Contacts of the helix formed by residues 56 - 74 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C GLN 3.4 2.3 + - - -
55C TYR* 1.3 71.1 - - - +
57C LYS* 1.3 58.3 + - - +
58C GLU* 3.1 15.6 + - - +
59C GLU* 3.0 45.7 + - + +
60C PHE* 3.1 24.8 + - - +
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Residues in contact with LYS 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 LEU 5.5 4.0 - - - +
55C TYR* 3.1 38.6 + - + +
56C ASP* 1.3 71.8 + - - +
58C GLU* 1.3 79.2 + - - +
59C GLU 3.3 0.2 - - - -
60C PHE* 3.5 8.6 - - - +
61C ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 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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56C ASP* 3.1 9.6 + - - +
57C LYS* 1.3 87.0 + - - +
59C GLU* 1.3 65.3 + - - +
61C ALA* 3.3 8.3 + - - +
62C ARG* 3.1 21.6 + - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 3.0 37.8 + - - +
58C GLU* 1.3 75.1 - - - +
60C PHE* 1.3 66.1 + - - +
62C ARG* 2.9 21.0 + - - +
63C ILE* 2.9 22.5 + - + +
199C PHE* 3.6 20.9 - - + -
200C VAL* 2.8 41.9 + - - +
214C PRO* 3.4 26.3 - - + +
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Residues in contact with PHE 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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55C TYR* 3.7 29.2 - + + -
56C ASP 3.1 16.4 + - - +
57C LYS* 3.5 7.0 - - - +
58C GLU 3.3 0.2 - - - -
59C GLU* 1.3 79.6 - - - +
61C ALA* 1.3 61.7 + - + +
63C ILE* 3.1 22.1 + - - +
64C GLN* 3.2 39.4 + - - +
217C LEU* 3.8 21.1 - - + -
227C ILE* 3.4 44.8 - - + +
228C GLU* 3.7 13.2 - - + -
231C MSE 3.7 23.1 - - + -
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Residues in contact with ALA 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 LYS 3.1 13.4 + - - +
58C GLU* 3.7 10.1 - - - +
59C GLU 3.2 0.2 - - - -
60C PHE* 1.3 77.3 - - + +
62C ARG* 1.3 57.1 + - - +
64C GLN* 3.3 18.8 + - - +
65C LYS* 3.1 26.0 + - - +
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Residues in contact with ARG 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 GLU 3.1 11.7 + - - +
59C GLU* 2.9 25.6 + - - +
61C ALA* 1.3 75.4 - - - +
63C ILE* 1.3 64.5 + - - +
65C LYS* 3.8 11.4 - - + +
66C CYS* 3.0 28.7 + - - -
197C GLU* 2.9 32.2 + - - +
198C THR 2.8 31.3 + - - +
199C PHE* 3.5 24.7 - - + +
200C VAL* 6.3 0.6 - - - +
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Residues in contact with ILE 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 GLU* 2.9 17.1 + - + +
60C PHE* 3.3 22.0 - - + +
62C ARG* 1.3 75.0 - - - +
64C GLN* 1.3 58.0 + - - +
66C CYS* 3.3 2.6 + - - +
67C ALA* 2.9 28.8 + - - +
199C PHE* 3.6 24.4 - - + -
214C PRO* 3.9 30.1 - - + -
217C LEU* 3.9 21.8 - - + +
218C LEU* 3.6 35.5 - - + +
221C ALA* 4.5 2.7 - - + -
227C ILE* 3.9 16.4 - - + -
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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 PHE* 3.2 33.0 + - - +
61C ALA* 3.5 22.5 - - - +
62C ARG 3.2 0.2 - - - -
63C ILE* 1.3 79.1 - - - +
65C LYS* 1.3 60.6 + - - +
67C ALA* 3.4 7.7 + - - +
68C GLU* 3.1 29.2 + - - +
221C ALA* 5.4 2.0 - - + -
226C ASN* 5.7 0.6 + - - -
227C ILE* 4.0 21.7 - - + +
228C GLU* 4.7 13.3 + - - +
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Residues in contact with LYS 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 ALA 3.1 16.1 + - - +
62C ARG* 3.8 13.0 - - + +
63C ILE 3.3 0.2 - - - -
64C GLN* 1.3 76.0 - - - +
66C CYS* 1.3 65.4 + - - +
68C GLU* 3.3 9.0 + - - +
69C LYS* 3.1 21.7 + - + +
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Residues in contact with CYS 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 ARG* 3.0 25.1 + - - +
63C ILE 3.8 3.6 - - - +
65C LYS* 1.3 76.4 - - - +
67C ALA* 1.3 65.4 + - - +
69C LYS* 3.3 9.4 + - - +
70C ILE* 3.0 30.2 + - - +
177C TYR* 3.9 24.0 + - + -
197C GLU* 3.9 26.9 - - - -
199C PHE* 3.8 17.3 - - + -
218C LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 67 (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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63C ILE 2.9 17.9 + - - +
64C GLN* 3.6 6.7 - - - +
66C CYS* 1.3 76.2 - - - +
68C GLU* 1.3 58.3 + - - +
70C ILE* 3.4 1.9 + - - +
71C LYS* 3.0 37.0 + - - +
218C LEU* 4.2 2.9 - - + +
221C ALA* 3.7 31.2 - - + +
222C VAL* 3.8 24.8 - - + +
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Residues in contact with GLU 68 (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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64C GLN* 3.1 18.9 + - + +
65C LYS* 3.6 9.2 - - - +
66C CYS 3.2 0.4 - - - -
67C ALA* 1.3 74.5 - - - +
69C LYS* 1.3 65.2 + - - +
71C LYS* 3.3 35.4 + - - +
72C ASN* 3.1 41.0 + - - +
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Residues in contact with LYS 69 (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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65C LYS* 3.1 13.1 + - + +
66C CYS* 3.5 12.1 - - - +
68C GLU* 1.3 74.9 - - - +
70C ILE* 1.3 59.4 + - - +
72C ASN* 3.2 7.5 + - - +
73C ASP* 2.5 62.1 + - + +
171C GLU* 5.3 2.4 + - - -
174C LYS* 3.1 36.7 + - - +
175C ARG* 4.7 4.9 - - - +
177C TYR* 3.3 18.8 + - + +
197C GLU* 6.5 0.2 - - + -
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Residues in contact with ILE 70 (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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66C CYS 3.0 23.5 + - - +
67C ALA 3.8 3.4 - - - +
69C LYS* 1.3 73.9 - - - +
71C LYS* 1.3 65.0 + - - +
73C ASP* 3.5 6.5 - - - -
74C SER* 2.9 40.7 + - - +
77C LEU* 4.4 16.6 - - + -
112C PRO* 4.1 2.6 - - + +
139C SER* 4.4 9.2 - - - +
141C ASN* 6.1 0.2 - - + -
177C TYR* 3.6 45.1 - - + +
218C LEU* 4.3 10.5 - - + -
222C VAL* 3.8 35.9 - - + -
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Residues in contact with LYS 71 (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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67C ALA* 3.0 27.6 + - - +
68C GLU* 3.3 35.5 + - - +
70C ILE* 1.3 76.9 - - - +
72C ASN* 1.3 66.2 + - - +
74C SER 4.1 8.5 - - - +
110C LYS 5.3 5.4 - - - +
111C THR* 4.4 11.3 - - + +
112C PRO* 3.8 19.5 - - + +
221C ALA 3.3 26.8 + - - -
222C VAL* 3.7 20.0 - - - +
224C GLY* 3.9 16.3 + - - -
225C LEU 5.7 0.4 + - - -
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Residues in contact with ASN 72 (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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68C GLU* 3.1 30.2 + - - +
69C LYS* 3.8 5.5 - - - +
71C LYS* 1.3 86.2 - - - +
73C ASP* 1.3 58.6 + - - +
74C SER 3.8 0.4 - - - -
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Residues in contact with ASP 73 (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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69C LYS* 2.5 56.0 + - + +
70C ILE* 3.5 5.7 - - - +
72C ASN* 1.3 78.6 - - + +
74C SER* 1.3 86.3 + - - +
137C ASP* 3.6 9.3 - - - +
139C SER* 3.8 3.2 + - - -
171C GLU* 5.6 0.3 - - - +
175C ARG* 3.0 38.8 + - - +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 2.9 19.6 + - - +
71C LYS 4.1 5.5 - - - +
72C ASN 3.8 1.4 - - - -
73C ASP* 1.3 97.5 + - - +
75C ASP* 1.3 64.7 + - - +
76C ILE 3.6 20.4 - - - -
112C PRO* 3.7 17.3 - - - +
137C ASP* 3.8 7.2 - - - -
138C PHE* 4.1 1.6 - - - -
139C SER* 2.7 21.4 + - - -
175C ARG* 3.4 2.9 + - - -
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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