Contacts of the helix formed by residues 54 - 66 (chain C) in PDB entry 4PIW
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 SER 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C THR* 2.7 21.6 + - - -
53C PRO* 1.3 83.1 - - - +
55C CYS* 1.3 59.2 + - - +
56C THR* 3.6 4.3 + - - -
57C ALA* 3.2 21.7 + - - +
58C SER 3.1 13.2 + - - -
181C LLP 3.3 20.0 + - - -
188C GLU* 4.6 6.7 - - - -
189C GLY 3.4 13.2 - - - -
190C GLY* 3.7 0.7 - - - -
232D SER* 3.8 20.0 + - - -
234D LEU 6.1 0.9 - - - -
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Residues in contact with CYS 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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54C SER* 1.3 70.0 - - - +
56C THR* 1.3 55.3 + - - +
58C SER* 3.2 4.3 + - - -
59C LEU* 2.8 35.6 + - - +
152C ASP* 3.5 24.7 - - - -
154C ALA* 3.8 15.3 - - - -
174C CYS* 4.1 12.6 - - - -
175C PHE 3.3 26.7 - - - +
176C SER* 3.6 9.9 - - - -
181C LLP 2.9 28.6 + - - +
189C GLY 3.7 2.8 + - - -
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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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54C SER* 3.7 0.2 - - - -
55C CYS* 1.3 78.4 - - - +
57C ALA* 1.3 50.9 + - - +
59C LEU* 3.1 6.3 + - - +
60C GLU* 2.8 59.7 + - + +
81C PHE* 4.6 0.2 - - - -
83C SER* 2.6 44.1 + - - +
86C ASN* 6.0 1.8 - - + -
87C ALA* 5.5 0.9 - - + +
181C LLP 2.4 23.5 + - - -
209D LYS* 4.6 1.5 - - + -
231D SER* 4.3 2.9 - - - +
232D SER* 3.5 29.6 - - - +
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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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52C THR* 4.3 1.1 - - - -
53C PRO* 4.2 13.7 - - + -
54C SER* 3.2 25.2 + - - +
56C THR* 1.3 79.7 - - - +
58C SER* 1.3 56.3 + - - +
60C GLU* 4.1 12.6 - - - +
61C MSE 2.8 30.8 + - - +
233C TYR* 3.3 25.7 - - + -
231D SER* 5.9 0.2 - - - -
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Residues in contact with SER 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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52C THR* 2.4 32.6 + - - +
54C SER 3.1 5.4 + - - -
55C CYS* 3.2 12.9 + - - -
57C ALA* 1.3 77.6 - - - +
59C LEU* 1.3 57.0 + - - +
61C MSE 3.4 3.4 + - - +
62C ALA* 2.9 27.9 + - - +
174C CYS* 3.8 17.4 - - - -
175C PHE 4.8 0.2 - - - -
191C ALA 3.4 16.6 + - - -
192C THR* 3.2 24.8 + - - +
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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 CYS* 2.8 22.1 + - - +
56C THR 3.1 6.5 + - - +
58C SER* 1.3 73.7 - - - +
60C GLU* 1.3 59.3 + - - +
62C ALA* 3.1 4.5 + - - +
63C ALA* 3.0 25.3 + - - +
83C SER* 3.4 35.9 - - - +
84C THR* 3.7 11.0 - - - +
87C ALA* 3.5 17.7 - - + +
88C PHE* 4.8 13.0 - - + -
124C VAL* 5.2 2.5 - - + -
150C VAL* 4.4 13.2 - - + -
152C ASP* 4.0 31.2 - - + +
174C CYS* 3.7 21.1 - - + -
181C LLP 5.1 1.8 - - - +
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Residues in contact with GLU 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* 2.8 34.9 + - + +
57C ALA* 3.7 12.0 - - - +
59C LEU* 1.3 72.1 - - - +
61C MSE 1.3 56.7 + - - +
63C ALA* 3.4 2.6 + - - +
64C LEU* 2.9 30.3 + - - +
86C ASN* 5.9 0.2 - - - +
87C ALA* 3.7 24.2 + - + +
90C LEU* 3.5 24.9 - - + +
91C ARG* 5.4 0.9 - - - +
233C TYR* 3.9 16.9 + - - +
60D GLU* 5.7 1.0 - - - +
230D GLY 4.2 0.9 - - - +
231D SER* 2.5 37.3 + - - -
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Residues in contact with MSE 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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50C LEU* 3.7 21.8 - - + -
52C THR* 4.2 13.0 - - - -
57C ALA 2.8 19.6 + - - +
58C SER 3.5 4.9 - - - +
60C GLU* 1.3 75.5 - - - +
62C ALA* 1.3 58.2 + - - +
64C LEU* 3.4 2.1 + - - -
65C LEU* 2.8 33.3 + - + +
192C THR* 3.4 32.1 - - + +
194C ILE* 4.9 0.7 - - + -
203C ALA* 3.3 39.3 - - + +
206C ILE* 3.6 14.8 - - + +
207C ARG* 4.2 6.3 - - + -
233C TYR* 3.8 31.3 + - + -
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Residues in contact with ALA 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 SER 2.9 14.2 + - - +
59C LEU* 3.1 10.9 + - - +
61C MSE 1.3 74.7 - - - +
63C ALA* 1.3 63.7 + - - +
65C LEU* 3.3 3.5 + - - +
66C LEU* 3.2 30.9 + - - +
88C PHE* 5.1 1.8 - - + -
150C VAL* 4.0 19.3 - - + -
172C ILE* 3.7 36.5 - - + +
174C CYS* 4.4 1.1 - - - -
192C THR* 5.3 0.9 - - - -
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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 10.5 + - - +
60C GLU 3.7 5.2 - - - +
62C ALA* 1.3 76.6 - - - +
64C LEU* 1.3 62.2 + - - +
65C LEU 3.2 0.9 + - - -
66C LEU* 3.4 6.1 + - - -
68C ILE* 3.2 32.5 + - + +
87C ALA 3.3 26.5 - - - +
88C PHE* 3.7 26.0 - - + -
91C ARG* 3.8 12.8 - - + -
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Residues in contact with LEU 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 GLU 2.9 17.3 + - - +
61C MSE 3.8 4.7 - - - +
63C ALA* 1.3 76.6 - - - +
65C LEU* 1.3 61.2 + - - +
67C ASP* 3.6 5.9 + - - -
68C ILE 5.3 0.2 - - - +
91C ARG* 3.3 41.4 - - - +
202C ARG* 3.5 18.0 + - - -
206C ILE* 4.5 10.8 - - + +
229C ILE* 4.2 19.5 - - + +
230C GLY* 4.3 20.9 - - - -
233C TYR* 3.9 22.7 - - + +
90D LEU* 3.8 26.2 - - + -
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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 MSE 2.8 21.0 + - + +
62C ALA* 3.5 7.9 - - - +
63C ALA 3.1 0.2 - - - -
64C LEU* 1.3 75.0 - - - +
66C LEU* 1.3 58.4 + - + +
67C ASP 3.0 9.6 + - - -
172C ILE* 3.8 11.2 - - + -
192C THR* 5.4 0.2 - - + -
194C ILE* 3.7 19.1 - - + -
199C LEU* 3.7 48.6 - - + +
202C ARG* 3.2 28.0 + - + +
203C ALA* 3.6 34.3 - - + +
206C ILE* 4.0 15.0 - - + +
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Residues in contact with LEU 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 ALA 3.2 15.0 + - - +
63C ALA 3.4 1.2 + - - +
65C LEU* 1.3 75.0 - - + +
67C ASP* 1.3 70.2 + - - +
68C ILE* 3.3 15.1 + - + +
88C PHE* 5.3 1.3 - - + -
121C ARG* 3.6 21.7 + - - +
122C VAL* 3.6 26.0 - - + -
148C PHE* 3.7 46.4 - - + -
150C VAL* 3.8 23.6 - - + -
171C HIS* 6.0 0.2 - - + -
172C ILE* 3.7 17.5 - - + -
199C LEU* 4.0 13.5 - - + -
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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