Contacts of the helix formed by residues 50 - 66 (chain C) in PDB entry 1YKB
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 PRO 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C GLN 3.0 3.6 - - - +
49C GLN* 1.4 84.4 - - - +
51C TYR* 1.3 65.2 + - - +
52C ILE* 3.1 1.3 - - - -
53C THR* 3.4 17.9 - - - +
54C ASN* 2.9 30.3 + - - +
1I NAG 3.3 23.1 - - - +
2I NAG 2.9 33.2 - - - +
5I FUC 5.3 4.5 - - - +
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 2.3 22.6 + - + +
50C PRO* 1.3 69.5 - - - +
52C ILE* 1.3 63.6 + - + +
54C ASN* 3.3 7.2 + - + +
55C ARG* 2.9 68.8 + - + +
117C GLU* 2.4 35.4 + - + -
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Residues in contact with ILE 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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47C PHE 5.5 2.7 - - - -
49C GLN* 2.7 48.1 + - + +
50C PRO 4.1 0.4 - - - -
51C TYR* 1.3 84.3 - - + +
53C THR* 1.3 62.8 + - - +
55C ARG* 3.5 5.5 + - + +
56C THR* 2.9 43.8 + - - +
117C GLU 4.3 4.9 - - - +
118C VAL* 4.2 17.0 - - + -
121C PHE* 3.5 55.6 - - + -
171C PHE* 4.3 6.1 - - + -
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Residues in contact with THR 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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47C PHE 4.9 0.3 + - - -
50C PRO* 3.1 18.8 + - - +
52C ILE* 1.3 78.9 - - - +
54C ASN* 1.3 66.2 + - - +
56C THR* 3.3 2.2 + - - -
57C PHE* 3.0 41.7 + - + -
171C PHE* 3.7 18.7 - - + -
172C MET* 5.5 1.8 - - - -
50D PRO* 4.1 22.9 - - + +
54D ASN* 5.9 0.2 - - + -
1I NAG 3.1 41.1 + - + +
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Residues in contact with ASN 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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50C PRO* 2.9 20.3 + - - +
51C TYR* 3.7 8.6 - - + +
53C THR* 1.3 76.1 - - - +
55C ARG* 1.3 58.1 + - - +
57C PHE* 3.3 5.7 + - - +
58C MET* 2.9 48.0 + - + +
50D PRO* 3.8 21.2 - - - +
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Residues in contact with ARG 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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51C TYR* 2.9 66.9 + - + +
52C ILE* 3.7 9.2 - - + +
54C ASN* 1.3 73.7 - - - +
56C THR* 1.3 59.8 + - - +
58C MET* 3.1 26.4 + - + +
59C LEU* 2.8 30.3 + - - +
113C PRO* 5.2 4.0 - - - +
114C TYR* 4.2 20.8 - - + +
117C GLU* 3.4 31.2 + - + +
118C VAL* 3.6 18.2 - - + +
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Residues in contact with THR 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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52C ILE* 2.9 25.0 + - - +
53C THR* 3.3 7.4 + - - -
55C ARG* 1.3 76.1 - - - +
57C PHE* 1.3 60.0 + - + +
59C LEU* 3.4 3.7 + - - +
60C ALA* 3.0 26.0 + - - +
118C VAL* 3.4 27.4 - - + +
121C PHE* 5.4 0.2 - - - -
122C LEU* 6.0 1.6 - - + -
167C LEU* 3.7 34.9 - - + +
168C ASP* 4.2 3.4 - - - +
171C PHE* 4.0 23.5 - - + -
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Residues in contact with PHE 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 THR* 3.0 40.4 + - + +
54C ASN 3.8 3.6 - - - +
56C THR* 1.3 77.0 - - - +
58C MET* 1.3 62.0 + - + +
60C ALA* 3.6 5.5 - - - +
61C LYS* 2.8 36.9 + - - +
168C ASP* 3.8 37.9 - - + -
171C PHE* 4.9 4.7 - + - -
172C MET* 4.2 12.6 - - + -
47D PHE 4.9 0.9 - - - -
48D GLN* 3.5 25.4 - - + +
49D GLN 3.8 0.9 - - - -
50D PRO* 3.5 41.7 - - + -
53D THR* 3.8 30.7 - - + -
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Residues in contact with MET 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 ASN* 2.9 44.2 + - + +
55C ARG* 3.3 45.8 - - - +
57C PHE* 1.3 76.0 - - + +
59C LEU* 1.3 59.0 + - - +
61C LYS* 3.3 15.1 + - + +
62C GLU* 3.0 29.8 + - - +
114C TYR* 3.9 32.9 - - + +
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Residues in contact with LEU 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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55C ARG 2.8 17.0 + - - +
56C THR* 3.6 6.5 - - - +
58C MET* 1.3 75.9 - - - +
60C ALA* 1.3 62.8 + - - +
62C GLU* 3.3 1.9 + - - +
63C ALA* 3.0 22.9 + - - +
104C LEU* 5.1 0.2 - - + -
111C PHE* 3.6 31.2 - - + -
114C TYR* 3.8 21.9 - - + -
115C MET* 4.1 26.9 - - + +
118C VAL* 4.0 21.5 - - + -
119C VAL* 5.5 0.9 - - + -
164C ILE* 3.8 16.4 - - + -
167C LEU* 3.5 25.8 - - + -
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Residues in contact with ALA 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 THR 3.0 17.5 + - - +
57C PHE 3.6 4.7 - - - +
59C LEU* 1.3 77.7 - - - +
61C LYS* 1.3 56.9 + - - +
64C SER* 2.9 33.5 + - - -
164C ILE 3.5 15.9 + - - +
165C GLY* 3.5 11.4 - - - +
167C LEU* 4.7 0.4 - - + +
168C ASP* 3.8 37.7 - - + +
48D GLN* 5.1 1.6 - - - +
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Residues in contact with LYS 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 PHE* 2.8 24.9 + - - +
58C MET* 3.5 14.2 - - + +
59C LEU 3.2 0.2 - - - -
60C ALA* 1.3 72.5 - - + +
62C GLU* 1.3 64.9 + - - +
64C SER* 3.3 3.5 + - - -
65C LEU* 3.3 25.8 + - - +
48D GLN* 3.1 54.7 + - + +
49D GLN* 3.5 23.4 + - - +
50D PRO* 4.8 5.3 - - - +
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Residues in contact with GLU 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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58C MET 3.0 16.4 + - - +
59C LEU* 3.3 4.5 + - - +
61C LYS* 1.3 76.1 - - - +
63C ALA* 1.3 62.8 + - - +
65C LEU* 3.1 38.0 + - - +
66C ALA* 3.8 2.9 + - - +
111C PHE* 3.6 29.0 - - + -
114C TYR* 4.2 27.0 + - + -
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Residues in contact with ALA 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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59C LEU 3.0 10.7 + - - +
62C GLU* 1.3 76.8 - - - +
64C SER* 1.3 62.1 + - - +
66C ALA 3.1 10.8 + - - +
67C ASP* 3.4 2.6 + - - +
111C PHE* 3.8 23.5 - - + -
161C ILE* 3.4 21.0 - - - +
164C ILE* 3.5 33.4 - - + -
165C GLY* 3.6 16.4 - - - +
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Residues in contact with SER 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 ALA 2.9 20.0 + - - -
61C LYS 3.5 6.5 - - - -
62C GLU 3.2 0.2 - - - -
63C ALA* 1.3 76.7 - - - +
65C LEU* 1.3 63.4 + - - +
67C ASP* 3.2 23.9 + - - +
165C GLY* 3.5 18.7 + - - -
44D LYS* 3.6 27.8 + - - +
48D GLN* 3.7 16.6 + - - -
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Residues in contact with LEU 65 (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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61C LYS 3.3 12.1 + - - +
62C GLU* 3.1 32.8 + - - +
64C SER* 1.3 79.9 - - - +
66C ALA* 1.3 60.4 + - - +
67C ASP 3.6 1.7 + - - -
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Residues in contact with ALA 66 (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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62C GLU 3.8 3.1 + - - +
63C ALA 3.1 11.8 + - - +
65C LEU* 1.3 79.4 - - + +
67C ASP* 1.3 57.1 + - - +
68C ASN* 3.1 10.1 + - - +
110C ARG* 5.9 1.3 - - - +
111C PHE* 5.0 10.5 - - + -
158C SER* 6.0 1.7 - - - -
161C ILE* 3.9 19.9 - - + +
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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