Contacts of the strand formed by residues 38 - 45 (chain D) 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 GLU 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LYS* 3.4 34.8 + - - -
30D CYS 3.4 7.0 - - - +
31D ARG* 2.7 49.7 + - + +
36D GLY 4.5 0.2 - - - +
37D LEU* 1.3 75.4 - - - +
39D TYR* 1.3 70.5 + - - +
95D LEU* 3.8 27.8 + - + +
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Residues in contact with TYR 39 (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 TYR* 4.2 14.8 - + - -
29D LYS* 3.7 4.9 - - - +
30D CYS* 2.7 34.9 + - - +
32D GLU* 3.5 19.7 + - + -
35D THR* 5.4 0.5 - - - +
37D LEU* 3.2 56.6 - - + +
38D GLU* 1.3 75.8 - - - +
40D ALA* 1.3 60.8 + - - +
80D HIS* 3.3 44.5 - + + -
92D ILE* 3.6 16.2 - - + -
93D LEU 3.4 15.9 - - - +
94D GLU* 4.7 5.6 - - - -
95D LEU* 3.8 14.4 - - - +
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Residues in contact with ALA 40 (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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19D LEU* 4.8 1.3 - - + -
27D VAL* 4.3 10.3 - - + -
28D LYS 3.7 4.5 - - - +
29D LYS* 4.7 0.4 - - - +
30D CYS* 4.3 2.0 - - - -
39D TYR* 1.3 74.0 - - - +
41D ALA* 1.3 58.1 + - - +
42D LYS 3.8 0.4 + - - -
91D LEU 3.5 0.9 - - - +
93D LEU* 2.5 49.5 + - + +
94D GLU 4.1 1.1 - - - +
95D LEU* 4.0 7.0 - - + +
1302D IQU 3.3 43.1 - - + +
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Residues in contact with ALA 41 (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 ILE* 4.9 3.1 - - + -
27D VAL* 4.4 2.2 - - - +
28D LYS 2.7 38.5 + - - +
30D CYS* 3.8 14.5 - - + -
40D ALA* 1.3 69.9 - - - +
42D LYS* 1.3 60.8 + - - +
43D PHE* 3.3 28.6 + - + -
90D VAL* 4.1 3.1 - - + -
91D LEU 3.4 4.7 - - - -
92D ILE* 3.7 22.9 - - + -
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Residues in contact with LYS 42 (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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25D ALA* 4.2 21.7 - - + +
26D ILE 3.8 2.7 - - - -
27D VAL* 4.0 24.5 - - + +
40D ALA 3.8 1.4 + - - -
41D ALA* 1.3 69.0 - - - +
43D PHE* 1.3 60.3 + - - +
44D ILE* 3.4 23.9 + - + +
64D GLU* 2.6 38.9 + - - +
89D VAL 3.5 0.7 - - - +
90D VAL* 3.5 1.7 - - - -
91D LEU* 2.7 46.5 + - + +
93D LEU* 4.0 20.2 - - + -
161D ASP* 4.0 24.8 + - - +
163D GLY* 4.8 1.2 - - - +
1302D IQU 5.9 4.5 - - + -
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Residues in contact with PHE 43 (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 VAL* 4.4 11.0 - - + -
15D ILE* 4.1 25.8 - - + -
24D PHE 4.3 0.2 - - - -
25D ALA* 3.2 4.7 - - - -
26D ILE* 2.8 46.5 + - + +
28D LYS* 4.2 29.8 - - + -
41D ALA* 3.3 28.3 - - + -
42D LYS* 1.3 69.5 - - - +
44D ILE* 1.3 62.5 + - - +
45D LYS* 3.8 1.2 + - - +
85D ASN* 5.7 2.5 - - - -
88D ASP* 3.5 22.6 - - + +
89D VAL 4.2 2.5 - - - -
90D VAL* 3.4 34.1 - - + -
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Residues in contact with ILE 44 (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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24D PHE 3.4 10.5 - - - +
25D ALA* 4.6 3.8 - - + -
42D LYS* 3.9 33.7 - - + +
43D PHE* 1.3 73.0 - - - +
45D LYS* 1.3 67.0 + - - +
46D LYS* 3.5 0.7 + - - +
56D VAL* 3.9 27.4 - - + -
61D ILE* 4.1 22.6 - - + +
64D GLU* 3.8 22.9 - - + +
88D ASP* 3.4 3.5 - - - -
89D VAL* 2.8 44.6 + - + +
91D LEU* 4.2 16.8 - - + -
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Residues in contact with LYS 45 (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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24D PHE* 3.0 28.4 + - + +
43D PHE 3.8 2.0 + - - -
44D ILE* 1.3 71.8 - - - +
46D LYS* 1.3 69.5 + - - +
48D GLN* 5.1 11.0 - - - +
54D ARG* 5.6 7.0 - - + +
55D GLY* 5.0 5.2 - - - +
56D VAL* 3.1 30.0 + - - +
87D THR* 4.3 18.5 - - - +
88D ASP* 3.6 24.1 + - - +
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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