Contacts of the helix formed by residues 56 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLN 3.6 1.9 + - - -
55A TYR* 1.3 71.1 - - - +
57A LYS* 1.3 58.7 + - - +
58A GLU* 3.1 14.7 + - - +
59A GLU* 3.0 43.6 + - + +
60A PHE* 3.0 26.3 + - - +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 6.2 0.2 - - - +
55A TYR* 3.0 32.3 + - + +
56A ASP* 1.3 70.6 + - - +
58A GLU* 1.3 75.5 + - - +
60A PHE* 3.3 8.8 + - - +
61A ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP* 3.1 9.3 + - - +
57A LYS* 1.3 85.3 + - - +
59A GLU* 1.3 62.9 + - - +
61A ALA* 3.4 7.1 + - - +
62A ARG* 3.1 21.8 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 3.0 35.7 + - - +
58A GLU* 1.3 73.8 - - - +
60A PHE* 1.3 61.8 + - - +
62A ARG* 3.0 20.7 + - - +
63A ILE* 2.8 28.0 + - + +
199A PHE* 3.6 20.0 - - + -
200A VAL* 2.9 39.5 + - - +
214A PRO* 3.3 27.9 - - + +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 3.5 32.3 - + + -
56A ASP 3.0 18.4 + - - +
57A LYS* 3.5 6.7 - - - +
58A GLU 3.3 0.2 - - - -
59A GLU* 1.3 76.2 - - - +
61A ALA* 1.3 62.9 + - - +
63A ILE* 3.1 20.8 + - + +
64A GLN* 3.1 41.2 + - - +
217A LEU* 3.8 24.7 - - + -
227A ILE* 3.5 37.7 - - + -
228A GLU* 3.8 12.8 - - + -
231A MSE 3.5 23.8 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS 3.0 12.7 + - - +
58A GLU* 3.7 10.5 - - - +
59A GLU 3.2 0.2 - - - -
60A PHE* 1.3 77.6 - - - +
62A ARG* 1.3 57.8 + - - +
64A GLN* 3.4 18.3 + - - +
65A LYS* 3.0 25.5 + - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU 3.1 10.9 + - - +
59A GLU* 3.0 24.6 + - - +
61A ALA* 1.3 76.5 - - - +
63A ILE* 1.3 58.2 + - - +
65A LYS* 3.6 15.6 - - + +
66A CYS* 2.9 33.9 + - - -
197A GLU* 3.0 30.9 + - - +
198A THR 2.9 34.3 + - - +
199A PHE* 3.6 26.0 - - + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 2.8 16.4 + - + +
60A PHE* 3.1 22.9 + - + +
62A ARG* 1.3 76.4 - - - +
64A GLN* 1.3 57.1 + - - +
66A CYS* 3.3 1.8 + - - +
67A ALA* 2.8 28.4 + - - +
199A PHE* 3.7 24.4 - - + -
214A PRO* 3.8 35.7 - - + -
217A LEU* 4.0 17.5 - - + +
218A LEU* 3.7 32.9 - - + +
221A ALA* 4.8 1.6 - - + -
227A ILE* 3.8 18.8 - - + -
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.1 22.8 + - - +
61A ALA* 3.5 19.5 - - - +
62A ARG 3.2 0.2 - - - -
63A ILE* 1.3 77.6 - - - +
65A LYS* 1.3 60.6 + - - +
67A ALA* 3.3 7.6 + - - +
68A GLU* 3.0 33.0 + - + +
221A ALA* 5.4 1.3 - - + -
227A ILE* 4.0 21.7 - - + +
228A GLU* 3.3 41.6 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 14.3 + - - +
62A ARG* 3.3 18.1 + - + +
64A GLN* 1.3 77.8 - - - +
66A CYS* 1.3 64.9 + - - +
68A GLU* 3.3 8.6 + - - +
69A LYS* 3.1 26.2 + - + +
197A GLU* 4.7 11.7 + - - -
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Residues in contact with CYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 2.9 27.1 + - - +
63A ILE 3.8 2.9 - - - +
65A LYS* 1.3 74.1 - - - +
67A ALA* 1.3 65.4 + - - +
69A LYS* 3.2 9.0 + - - +
70A ILE* 3.0 29.8 + - - +
177A TYR* 3.8 18.6 - - + -
197A GLU* 3.8 35.0 - - - -
199A PHE* 3.7 21.8 - - + -
218A LEU* 4.3 6.1 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE 2.8 18.1 + - - +
64A GLN* 3.5 6.3 - - - +
65A LYS 3.3 0.2 - - - -
66A CYS* 1.3 77.0 - - - +
68A GLU* 1.3 57.8 + - + +
70A ILE* 3.4 2.3 + - - +
71A LYS* 2.9 36.7 + - - +
218A LEU* 3.9 4.4 - - + +
221A ALA* 3.6 31.0 - - + +
222A VAL* 3.9 23.2 - - + +
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLN* 3.0 23.7 + - + +
65A LYS* 3.7 8.3 - - - +
66A CYS 3.2 0.4 - - - -
67A ALA* 1.3 74.9 - - - +
69A LYS* 1.3 66.0 + - - +
71A LYS* 3.4 32.9 + - - +
72A ASN* 3.0 39.7 + - - +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.1 17.6 + - + +
66A CYS* 3.5 11.9 - - - +
68A GLU* 1.3 77.1 - - - +
70A ILE* 1.3 61.2 + - - +
72A ASN* 3.2 7.0 + - - +
73A ASP* 2.8 51.8 + - - +
171A GLU* 5.2 2.0 + - - -
174A LYS* 2.8 40.6 + - - +
175A ARG* 4.5 5.5 - - - +
177A TYR* 3.3 17.0 + - + +
197A GLU* 6.4 0.9 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A CYS 3.0 18.7 + - - +
67A ALA 3.7 5.8 - - - +
69A LYS* 1.3 74.1 - - - +
71A LYS* 1.3 65.4 + - - +
73A ASP* 3.5 6.3 - - - -
74A SER* 2.9 41.5 + - - +
77A LEU* 4.3 22.9 - - + -
112A PRO* 4.1 1.7 - - + +
139A SER* 4.3 5.8 - - - +
177A TYR* 3.6 41.5 - - + +
218A LEU* 4.3 10.8 - - + -
222A VAL* 3.8 36.1 - - + -
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 2.9 23.9 + - - +
68A GLU* 3.5 38.0 + - - +
69A LYS 3.4 0.2 - - - -
70A ILE* 1.3 76.4 - - - +
72A ASN* 1.3 66.6 + - - +
73A ASP 3.5 0.4 + - - -
74A SER 4.1 7.4 - - - +
110A LYS 5.2 4.3 - - - +
111A THR* 4.5 10.6 - - + +
112A PRO* 3.8 18.2 - - + +
221A ALA 3.1 26.7 + - - -
222A VAL* 3.6 21.3 - - + +
224A GLY* 4.1 16.0 + - - -
225A LEU 5.8 0.2 + - - -
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Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.0 34.7 + - - +
69A LYS* 3.9 3.6 - - - +
70A ILE 3.1 0.8 - - - -
71A LYS* 1.3 85.3 - - - +
73A ASP* 1.3 59.3 + - - +
74A SER 3.8 0.4 - - - -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS* 2.8 56.4 + - - +
70A ILE* 3.5 5.7 - - - +
72A ASN* 1.3 79.3 - - - +
74A SER* 1.3 74.5 + - - +
137A ASP* 3.5 11.5 - - - +
139A SER* 3.9 2.4 + - - -
171A GLU* 5.4 0.5 - - - +
175A ARG* 2.9 38.9 + - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 2.9 19.4 + - - +
71A LYS 4.1 5.5 - - - +
72A ASN 3.8 0.4 - - - -
73A ASP* 1.3 92.2 + - - +
75A ASP* 1.3 64.4 + - - +
76A ILE 3.6 20.2 - - - -
112A PRO* 3.6 17.2 - - - +
137A ASP* 3.8 7.0 - - - -
138A PHE* 4.2 1.3 - - - -
139A SER* 2.6 27.4 + - - -
175A ARG* 3.3 4.3 + - - -
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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