Contacts of the helix formed by residues 61 - 82 (chain A) in PDB entry 1FIU
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 PRO 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG 3.8 2.0 - - - +
60A LEU* 1.3 94.1 - - + +
62A GLY* 1.3 66.1 + - - +
63A GLN* 3.5 14.8 - - - +
64A THR* 2.9 29.4 + - + +
65A SER* 3.1 8.7 + - - -
9I C 6.3 0.2 - - - -
10I G 3.7 24.2 - - - +
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Residues in contact with GLY 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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60A LEU 3.4 3.0 + - - -
61A PRO* 1.3 72.7 - - - +
63A GLN* 1.3 59.7 + - - +
65A SER* 3.5 4.9 - - - -
66A GLY* 2.9 24.6 + - - -
8I G 5.7 1.8 - - - +
5J C 4.3 2.3 - - - +
6J C 3.2 37.5 - - - +
7J G 4.1 16.7 - - - -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.5 19.6 - - - +
62A GLY* 1.3 75.2 + - - +
64A THR* 1.3 56.6 + - - +
66A GLY* 4.1 0.2 - - - -
67A ASN* 3.1 30.1 + - - +
4F G 3.9 6.5 - - - +
8I G 3.4 16.0 + - - +
9I C 2.8 52.2 + - - +
10I G 3.3 33.5 - - - +
11I C 3.9 8.8 - - - +
5J C 3.9 22.7 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 5.2 2.9 - - + -
60A LEU* 3.9 23.6 - - + -
61A PRO* 2.9 29.3 + - + +
63A GLN* 1.3 76.3 - - - +
65A SER* 1.3 61.3 + - - +
67A ASN* 3.4 1.6 + - - +
68A ALA* 2.9 33.6 + - + +
10I G 3.2 7.6 + - - -
11I C 2.8 29.5 + - - +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.2 21.9 - - - +
60A LEU* 4.6 11.6 + - - +
61A PRO 3.1 5.1 + - - -
62A GLY* 3.2 18.7 + - - -
64A THR* 1.3 79.8 - - - +
66A GLY* 1.3 60.2 + - - +
68A ALA* 4.1 1.7 - - - +
69A PHE* 2.8 34.1 + - - +
188A TRP* 3.5 34.0 - - - +
6J C 3.9 2.4 + - - -
7J G 4.9 0.9 + - - -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY 2.9 15.3 + - - -
63A GLN 4.1 0.4 - - - -
65A SER* 1.3 79.8 + - - +
67A ASN* 1.3 61.7 + - - +
69A PHE* 3.5 2.6 + - - +
70A GLU* 3.2 29.2 + - - +
188A TRP* 4.7 0.7 - - - -
5J C 3.4 28.3 - - - -
6J C 3.6 12.7 + - - -
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Residues in contact with ASN 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 GLN 3.1 18.6 + - - +
64A THR 4.0 2.0 - - - +
66A GLY* 1.3 76.2 - - - +
68A ALA* 1.3 64.2 + - - +
70A GLU* 3.2 7.2 + - - -
71A ALA* 3.0 21.0 + - - +
96A GLN* 2.9 36.7 + - - +
11I C 4.0 36.4 + - - +
5J C 5.5 1.2 - - - -
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Residues in contact with ALA 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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21A ILE* 3.5 31.2 - - + -
64A THR* 2.9 21.4 + - + +
65A SER 4.1 1.3 - - - +
67A ASN* 1.3 78.3 + - - +
69A PHE* 1.3 57.6 + - - +
71A ALA* 3.2 6.2 + - - +
72A ILE* 2.9 40.6 + - + +
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Residues in contact with PHE 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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12A PHE* 4.2 14.6 - + - -
16A LEU* 4.1 14.6 - - + -
21A ILE* 5.1 1.0 - - + +
65A SER 2.8 20.1 + - - +
66A GLY 3.8 3.8 - - - +
68A ALA* 1.3 76.0 - - - +
70A GLU* 1.3 62.7 + - - +
72A ILE* 4.7 2.2 - - - -
73A CYS* 2.9 52.5 + - - +
186A CYS* 3.9 13.0 - - + -
187A LYS 3.7 11.7 - - - -
188A TRP* 3.6 47.1 - + + -
219A VAL* 3.7 31.0 - - + -
220A THR 3.9 1.3 - - - -
221A ALA* 3.9 18.4 - - + -
244A PHE* 4.3 4.7 - - + -
6J C 5.1 0.7 - - - -
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Residues in contact with GLU 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 GLY 3.2 15.0 + - - +
67A ASN* 3.2 7.6 + - - +
69A PHE* 1.3 79.4 - - - +
71A ALA* 1.3 57.5 + - - +
73A CYS 3.3 0.2 + - - -
74A SER* 2.9 26.9 + - - -
96A GLN* 2.9 35.8 + - + +
98A GLY* 5.2 5.2 + - - -
140A ASP* 3.4 35.0 - - + +
141A ILE* 3.4 11.2 - - + +
186A CYS* 4.0 27.8 - - + +
5555A MG 4.2 0.7 - - - -
5J C 4.0 18.0 - - - +
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Residues in contact with ALA 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 ASN* 3.0 13.2 + - - +
68A ALA* 3.2 10.7 + - - +
70A GLU* 1.3 78.0 - - - +
72A ILE* 1.3 63.9 + - + +
74A SER* 3.2 7.4 + - - -
75A GLU* 3.0 34.2 + - - +
96A GLN* 3.5 22.4 - - - +
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Residues in contact with ILE 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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12A PHE* 3.6 37.4 - - + +
15A LYS* 3.8 41.5 + - + +
16A LEU* 3.7 26.0 - - + -
21A ILE* 4.3 10.3 - - + -
68A ALA* 2.9 23.4 + - + +
69A PHE 4.1 2.2 - - - +
71A ALA* 1.3 75.2 - - + +
73A CYS* 1.3 65.3 + - - +
75A GLU* 3.4 10.8 + - - +
76A PHE* 3.1 22.2 + - - +
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Residues in contact with CYS 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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12A PHE* 3.9 14.8 - - - -
69A PHE* 2.9 58.0 + - - +
70A GLU 3.6 4.0 - - - +
72A ILE* 1.3 75.2 - - - +
74A SER* 1.3 62.9 + - - +
76A PHE* 3.3 4.0 + - - +
77A VAL* 3.0 30.5 + - + +
141A ILE* 3.9 13.5 - - + -
184A ILE* 5.7 0.7 - - + -
186A CYS* 3.9 6.5 - - - -
219A VAL* 3.7 22.9 - - + -
277A ILE* 5.0 2.6 - - + +
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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 GLU 2.9 14.1 + - - -
71A ALA* 3.3 11.7 - - - -
73A CYS* 1.3 77.6 - - - +
75A GLU* 1.3 58.1 + - - +
77A VAL* 3.3 1.6 + - - -
78A GLN* 2.9 31.1 + - - +
94A VAL* 3.6 24.1 + - - +
95A LYS* 3.9 3.3 - - - -
96A GLN* 3.8 21.0 + - - -
141A ILE* 3.7 16.2 - - - +
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Residues in contact with GLU 75 (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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15A LYS* 2.6 48.0 + - - +
71A ALA* 3.0 22.5 + - + +
72A ILE* 3.8 8.0 - - - +
73A CYS 3.3 0.2 - - - -
74A SER* 1.3 73.6 - - - +
76A PHE* 1.3 65.1 + - - +
78A GLN* 3.5 12.2 + - - +
79A SER* 3.0 26.7 + - - -
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Residues in contact with PHE 76 (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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5A PHE* 4.8 4.7 - + + -
8A GLU* 3.6 46.4 - - + -
9A ARG* 3.9 8.5 - - + -
12A PHE* 3.8 23.1 - + + -
15A LYS* 5.1 1.3 - - - +
72A ILE 3.1 13.6 + - - +
73A CYS 3.6 6.5 - - - +
75A GLU* 1.3 76.7 - - - +
77A VAL* 1.3 72.7 + - + +
79A SER* 3.9 3.6 - - - -
80A ALA* 3.0 27.0 + - + +
277A ILE* 3.4 50.3 - - + -
278A SER* 4.1 11.2 - - - -
280A LEU* 5.1 0.2 - - + -
281A PRO* 3.7 25.1 - - + -
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Residues in contact with VAL 77 (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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73A CYS* 3.0 22.9 + - + +
74A SER* 3.8 4.7 - - - +
76A PHE* 1.3 87.0 - - + +
78A GLN* 1.3 64.0 + - - +
81A PHE* 2.9 33.3 + - + +
94A VAL* 4.1 21.1 - - + -
141A ILE* 5.9 0.7 - - + -
143A VAL* 4.4 2.0 - - + -
184A ILE* 4.3 15.9 - - + -
277A ILE* 5.4 1.3 - - + -
280A LEU* 3.8 29.2 - - + -
281A PRO* 5.0 4.5 - - + -
284A LEU* 3.8 25.1 - - + -
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Residues in contact with GLN 78 (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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74A SER* 2.9 18.8 + - - +
75A GLU* 3.7 12.5 - - - +
77A VAL* 1.3 76.9 - - - +
79A SER* 1.3 62.8 + - - +
81A PHE* 4.2 1.3 - - - +
82A GLU* 3.2 30.3 + - + +
93A ASN* 5.9 0.8 - - - +
94A VAL* 3.8 43.8 + - + +
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Residues in contact with SER 79 (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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8A GLU* 3.2 32.5 + - - -
75A GLU 3.0 18.1 + - - -
76A PHE 4.0 0.9 - - - -
78A GLN* 1.3 80.7 - - - +
80A ALA* 1.3 62.5 + - - +
82A GLU* 3.6 18.8 + - - +
83A LYS* 3.7 16.5 - - - +
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Residues in contact with ALA 80 (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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5A PHE* 3.5 30.9 - - + -
8A GLU* 4.6 8.0 + - + -
76A PHE* 3.0 26.4 + - + +
79A SER* 1.3 74.9 - - - +
81A PHE* 1.3 66.2 + - - +
83A LYS* 3.1 19.7 + - - +
84A LEU* 4.0 1.4 + - - +
281A PRO* 3.4 29.8 - - + -
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Residues in contact with PHE 81 (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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77A VAL* 2.9 26.3 + - + +
78A GLN* 4.3 2.5 - - - +
80A ALA* 1.3 77.7 - - - +
82A GLU* 1.3 63.4 + - - +
84A LEU* 2.9 27.0 + - + +
85A GLN* 4.2 0.7 + - - -
88A ARG* 4.2 10.8 - - + -
92A TRP* 3.6 57.1 - + + -
94A VAL* 5.2 4.9 - - + -
143A VAL* 4.5 13.0 - - + -
181A HIS* 4.1 7.4 - + - -
281A PRO* 3.6 24.3 - - + +
284A LEU* 3.6 40.8 - - + -
285A ALA* 4.0 10.1 - - + -
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Residues in contact with GLU 82 (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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78A GLN* 3.2 22.6 + - + +
79A SER* 3.6 13.7 + - - +
80A ALA 3.2 0.6 - - - -
81A PHE* 1.3 79.3 - - - +
83A LYS* 1.3 60.4 + - + +
84A LEU 3.2 1.3 + - - -
85A GLN* 3.8 17.1 + - - +
92A TRP* 6.5 1.1 - - - -
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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