Contacts of the strand formed by residues 13 - 22 (chain C) in PDB entry 2CKE
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 TYR 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C VAL* 2.8 27.4 + - + +
10C GLU* 3.0 26.5 + - - +
12C PHE* 1.3 86.8 - - + +
14C ASP* 1.3 63.0 + - - +
15C ILE* 3.4 19.8 + - + +
30C CYS* 3.8 15.0 - - + -
31C ARG 3.2 6.7 - - - +
32C GLU* 3.1 56.0 + - + -
33C LYS* 4.1 2.5 - - - -
39C TYR* 4.2 6.5 - + - -
80C HIS* 3.2 21.1 - - - -
81C ASP* 4.6 2.9 + - - +
83C TYR* 3.7 32.4 + + - -
92C ILE* 3.8 23.1 - - + +
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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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13C TYR* 1.3 69.2 - - - +
15C ILE* 1.3 62.1 + - - +
16C GLY 3.8 0.2 + - - -
30C CYS* 3.3 4.1 - - - -
31C ARG* 2.9 62.1 + - - +
33C LYS* 2.9 40.7 + - - +
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Residues in contact with ILE 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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9C VAL* 4.8 12.1 - - + -
10C GLU* 5.0 10.1 - - + -
13C TYR* 3.4 19.6 + - + +
14C ASP* 1.3 73.5 - - - +
16C GLY* 1.3 62.1 + - - +
28C LYS* 3.7 35.2 - - + +
29C LYS 3.8 1.3 - - - +
30C CYS* 3.4 24.5 - - + -
41C ALA* 4.2 8.3 - - + -
43C PHE* 4.1 23.1 - - + -
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Residues in contact with GLY 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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14C ASP 3.8 1.6 + - - -
15C ILE* 1.3 78.0 - - - +
17C GLU* 1.3 68.9 + - - +
18C GLU 3.6 1.0 + - - -
28C LYS* 3.9 16.3 + - - +
29C LYS* 2.7 18.6 + - - +
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Residues in contact with GLU 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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16C GLY* 1.3 70.1 - - - -
18C GLU* 1.3 73.2 + - - +
19C LEU* 3.4 9.5 - - + +
28C LYS* 3.5 0.2 - - - -
29C LYS* 2.7 43.3 + - + +
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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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16C GLY 3.6 2.0 + - - -
17C GLU* 1.3 85.8 - - - +
19C LEU* 1.3 68.1 + - - +
20C GLY* 3.7 10.6 - - - +
21C SER* 3.2 28.2 - - - -
26C ILE* 4.3 13.6 - - + +
27C VAL 3.4 14.6 - - - +
28C LYS* 4.0 16.5 + - + +
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Residues in contact with LEU 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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17C GLU* 3.4 16.8 + - + +
18C GLU* 1.3 83.4 - - - +
20C GLY* 1.3 59.4 + - - +
27C VAL* 2.9 12.0 + - + +
28C LYS 4.2 2.9 - - - -
29C LYS* 3.7 41.7 - - + +
40C ALA* 4.4 5.4 - - + -
95C LEU* 3.9 8.7 - - + -
1302C IQU 3.3 48.4 + - + +
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Residues in contact with GLY 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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18C GLU* 3.7 8.4 - - - +
19C LEU* 1.3 78.7 - - - +
21C SER* 1.3 63.8 + - - -
26C ILE* 3.8 0.5 - - - -
27C VAL* 2.9 28.6 + - - +
1302C IQU 3.0 24.6 + - - -
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Residues in contact with SER 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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18C GLU* 3.2 18.6 - - - -
20C GLY* 1.3 74.2 - - - -
22C GLY* 1.3 60.6 + - - +
25C ALA 3.6 6.9 + - - -
26C ILE* 3.9 21.6 - - - +
27C VAL* 5.9 0.2 - - - -
1302C IQU 4.2 12.1 + - - -
54D ARG* 5.6 4.5 + - - -
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Residues in contact with GLY 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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21C SER* 1.3 79.2 + - - +
23C GLN* 1.3 74.0 + - - +
24C PHE 3.0 7.1 + - - -
25C ALA* 3.3 17.4 + - - +
1302C IQU 4.3 10.9 + - - -
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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