Contacts of the helix formed by residues 51 - 64 (chain C) in PDB entry 1KFY
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 ASN 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.0 21.4 + - - +
48C ALA* 3.3 2.6 + - - -
50C LYS* 1.3 77.6 + - - +
52C GLY* 1.3 63.2 + - - +
54C GLU* 4.7 3.3 + - - +
55C ALA* 3.4 22.6 + - + +
118D ILE* 4.0 18.2 - - - +
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Residues in contact with GLY 52 (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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48C ALA 3.6 0.4 + - - +
49C LEU 3.7 2.2 + - - -
50C LYS 3.0 10.3 + - - -
51C ASN* 1.3 74.2 - - - +
53C PRO* 1.3 68.9 - - - +
54C GLU* 2.9 2.9 - - - -
55C ALA 2.6 28.2 + - - -
56C TRP 3.0 8.8 + - - -
51D TYR* 3.5 15.7 - - - -
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Residues in contact with PRO 53 (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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52C GLY* 1.3 81.8 - - - +
54C GLU* 1.3 64.3 + - + +
56C TRP* 3.8 1.5 - - + +
57C ALA* 3.0 26.0 + - - +
51D TYR* 3.3 49.0 - - + +
52D GLU* 5.1 4.3 - - - +
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Residues in contact with GLU 54 (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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51C ASN 4.8 3.8 - - - +
52C GLY 2.7 6.8 + - - +
53C PRO* 1.3 81.9 - - + +
55C ALA* 1.3 60.7 + - + +
57C ALA* 3.6 6.4 + - - +
58C GLY* 3.5 13.2 + - - -
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Residues in contact with ALA 55 (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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48C ALA* 3.4 24.9 - - + +
51C ASN* 3.4 23.3 - - + +
52C GLY 2.6 13.5 + - - +
54C GLU* 1.3 73.9 - - - +
56C TRP* 1.3 66.0 + - - +
57C ALA 3.1 1.8 - - - -
58C GLY* 2.9 13.0 + - - +
59C PHE 3.0 10.0 + - - -
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Residues in contact with TRP 56 (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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45C GLY 3.7 16.8 - - - -
48C ALA* 3.4 13.3 + - - +
49C LEU* 3.3 37.9 - - + -
52C GLY 3.0 5.8 + - - +
53C PRO 3.9 4.0 - - - +
55C ALA* 1.3 76.6 - - - +
57C ALA* 1.3 65.5 + - + +
59C PHE* 3.0 26.3 + + - +
60C VAL* 3.0 51.5 + - + +
35D VAL* 6.2 0.7 - - + -
39D LEU* 4.1 20.6 - - + +
49D LEU 4.7 3.6 + - - -
51D TYR* 3.5 51.0 - + + +
54D VAL* 4.1 27.6 - - + -
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Residues in contact with ALA 57 (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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53C PRO 3.0 17.9 + - - +
54C GLU* 3.7 7.2 - - - +
55C ALA 3.1 0.2 - - - -
56C TRP* 1.3 81.1 - - + +
58C GLY* 1.3 57.1 + - - +
60C VAL* 3.9 6.8 - - - +
61C ASP* 3.0 26.3 + - - +
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Residues in contact with GLY 58 (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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54C GLU 3.5 6.7 + - - -
55C ALA* 2.9 10.0 + - - -
57C ALA* 1.3 79.7 - - - +
59C PHE* 1.3 63.4 + - - +
61C ASP* 3.4 8.2 + - - +
62C PHE* 3.1 19.6 + - - +
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Residues in contact with PHE 59 (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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41C GLU* 3.7 16.4 - - + -
42C LEU* 5.5 1.8 - - + -
44C PHE* 4.1 12.3 - + + -
45C GLY* 3.4 39.0 - - - -
48C ALA* 3.8 18.4 - - + -
55C ALA 3.0 4.6 + - - -
56C TRP* 3.0 38.8 + + - +
58C GLY* 1.3 74.6 - - - +
60C VAL* 1.3 59.6 + - + +
61C ASP 3.0 0.9 - - - -
62C PHE* 2.8 34.6 + + + +
63C LEU* 2.9 51.7 + - + +
35D VAL* 4.6 14.6 - - + -
39D LEU* 4.7 0.4 - - + -
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Residues in contact with VAL 60 (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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56C TRP* 3.0 50.8 + - + +
57C ALA* 3.9 7.4 - - - +
59C PHE* 1.3 77.0 - - + +
61C ASP* 1.3 63.2 + - - +
63C LEU* 3.3 11.2 + - - +
64C GLN* 3.2 31.6 + - - +
39D LEU* 4.6 16.6 - - + +
40D PRO* 4.4 18.6 - - + -
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Residues in contact with ASP 61 (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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57C ALA 3.0 19.6 + - - +
58C GLY* 3.5 10.5 - - - +
59C PHE 3.0 0.2 - - - -
60C VAL* 1.3 77.0 - - - +
62C PHE* 1.3 63.1 + - - +
64C GLN* 3.1 30.2 + - - +
65C ASN* 3.5 4.9 + - - -
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Residues in contact with PHE 62 (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 TRP* 4.0 14.1 - + - -
41C GLU* 4.1 15.7 - - + -
44C PHE* 5.2 19.7 - + - -
58C GLY 3.1 12.9 + - - +
59C PHE* 2.8 22.0 + + + +
61C ASP* 1.3 76.5 - - - +
63C LEU* 1.3 68.8 + - + -
65C ASN* 2.9 33.0 + - - +
68C ILE* 3.4 46.7 - - + +
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Residues in contact with LEU 63 (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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41C GLU* 4.5 9.0 - - - +
59C PHE* 2.9 49.9 + - + +
60C VAL* 3.3 8.0 + - - +
62C PHE* 1.3 93.8 - - + +
64C GLN* 1.3 56.0 + - - +
65C ASN 3.2 1.1 + - - -
68C ILE* 4.0 6.5 - - + +
69C VAL* 3.0 27.2 + - - +
72C ASN* 4.2 17.8 - - - +
35D VAL* 4.0 13.9 - - + +
36D GLY* 5.1 1.7 - - - +
39D LEU* 3.9 21.3 - - + -
40D PRO* 3.6 24.4 - - + +
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Residues in contact with GLN 64 (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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60C VAL* 3.2 25.0 + - - +
61C ASP* 3.1 24.6 + - - +
62C PHE 3.0 1.4 + - - -
63C LEU* 1.3 75.5 - - - +
65C ASN* 1.3 63.7 + - - +
66C PRO* 3.1 12.3 - - - +
69C VAL* 4.2 5.0 - - - +
40D PRO* 3.4 30.6 + - + +
41D LEU* 5.6 1.1 - - + -
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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