Contacts of the helix formed by residues 56 - 74 (chain F) in PDB entry 3IFS
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 ASP 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F GLN 3.6 2.1 + - - -
55F TYR* 1.3 71.1 - - - +
57F LYS* 1.3 57.8 + - - +
58F GLU* 3.0 26.8 + - - +
59F GLU* 3.1 33.8 + - + +
60F PHE* 3.0 26.9 + - - +
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Residues in contact with LYS 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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55F TYR* 3.1 26.6 + - + +
56F ASP* 1.3 70.8 + - - +
58F GLU* 1.3 77.9 + - - +
60F PHE* 3.4 9.0 + - - +
61F ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 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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56F ASP* 3.0 12.9 + - - +
57F LYS* 1.3 82.4 + - - +
59F GLU* 1.3 65.7 + - - +
61F ALA* 3.3 8.3 + - - +
62F ARG* 3.2 20.9 + - - +
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ASP* 3.1 37.1 + - - +
58F GLU* 1.3 77.1 - - - +
60F PHE* 1.3 63.8 + - - +
62F ARG* 3.0 20.5 + - - +
63F ILE* 2.9 26.7 + - + +
199F PHE* 3.6 20.5 - - + -
200F VAL* 2.8 41.1 + - - +
214F PRO* 3.4 25.8 - - + +
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Residues in contact with PHE 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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55F TYR* 3.6 33.4 - + + -
56F ASP 3.0 18.5 + - - +
57F LYS* 3.5 7.2 - - - +
58F GLU 3.3 0.2 - - - -
59F GLU* 1.3 76.5 - - - +
61F ALA* 1.3 61.9 + - + +
63F ILE* 3.3 19.7 + - - +
64F GLN* 3.3 26.8 + - - +
217F LEU* 3.9 20.2 - - + -
227F ILE* 3.6 42.3 - - + +
228F GLU* 3.8 24.2 - - + -
231F MSE 3.7 24.2 - - + -
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Residues in contact with ALA 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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57F LYS 3.1 13.0 + - - +
58F GLU* 3.6 10.5 - - - +
59F GLU 3.2 0.2 - - - -
60F PHE* 1.3 77.4 - - + +
62F ARG* 1.3 58.4 + - - +
64F GLN* 3.2 17.0 + - - +
65F LYS* 3.0 24.8 + - - +
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Residues in contact with ARG 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 GLU 3.2 11.8 + - - +
59F GLU* 3.0 24.0 + - - +
61F ALA* 1.3 74.1 - - - +
63F ILE* 1.3 60.5 + - - +
65F LYS* 3.5 32.7 - - - +
66F CYS* 2.8 33.9 + - - -
197F GLU* 2.6 38.9 + - - +
198F THR 2.8 33.7 + - - +
199F PHE* 3.9 20.5 - - + +
200F VAL* 6.3 0.2 - - - +
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Residues in contact with ILE 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 GLU* 2.9 22.0 + - + +
60F PHE* 3.4 15.3 - - + +
62F ARG* 1.3 75.8 - - - +
64F GLN* 1.3 58.6 + - - +
66F CYS 3.3 0.3 + - - -
67F ALA* 2.8 29.5 + - - +
199F PHE* 3.5 22.9 - - + -
214F PRO* 4.0 24.7 - - + -
217F LEU* 3.8 37.2 - - + +
218F LEU* 3.6 35.0 - - + +
221F ALA* 4.6 2.0 - - + -
227F ILE* 4.1 9.9 - - + -
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Residues in contact with GLN 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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60F PHE* 3.3 22.2 + - - +
61F ALA* 3.2 19.3 + - - +
63F ILE* 1.3 81.2 - - - +
65F LYS* 1.3 61.5 + - - +
67F ALA* 3.3 6.5 + - - +
68F GLU* 3.1 29.2 + - + +
221F ALA* 5.4 2.2 - - + -
226F ASN* 5.6 0.2 + - - -
227F ILE* 3.9 20.9 - - + +
228F GLU* 2.8 42.7 + - - +
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Residues in contact with LYS 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 ALA 3.0 13.0 + - - +
62F ARG* 3.5 37.1 - - - +
64F GLN* 1.3 74.5 - - - +
66F CYS* 1.3 65.3 + - - +
68F GLU* 3.3 8.0 + - - +
69F LYS* 3.1 21.5 + - + +
197F GLU* 5.3 5.6 + - - -
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Residues in contact with CYS 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 ARG* 2.8 27.6 + - - +
63F ILE 3.8 3.1 - - - +
65F LYS* 1.3 72.0 - - - +
67F ALA* 1.3 67.9 + - - +
69F LYS* 3.1 9.1 + - - +
70F ILE* 3.0 28.1 + - - +
177F TYR* 3.9 24.9 - - + -
197F GLU* 3.9 27.6 - - - -
199F PHE* 3.7 18.4 - - + -
218F LEU* 4.2 9.9 - - + -
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Residues in contact with ALA 67 (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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63F ILE 2.8 18.1 + - - +
64F GLN* 3.6 5.8 - - - +
66F CYS* 1.3 75.6 - - - +
68F GLU* 1.3 60.1 + - - +
70F ILE* 3.3 1.7 + - - +
71F LYS* 2.9 37.5 + - - +
218F LEU* 4.1 2.4 - - + +
221F ALA* 3.7 39.0 - - + +
222F VAL* 3.8 16.7 - - + +
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Residues in contact with GLU 68 (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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64F GLN* 3.1 17.2 + - + +
65F LYS* 3.7 9.2 - - - +
66F CYS 3.2 0.2 - - - -
67F ALA* 1.3 75.8 - - - +
69F LYS* 1.3 65.1 + - - +
71F LYS* 3.1 36.7 + - - +
72F ASN* 3.0 37.5 + - - +
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Residues in contact with LYS 69 (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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65F LYS* 3.1 12.3 + - + +
66F CYS* 3.1 13.5 + - - +
68F GLU* 1.3 77.0 - - - +
70F ILE* 1.3 62.9 + - - +
72F ASN* 3.1 8.4 + - - +
73F ASP* 2.5 54.9 + - - +
171F GLU* 5.1 2.6 + - - -
174F LYS* 3.1 42.0 + - - +
175F ARG* 4.7 4.8 - - - +
177F TYR* 3.4 17.2 + - + +
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Residues in contact with ILE 70 (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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66F CYS 3.0 21.0 + - - +
67F ALA 3.8 3.6 - - - +
69F LYS* 1.3 75.0 - - - +
71F LYS* 1.3 63.6 + - - +
73F ASP* 3.5 7.4 - - - -
74F SER* 2.9 40.7 + - - +
77F LEU* 4.3 19.7 - - + -
112F PRO* 4.1 2.0 - - + +
139F SER* 4.3 9.0 - - - +
177F TYR* 3.5 47.3 - - + +
218F LEU* 4.7 7.6 - - + -
222F VAL* 4.0 35.0 - - + -
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Residues in contact with LYS 71 (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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67F ALA* 2.9 21.1 + - - +
68F GLU* 3.1 37.9 + - - +
70F ILE* 1.3 76.7 - - - +
72F ASN* 1.3 65.4 + - - +
74F SER 4.1 8.1 - - - +
110F LYS 5.5 3.8 - - - +
111F THR* 4.5 10.4 - - + +
112F PRO* 3.8 20.0 - - + +
221F ALA 3.0 29.5 + - - -
222F VAL* 3.5 21.1 - - - +
224F GLY* 3.8 17.3 + - - +
225F LEU 5.6 0.6 + - - -
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Residues in contact with ASN 72 (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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68F GLU* 3.0 26.7 + - - +
69F LYS* 3.1 7.5 + - - +
71F LYS* 1.3 83.1 + - - +
73F ASP* 1.3 58.0 + - + +
74F SER 3.8 0.2 - - - -
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Residues in contact with ASP 73 (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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69F LYS* 2.5 56.1 + - + +
70F ILE* 3.5 6.9 - - - -
72F ASN* 1.3 77.6 - - + +
74F SER* 1.3 83.3 + - - +
137F ASP* 3.5 9.9 - - - +
139F SER* 3.8 2.4 + - - -
171F GLU* 5.2 0.9 - - - +
175F ARG* 2.9 38.3 + - - +
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Residues in contact with SER 74 (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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70F ILE* 2.9 19.6 + - - +
71F LYS 4.1 5.5 - - - +
72F ASN 3.8 0.8 - - - -
73F ASP* 1.3 92.6 + - - +
75F ASP* 1.3 62.9 + - - +
76F ILE 3.6 20.4 - - - -
112F PRO* 3.6 17.5 - - - +
137F ASP* 3.6 7.0 - - - -
138F PHE* 4.1 1.1 - - - -
139F SER* 2.7 26.9 + - - -
175F ARG* 3.2 4.9 + - - -
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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