Contacts of the helix formed by residues 37 - 45 (chain C) in PDB entry 2KI4
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.2 24.7 - - - +
24C ALA* 2.9 35.1 - - - +
26C GLN* 3.4 7.6 - - + -
27C GLU* 2.8 29.3 + - - +
28C GLY 3.3 2.1 - - - +
32C SER 3.2 2.1 - - - +
33C LEU* 3.5 10.6 - - + +
34C SER* 2.9 42.6 + - - +
36C ASN* 1.3 83.3 - - - +
38C PHE* 1.3 60.3 + - - +
39C LYS 3.6 1.0 - - - +
40C GLU* 3.9 9.2 - - - +
41C LEU* 3.1 27.5 + - - +
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Residues in contact with PHE 38 (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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33C LEU* 3.6 19.0 - - + +
34C SER 2.8 15.5 + - - +
35C VAL* 4.5 9.4 - - + -
37C GLU* 1.3 74.5 - - - +
39C LYS* 1.3 65.7 + - - +
41C LEU* 2.9 17.8 + - + +
42C VAL* 3.0 14.8 + - + +
56C LEU* 3.8 26.5 - - + -
60C MET* 5.8 2.7 - - + -
63C LEU* 3.5 21.8 - - + -
71C LEU* 3.5 40.4 - - + -
76C TYR* 3.7 29.8 - + + -
79C LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 39 (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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34C SER 4.9 0.2 + - - -
35C VAL* 4.9 15.8 - - + +
36C ASN* 4.9 3.5 - - - +
37C GLU 3.6 2.0 - - - +
38C PHE* 1.3 77.1 - - - +
40C GLU* 1.3 57.2 + - + +
42C VAL* 3.2 9.4 - - + +
43C THR* 2.8 44.0 + - - +
53C VAL 3.1 24.1 + - - -
54C GLY* 3.8 12.9 + - - -
56C LEU* 3.9 24.3 - - + +
57C ASP* 2.9 26.6 + - - +
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Residues in contact with GLU 40 (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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23C PHE* 4.6 3.1 - - + -
26C GLN* 3.4 22.5 + - - +
36C ASN* 3.1 47.8 + - - +
37C GLU* 3.8 9.8 + - - +
38C PHE 3.2 0.2 - - - -
39C LYS* 1.3 77.7 - - + +
41C LEU* 1.3 56.4 - - - +
43C THR* 4.0 4.8 - - - -
44C GLN* 3.1 33.8 + - - +
114D PRO* 5.5 3.8 - - - +
115D ARG* 3.7 21.1 + - - +
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Residues in contact with LEU 41 (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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19C THR* 4.4 15.0 - - + +
20C PHE* 5.5 3.6 - - - +
23C PHE* 3.8 30.1 - - + -
33C LEU* 4.9 9.0 - - + -
37C GLU 3.1 16.2 + - - +
38C PHE* 2.9 14.5 + - + +
40C GLU* 1.3 75.6 - - - +
42C VAL* 1.3 60.2 + - - +
45C GLN* 2.8 43.4 + - + +
46C LEU* 3.2 13.5 + - + +
76C TYR* 3.7 37.5 - - + +
79C LEU* 4.5 11.2 - - + -
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Residues in contact with VAL 42 (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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38C PHE* 3.0 34.7 + - + +
39C LYS* 3.2 28.3 - - + +
41C LEU* 1.3 76.9 - - + +
43C THR* 1.3 60.6 + - - +
46C LEU* 2.8 40.5 + - + +
47C PRO 3.2 0.2 - - - -
50C LEU* 3.9 27.4 - - + -
52C ASP 5.7 1.1 - - - +
53C VAL* 3.6 17.1 - - + +
56C LEU* 4.0 24.2 - - + -
79C LEU* 4.3 7.9 - - + -
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Residues in contact with THR 43 (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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39C LYS* 2.8 31.9 + - - +
40C GLU* 4.2 4.5 - - - -
42C VAL* 1.3 77.1 - - - +
44C GLN* 1.3 56.8 + - - +
47C PRO* 3.5 17.6 - - - +
53C VAL* 4.0 24.6 + - + +
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Residues in contact with GLN 44 (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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23C PHE* 3.5 20.9 - - + -
40C GLU 3.1 13.9 + - - +
43C THR* 1.3 79.8 - - - +
45C GLN* 1.3 72.5 + - - +
46C LEU 3.5 0.4 - - - -
47C PRO* 3.3 17.9 - - - +
112D ARG* 3.6 21.3 + - - +
115D ARG* 3.0 39.3 - - - +
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Residues in contact with GLN 45 (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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7B THR* 4.4 17.2 + - - +
8B GLU* 3.5 23.2 + - - -
9B LEU* 4.2 18.7 - - + +
19C THR* 3.5 23.8 - - + +
23C PHE* 5.0 6.0 - - + -
41C LEU* 2.8 25.4 + - + +
44C GLN* 1.3 91.5 + - - +
46C LEU* 1.3 76.9 + - + +
47C PRO* 3.2 10.5 - - - +
49C LEU* 5.4 0.5 - - - +
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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