9 20.3 + - - +
15D ASP* 3.7 10.5 - - + -
16D LEU 3.2 0.2 - - - -
17D ILE* 1.3 77.3 - - - +
19D THR* 1.3 60.7 + - - +
21D SER* 3.4 13.7 + - - -
22D ASN* 3.8 7.1 + - - +
77D LYS* 3.8 39.9 + - + +
81D LYS* 6.1 5.4 - - + +
209D LYS* 5.0 5.1 - - - -
210D GLY* 5.7 2.0 - - - -
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Residues in contact with THR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASP 2.3 27.6 + - - -
16D LEU* 3.1 8.6 + - - -
18D ALA* 1.3 76.7 - - - +
20D ALA* 1.3 61.7 + - - +
21D SER 3.3 1.2 + - - -
22D ASN* 3.5 16.3 + - - +
23D LEU* 4.4 8.3 + - - +
206D ASP 5.7 0.9 - - - -
207D MET* 3.6 39.6 - - + +
209D LYS* 6.4 0.4 - - - +
210D GLY* 2.9 28.5 + - - +
211D ILE* 4.6 8.7 - - + +
231D TYR* 4.9 6.1 + - - +
239D LEU* 5.9 0.2 - - + -
241D PHE* 4.7 12.7 - - + -
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.0 15.9 + - + +
17D ILE* 3.3 4.0 + - + +
19D THR* 1.3 75.6 - - - +
21D SER* 1.3 59.7 + - - +
22D ASN 3.4 0.6 + - - -
23D LEU* 3.9 6.4 + - - +
24D ILE* 3.5 21.9 + - + +
38D MET* 4.5 6.1 - - + -
49D ILE* 3.9 29.6 - - + +
73D MET* 3.5 30.0 - - + +
239D LEU* 6.3 1.1 - - + -
241D PHE* 5.8 0.4 - - - -
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE 2.9 15.7 + - - -
18D ALA 3.7 7.6 - - - -
19D THR 3.2 1.4 - - - -
20D ALA* 1.3 78.1 - - - +
22D ASN* 1.3 60.1 + - - +
23D LEU 3.4 0.7 - - - -
24D ILE 2.9 19.2 - - - +
25D ASP* 4.6 5.5 - - - +
73D MET* 3.4 33.6 + - - +
74D ASP* 4.2 7.6 + - - +
77D LYS* 3.8 20.9 + - - +
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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