Contacts of the helix formed by residues 37 - 45 (chain D) in PDB entry 2KI6
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 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.2 24.7 - - - +
24D ALA* 2.9 35.1 - - - +
26D GLN* 3.4 7.6 - - + -
27D GLU* 2.8 29.3 + - - +
28D GLY 3.3 2.1 - - - +
32D SER 3.2 2.1 - - - +
33D LEU* 3.5 10.6 - - + +
34D SER* 2.9 42.6 + - - +
36D ASN* 1.3 83.3 - - - +
38D PHE* 1.3 60.3 + - - +
39D LYS 3.6 1.0 - - - +
40D GLU* 3.9 9.2 - - - +
41D LEU* 3.1 27.5 + - - +
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Residues in contact with PHE 38 (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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33D LEU* 3.6 19.0 - - + +
34D SER 2.8 15.5 + - - +
35D VAL* 4.5 9.4 - - + -
37D GLU* 1.3 74.5 - - - +
39D LYS* 1.3 65.7 + - - +
41D LEU* 2.9 17.8 + - + +
42D VAL* 3.0 14.8 + - + +
56D LEU* 3.8 26.5 - - + -
60D MET* 5.8 2.7 - - + -
63D LEU* 3.5 21.8 - - + -
71D LEU* 3.5 40.4 - - + -
76D TYR* 3.7 29.8 - + + -
79D LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 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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34D SER 4.9 0.2 + - - -
35D VAL* 4.9 15.8 - - + +
36D ASN* 4.9 3.5 - - - +
37D GLU 3.6 2.0 - - - +
38D PHE* 1.3 77.1 - - - +
40D GLU* 1.3 57.2 + - + +
42D VAL* 3.2 9.4 - - + +
43D THR* 2.8 44.0 + - - +
53D VAL 3.1 24.1 + - - -
54D GLY* 3.8 12.9 + - - -
56D LEU* 3.9 24.3 - - + +
57D ASP* 2.9 26.6 + - - +
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Residues in contact with GLU 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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23D PHE* 4.6 3.1 - - + -
26D GLN* 3.4 22.5 + - - +
36D ASN* 3.1 47.8 + - - +
37D GLU* 3.8 9.8 + - - +
38D PHE 3.2 0.2 - - - -
39D LYS* 1.3 77.7 - - + +
41D LEU* 1.3 56.4 - - - +
43D THR* 4.0 4.8 - - - -
44D GLN* 3.1 33.8 + - - +
114E PRO* 5.5 3.8 - - - +
115E ARG* 3.7 21.1 + - - +
127F GLU* 4.7 2.6 - - - +
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Residues in contact with LEU 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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19D THR* 4.4 15.0 - - + +
20D PHE* 5.5 3.6 - - - +
23D PHE* 3.8 30.1 - - + -
33D LEU* 4.9 9.0 - - + -
37D GLU 3.1 16.2 + - - +
38D PHE* 2.9 14.5 + - + +
40D GLU* 1.3 75.6 - - - +
42D VAL* 1.3 60.2 + - - +
45D GLN* 2.8 43.4 + - + +
46D LEU* 3.2 13.5 + - + +
76D TYR* 3.7 37.5 - - + +
79D LEU* 4.5 11.2 - - + -
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Residues in contact with VAL 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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38D PHE* 3.0 34.7 + - + +
39D LYS* 3.2 28.3 - - + +
41D LEU* 1.3 76.9 - - + +
43D THR* 1.3 60.6 + - - +
46D LEU* 2.8 40.5 + - + +
47D PRO 3.2 0.2 - - - -
50D LEU* 3.9 27.4 - - + -
52D ASP 5.7 1.1 - - - +
53D VAL* 3.6 17.1 - - + +
56D LEU* 4.0 24.2 - - + -
79D LEU* 4.3 7.9 - - + -
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Residues in contact with THR 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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39D LYS* 2.8 31.9 + - - +
40D GLU* 4.2 4.5 - - - -
42D VAL* 1.3 77.1 - - - +
44D GLN* 1.3 56.8 + - - +
47D PRO* 3.5 17.6 - - - +
53D VAL* 4.0 24.6 + - + +
32F LEU* 6.5 1.1 - - + -
99F ASP* 5.6 7.4 - - - +
127F GLU* 5.2 6.1 - - - +
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Residues in contact with GLN 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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23D PHE* 3.5 20.9 - - + -
40D GLU 3.1 13.9 + - - +
43D THR* 1.3 78.9 - - - +
45D GLN* 1.3 72.5 + - - +
46D LEU 3.5 0.4 - - - -
47D PRO* 3.3 17.9 - - - +
112E ARG* 3.6 13.0 + - - -
115E ARG* 3.0 36.1 - - - +
1F GLU* 4.2 14.4 + - + +
2F LYS* 4.4 5.2 + - - +
125F SER* 4.1 19.0 + - - +
127F GLU* 3.1 38.0 + - + +
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Residues in contact with GLN 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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7C THR* 4.4 13.2 + - - +
8C GLU* 3.5 23.2 + - - -
9C LEU* 4.2 18.7 - - + +
19D THR* 3.5 23.8 - - + +
23D PHE* 5.0 6.0 - - + -
41D LEU* 2.8 25.4 + - + +
44D GLN* 1.3 91.5 + - - +
46D LEU* 1.3 76.9 + - + +
47D PRO* 3.2 10.5 - - - +
49D LEU* 5.4 0.5 - - - +
1F GLU 4.2 14.4 + - - +
2F LYS* 4.3 15.4 + - + +
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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