Contacts of the helix formed by residues 54 - 66 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232E SER* 3.8 17.0 + - - -
52F THR* 2.6 25.3 + - - -
53F PRO* 1.3 83.1 - - - +
55F CYS* 1.3 58.2 + - - +
56F THR* 3.5 8.1 + - - -
57F ALA* 3.2 22.4 + - - +
58F SER 3.0 13.3 + - - -
181F LLP 3.3 21.5 - - - -
188F GLU* 4.5 4.5 - - - -
189F GLY 3.6 9.6 - - - -
190F GLY* 3.6 2.7 - - - -
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Residues in contact with CYS 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F SER* 1.3 70.5 - - - +
56F THR* 1.3 53.9 + - - +
58F SER* 3.1 4.6 + - - -
59F LEU* 2.7 46.0 + - - +
152F ASP* 4.2 2.5 - - - -
154F ALA* 4.0 19.5 - - + -
174F CYS* 3.9 22.4 - - - -
175F PHE 3.2 29.8 - - - +
176F SER* 3.5 12.1 - - - -
181F LLP 3.1 18.9 + - + +
189F GLY 3.8 2.4 + - - -
190F GLY* 3.7 3.8 - - - -
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Residues in contact with THR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E LYS* 4.8 2.3 + - + -
230E GLY 5.5 0.9 - - - +
231E SER* 4.3 2.5 - - - +
232E SER* 3.7 27.8 - - - +
54F SER* 3.1 8.7 - - - -
55F CYS* 1.3 79.1 - - - +
57F ALA* 1.3 56.5 + - - +
59F LEU* 3.2 5.4 + - - +
60F GLU* 2.8 53.7 + - + +
83F SER* 2.8 44.7 + - - +
86F ASN* 6.1 1.8 - - + -
87F ALA* 5.7 0.7 - - + +
181F LLP 3.3 12.2 + - - -
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E SER* 5.6 0.9 + - - +
52F THR* 4.2 4.9 - - - -
53F PRO* 4.4 7.9 - - + -
54F SER* 3.2 25.0 + - - +
56F THR* 1.3 79.6 - - - +
58F SER* 1.3 57.5 + - - +
60F GLU* 3.7 13.4 - - - +
61F MSE 2.8 24.9 + - - +
233F TYR* 3.1 33.4 - - + -
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Residues in contact with SER 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F THR* 2.3 31.7 + - - -
54F SER 3.0 6.0 + - - -
55F CYS* 3.3 13.5 - - - -
57F ALA* 1.3 77.9 - - - +
59F LEU* 1.3 56.4 + - - +
61F MSE 3.3 3.9 + - - +
62F ALA* 2.9 27.4 + - - +
174F CYS* 3.6 13.5 - - - -
191F ALA 3.3 21.3 + - - -
192F THR* 3.1 25.3 + - - +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F CYS* 2.7 33.9 + - - +
56F THR 3.5 4.0 - - - +
58F SER* 1.3 70.4 - - - +
60F GLU* 1.3 64.9 + - - +
62F ALA* 3.3 4.3 + - - +
63F ALA* 3.1 18.9 + - - +
83F SER* 3.6 25.8 - - - +
84F THR* 3.7 16.6 - - + +
87F ALA* 3.4 19.3 - - + +
88F PHE* 4.7 13.4 - - + -
124F VAL* 5.2 1.1 - - + -
150F VAL* 4.4 13.2 - - + -
151F GLU 4.8 0.2 - - - +
152F ASP* 4.0 24.2 - - + +
174F CYS* 3.6 24.5 - - + -
181F LLP 4.9 2.5 - - - +
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU* 5.8 0.3 - - - +
230E GLY 4.2 0.9 - - - +
231E SER* 2.6 37.7 + - - -
56F THR* 2.8 30.2 + - + +
57F ALA* 3.7 11.7 - - - +
59F LEU* 1.3 73.0 - - - +
61F MSE 1.3 65.3 + - - +
63F ALA* 3.3 4.3 + - - +
64F LEU* 3.1 22.9 + - - +
86F ASN* 5.8 0.5 - - - +
87F ALA* 3.7 29.3 + - + +
90F LEU* 3.9 18.8 - - + +
91F ARG* 5.3 1.2 - - - +
233F TYR* 4.0 12.6 + - - +
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Residues in contact with MSE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 3.8 15.3 - - + -
52F THR* 4.4 5.6 - - - -
57F ALA 2.8 18.4 + - - +
58F SER 3.5 5.2 - - - +
60F GLU* 1.3 73.8 - - - +
62F ALA* 1.3 56.2 + - - +
64F LEU* 3.1 4.2 + - - +
65F LEU* 2.7 35.0 + - + +
192F THR* 3.7 22.2 - - + +
194F ILE* 4.4 11.0 - - + -
203F ALA* 3.2 47.6 - - + +
206F ILE* 3.6 13.9 - - + +
207F ARG* 4.5 4.3 - - + -
233F TYR* 3.6 39.2 + - + -
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Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F SER 2.9 14.1 + - - +
59F LEU* 3.4 11.4 - - - +
60F GLU 3.2 0.4 - - - -
61F MSE 1.3 77.8 - - - +
63F ALA* 1.3 61.6 + - - +
65F LEU* 3.4 3.0 + - - +
66F LEU* 3.3 32.1 + - - +
88F PHE* 5.1 2.0 - - + -
150F VAL* 3.9 21.5 - - + -
172F ILE* 3.7 33.4 - - + -
174F CYS* 4.4 0.7 - - - -
192F THR* 5.4 0.2 - - - -
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU 3.1 9.6 + - - +
60F GLU 3.7 4.9 - - - +
61F MSE 3.3 0.2 - - - -
62F ALA* 1.3 76.5 - - - +
64F LEU* 1.3 59.8 + - - +
66F LEU 3.9 0.4 + - - -
67F ASP 3.8 1.6 + - - -
68F ILE* 3.3 41.2 + - + +
87F ALA 3.3 26.7 - - - +
88F PHE* 3.7 24.4 - - + -
91F ARG* 3.7 11.3 - - + +
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 3.9 20.2 - - + -
60F GLU 3.1 16.1 + - - +
61F MSE 3.6 5.6 - - - +
63F ALA* 1.3 76.5 - - - +
65F LEU* 1.3 64.1 + - - +
66F LEU 3.3 0.2 - - - -
67F ASP* 3.4 5.8 + - - +
91F ARG* 3.3 38.8 - - - +
202F ARG* 3.2 23.2 + - - +
206F ILE* 4.5 16.8 - - + +
229F ILE* 3.7 19.7 - - + +
230F GLY* 4.4 21.3 - - - +
233F TYR* 4.2 15.7 - - + +
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F MSE 2.7 17.6 + - + +
62F ALA* 3.4 7.2 + - - +
64F LEU* 1.3 79.8 - - - +
66F LEU* 1.3 55.1 + - - +
67F ASP 3.2 0.7 - - - -
172F ILE* 3.7 20.0 - - + -
194F ILE* 3.7 31.0 - - + -
199F LEU* 3.7 35.5 - - + +
202F ARG* 2.8 42.0 + - + +
203F ALA* 3.6 29.6 - - + +
206F ILE* 3.8 9.4 - - + +
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ALA 3.3 19.1 + - - +
63F ALA* 3.9 0.4 + - - -
64F LEU 3.3 0.4 - - - -
65F LEU* 1.3 75.6 - - - +
67F ASP* 1.3 72.4 + - - +
68F ILE* 3.6 15.2 - - + +
88F PHE* 5.2 0.4 - - + -
122F VAL* 3.6 39.0 - - + -
148F PHE* 3.7 43.0 - - + -
150F VAL* 3.9 14.8 - - + -
172F ILE* 3.8 16.8 - - + -
199F LEU* 3.9 15.7 - - + -
202F ARG* 4.1 0.7 - - - -
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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