Contacts of the helix formed by residues 29 - 43 (chain C) in PDB entry 3K9S
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 LYS 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C ILE* 2.8 29.9 + - + +
28C THR* 1.3 91.1 - - - +
30C HIS* 1.3 65.3 + - - +
31C HIS 3.6 0.2 - - - -
32C GLN* 3.6 1.6 + - - +
33C THR* 2.9 31.8 + - - -
179D ASN* 3.8 38.4 - - - +
180D ARG* 6.3 0.9 - - - +
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Residues in contact with HIS 30 (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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25C ILE* 3.3 17.4 + - + -
26C HIS* 3.4 24.0 - + + +
29C LYS* 1.3 76.0 - - - +
31C HIS* 1.3 62.5 + - - +
33C THR* 3.2 15.4 + - - -
34C TYR* 3.2 31.6 + - + +
169C TRP* 6.1 0.4 - - - -
171C HIS* 3.5 35.3 + + + +
170D GLU* 3.7 11.4 - - - -
174D TYR* 2.7 30.2 + + - -
179D ASN* 3.4 23.9 - - + +
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Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.4 12.2 - - + +
5C PRO* 3.7 15.5 - - + -
26C HIS 3.0 13.2 + - - +
27C HIS* 3.4 15.5 - - - +
30C HIS* 1.3 73.2 - - - +
32C GLN* 1.3 67.5 + - - +
34C TYR* 3.1 21.2 + + - +
35C VAL* 3.1 8.0 + - + +
78C HIS* 3.0 39.9 + - - -
81C HIS* 3.4 15.8 - - + +
82C SER* 3.6 28.0 - - - -
85C TRP* 2.8 30.4 + - + +
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Residues in contact with GLN 32 (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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4C LEU* 3.4 32.7 - - + +
27C HIS 3.3 6.3 + - - +
28C THR* 3.3 27.3 - - - +
29C LYS 3.8 1.8 - - - +
30C HIS 3.3 0.4 - - - -
31C HIS* 1.3 78.2 - - - +
33C THR* 1.3 58.4 + - - +
35C VAL* 3.1 19.4 + - - +
36C ASN* 2.9 63.4 + - - +
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Residues in contact with THR 33 (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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29C LYS* 2.9 22.8 + - - -
30C HIS* 3.5 6.5 - - - -
31C HIS 3.2 0.2 - - - -
32C GLN* 1.3 73.1 - - - +
34C TYR* 1.3 68.4 + - + +
36C ASN* 3.2 11.5 + - + +
37C ASN* 2.9 45.3 + - - +
74C ASN* 5.2 0.7 - - - +
179D ASN* 5.9 0.7 + - - -
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Residues in contact with TYR 34 (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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30C HIS* 3.2 31.7 + - + +
31C HIS* 3.1 15.1 + + - +
33C THR* 1.3 78.6 - - + +
35C VAL* 1.3 57.4 + - - +
37C ASN 3.3 0.2 + - - -
38C ALA* 2.8 33.7 + - - +
73C ASN 4.4 3.6 - - - -
74C ASN* 3.4 37.0 - - - +
77C GLY* 3.7 21.1 - - - -
78C HIS* 3.8 7.0 - - - +
81C HIS* 3.2 27.5 - + - -
146C GLN* 2.9 23.5 + - + -
169C TRP* 4.7 4.1 - + - -
171C HIS* 3.8 11.4 - - - -
207C PEO 3.7 4.3 + - - -
124D PHE* 4.0 24.9 - + - -
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Residues in contact with VAL 35 (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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2C TYR* 3.7 31.0 - - + +
3C THR* 4.2 5.6 - - - -
4C LEU* 4.2 13.7 - - + +
31C HIS* 3.1 17.0 + - + +
32C GLN* 3.1 23.7 + - - +
34C TYR* 1.3 77.6 - - - +
36C ASN* 1.3 65.0 + - - +
38C ALA* 3.9 4.0 - - - +
39C ASN* 3.0 29.6 + - - +
78C HIS* 3.4 36.1 - - + +
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Residues in contact with ASN 36 (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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32C GLN* 2.9 48.5 + - - +
33C THR* 3.2 11.5 + - + +
35C VAL* 1.3 77.2 - - - +
37C ASN* 1.3 65.1 + - - +
39C ASN* 3.4 6.5 + - - +
40C ALA* 3.0 29.2 + - - +
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Residues in contact with ASN 37 (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 THR* 2.9 34.7 + - - +
36C ASN* 1.3 81.9 - - - +
38C ALA* 1.3 61.4 - - - +
40C ALA* 3.5 9.2 + - - +
41C ALA* 3.2 22.3 + - - +
70C VAL* 4.5 7.8 - - + +
74C ASN* 3.2 39.1 + - - +
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Residues in contact with ALA 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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2C TYR* 3.7 29.8 - - + -
34C TYR 2.8 18.5 + - - +
35C VAL 3.9 0.7 - - - +
37C ASN* 1.3 73.2 - - - +
39C ASN* 1.3 65.1 + - - +
41C ALA* 3.2 3.5 + - - +
42C LEU* 3.0 29.4 + - - +
71C LEU* 4.0 12.6 - - + -
74C ASN* 3.8 14.2 - - + +
75C ALA 4.1 10.8 - - - +
78C HIS* 5.4 0.4 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 2.8 26.1 + - - +
2C TYR* 2.7 55.1 + - - +
35C VAL* 3.0 26.0 + - - +
36C ASN* 3.7 6.1 + - - +
38C ALA* 1.3 76.6 - - - +
40C ALA* 1.3 64.5 - - - +
42C LEU* 3.3 6.3 + - - +
43C GLU* 3.2 23.9 + - - +
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Residues in contact with ALA 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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36C ASN 3.0 18.0 + - - +
37C ASN* 3.5 10.8 - - - +
38C ALA 3.2 0.2 - - - -
39C ASN* 1.3 78.7 - - - +
41C ALA* 1.3 60.6 + - - +
43C GLU* 3.5 15.8 + - - +
44C SER 4.9 0.3 + - - -
67C LYS* 4.8 2.3 + - - -
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Residues in contact with ALA 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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37C ASN 3.2 9.7 + - - +
38C ALA 3.2 8.5 + - - +
40C ALA* 1.3 78.7 - - - +
42C LEU* 1.3 62.3 + - - +
43C GLU 3.5 0.3 + - - -
44C SER* 3.9 3.1 + - - -
45C LEU* 4.0 2.6 - - - +
67C LYS* 2.8 38.3 + - + +
70C VAL* 3.9 30.7 - - + -
71C LEU* 3.9 16.4 - - + -
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Residues in contact with LEU 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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1C SER* 5.9 3.8 - - - -
2C TYR* 3.6 38.8 - - + +
38C ALA 3.0 20.2 + - - +
39C ASN* 3.3 7.8 + - - +
41C ALA* 1.3 74.9 - - - +
43C GLU* 1.3 63.3 + - - +
44C SER 3.2 3.1 - - - -
45C LEU* 2.9 26.2 + - + +
48C PHE* 3.8 32.3 - - + -
49C ALA* 3.7 24.9 - - + +
56C LEU* 3.8 11.7 - - + -
71C LEU* 3.7 28.3 - - + -
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Residues in contact with GLU 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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1C SER* 5.2 6.5 + - - -
39C ASN 3.2 10.4 + - - +
40C ALA* 3.7 14.4 - - - +
41C ALA 3.3 1.2 - - - -
42C LEU* 1.3 78.0 - - - +
44C SER* 1.3 61.4 + - - +
45C LEU 3.3 0.5 + - - -
46C PRO* 4.6 6.1 - - - +
49C ALA* 5.7 0.4 - - - -
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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