Contacts of the helix formed by residues 66 - 83 (chain A) in PDB entry 1FF1
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.6 1.1 - - - -
29A GLY 2.8 26.5 - - - +
30A PHE* 3.4 19.4 - - + +
59A ILE* 5.1 0.2 - - - +
60A ASP* 3.6 5.5 - - - +
65A LEU* 1.3 73.0 - - - +
67A ARG* 1.3 63.8 + - + +
68A ASP* 2.6 16.1 + - - +
69A GLU* 2.4 72.0 + - - +
70A PHE 2.5 32.4 + - - -
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Residues in contact with ARG 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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14A LYS* 3.2 12.7 + - - +
17A TYR* 5.5 0.5 - - - +
18A ASP* 3.6 19.5 - - - +
21A PHE* 2.9 36.9 - - + +
28A ASN 4.2 4.9 + - - -
29A GLY* 3.7 27.0 + - - -
30A PHE* 5.2 3.2 - - - -
66A ASP* 1.3 75.2 + - + +
68A ASP* 1.3 81.7 + - + +
70A PHE* 4.0 0.7 - - - +
71A ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.7 16.8 - - + -
14A LYS* 3.7 15.5 - - - -
59A ILE* 5.3 0.9 - - - -
66A ASP* 2.6 18.4 + - - +
67A ARG* 1.3 87.3 + - + +
69A GLU* 1.3 62.8 + - + -
71A ALA* 3.4 5.2 - - - +
72A VAL* 3.2 26.6 + - - +
96A PRO* 5.1 21.0 - - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.9 2.1 - - - -
57A SER* 2.7 37.0 + - - +
59A ILE* 3.1 22.7 + - + +
60A ASP* 2.3 41.1 + - - +
65A LEU* 3.4 7.2 - - + -
66A ASP* 2.4 65.7 + - - +
68A ASP* 1.3 69.2 - - + +
70A PHE* 1.3 59.1 + - - +
71A ALA 3.0 5.4 + - - -
72A VAL* 3.3 10.4 + - - +
73A ALA 3.3 0.3 + - - -
113A CA 2.5 21.9 - - - -
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Residues in contact with PHE 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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17A TYR 3.9 1.6 - - - -
20A ILE* 3.0 30.3 - - + -
21A PHE* 3.7 22.7 - - + -
24A LEU* 3.2 10.8 - - + -
31A LEU* 2.9 31.2 - - + -
36A VAL* 3.1 35.2 - - + -
39A VAL* 3.2 25.1 - - + -
40A LEU* 6.0 0.2 - - + -
65A LEU* 3.5 16.3 - - + +
66A ASP 2.5 19.5 + - - +
67A ARG 4.1 1.1 - - - +
69A GLU* 1.3 75.2 - - - +
71A ALA* 1.3 57.9 + - - +
73A ALA* 3.5 2.3 + - + +
74A MET* 2.8 48.6 + - + +
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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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7A TRP* 4.3 9.9 - - + -
9A VAL* 4.4 2.9 - - + -
14A LYS* 3.3 28.5 - - + -
17A TYR* 3.1 33.5 - - + -
67A ARG 3.1 19.7 + - - +
68A ASP* 3.4 7.4 - - - +
69A GLU 3.0 0.4 - - - -
70A PHE* 1.3 75.5 - - - +
72A VAL* 1.3 67.0 + - - +
73A ALA 3.0 1.6 - - - -
74A MET 2.9 11.3 + - - -
75A PHE* 3.5 1.9 + - - -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 4.5 13.7 - - + +
9A VAL* 4.3 2.2 - - - -
56A LEU 3.4 19.1 - - - +
57A SER* 3.9 5.2 - - - -
59A ILE* 4.9 8.1 - - + -
68A ASP 3.2 16.8 - - - +
69A GLU* 3.3 8.7 + - - +
71A ALA* 1.3 76.9 - - - +
73A ALA* 1.3 57.7 + - - +
75A PHE* 2.7 31.0 - - - -
76A LEU* 3.1 10.6 - - + +
94A LEU* 3.1 53.8 - - + +
96A PRO* 5.3 2.7 - - + -
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Residues in contact with ALA 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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36A VAL* 5.1 0.4 - - + -
40A LEU* 3.9 7.4 - - + +
53A VAL* 3.2 18.8 - - + +
54A TRP* 4.8 0.7 - - - -
57A SER* 2.7 32.1 - - - +
65A LEU* 4.0 12.1 - - + -
69A GLU 3.3 4.1 + - - +
70A PHE* 3.8 6.5 - - + +
71A ALA 3.0 0.8 - - - -
72A VAL* 1.3 79.2 - - - +
74A MET* 1.3 56.9 + - - +
76A LEU 3.9 0.9 - - - -
77A VAL* 2.6 36.9 - - - +
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Residues in contact with MET 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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17A TYR* 3.0 42.6 - - + -
20A ILE* 3.0 37.2 - - + -
39A VAL* 3.5 21.5 - - + +
40A LEU* 4.7 4.0 - - + -
70A PHE* 2.8 49.6 - - + +
71A ALA 2.9 1.0 + - - -
73A ALA* 1.3 82.7 - - + +
75A PHE* 1.3 61.6 + - - +
76A LEU 3.2 1.1 - - - -
77A VAL* 3.1 10.3 + - + +
78A TYR* 2.9 36.9 + - + +
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Residues in contact with PHE 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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8A ALA* 4.5 16.2 - - + +
9A VAL* 3.5 23.1 - - + -
13A ASP* 5.5 1.6 - - + -
17A TYR* 2.7 28.7 + - + +
71A ALA 3.7 0.2 - - - -
72A VAL* 2.7 33.7 - - - -
74A MET* 1.3 73.2 - - - +
76A LEU* 1.3 84.6 + - + +
77A VAL 3.0 1.6 - - - -
78A TYR* 4.2 2.9 - - - +
79A CYS* 2.6 58.7 + - + +
91A PRO* 5.7 2.0 - - + -
94A LEU* 2.8 37.0 - - + -
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Residues in contact with LEU 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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53A VAL* 3.4 45.8 - - + +
56A LEU* 3.9 24.2 - - + -
72A VAL* 3.1 28.0 - - + +
73A ALA* 3.9 0.2 - - - -
75A PHE* 1.3 105.3 - - + +
77A VAL* 1.3 57.1 + - - +
79A CYS* 4.2 2.2 - - + -
80A ALA* 3.1 22.9 + - - +
86A VAL* 3.5 31.2 - - + +
87A PRO* 5.2 5.2 - - + -
91A PRO* 6.2 1.3 - - + -
94A LEU* 4.9 1.6 - - + -
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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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39A VAL 4.8 2.2 - - - +
40A LEU* 3.1 27.4 - - + -
43A SER* 2.7 39.9 - - - +
45A LEU* 3.7 3.3 - - + +
50A LEU* 4.7 2.9 - - + -
53A VAL* 3.2 14.6 - - + -
73A ALA 2.6 26.7 - - - +
74A MET* 3.1 12.1 + - + +
75A PHE 3.0 0.2 - - - -
76A LEU* 1.3 79.1 - - - +
78A TYR* 1.3 67.9 + - + +
79A CYS 3.2 0.9 - - - -
80A ALA* 3.2 10.1 + - - +
81A LEU* 2.8 26.7 - - + +
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Residues in contact with TYR 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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16A LYS* 4.4 22.2 - - + +
17A TYR* 4.5 11.2 - + - +
20A ILE* 4.4 20.3 - - + +
74A MET* 2.9 30.3 + - + +
75A PHE* 4.1 5.4 - - - +
77A VAL* 1.3 81.3 - - + +
79A CYS* 1.3 64.5 + - - +
80A ALA 3.4 0.7 + - - -
81A LEU* 3.3 26.4 + - + +
82A GLU* 3.5 19.6 + - + +
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Residues in contact with CYS 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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17A TYR* 5.3 0.4 - - - -
75A PHE* 2.6 54.5 + - + +
76A LEU* 4.7 2.5 - - + -
78A TYR* 1.3 73.9 - - - +
80A ALA* 1.3 58.8 + - - +
81A LEU 3.2 1.3 - - - -
83A LYS* 2.6 62.9 + - + +
84A GLU 2.8 11.2 + - - +
86A VAL* 5.8 0.2 - - - -
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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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45A LEU* 3.2 35.3 - - + +
49A ILE* 3.7 2.2 - - + -
76A LEU 3.1 21.8 + - - +
77A VAL 3.2 1.5 + - - +
79A CYS* 1.3 79.8 - - - +
81A LEU* 1.3 61.0 + - - +
83A LYS 4.5 0.2 - - - -
84A GLU 3.2 16.8 + - - +
85A PRO* 5.6 0.3 - - - +
86A VAL* 3.5 19.7 - - + -
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Residues in contact with LEU 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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43A SER* 2.6 41.7 - - - +
44A LYS* 4.7 2.0 - - + -
45A LEU* 3.5 20.9 - - + -
77A VAL* 2.8 22.7 - - + +
78A TYR* 3.3 32.5 - - + +
79A CYS 3.2 0.2 - - - -
80A ALA* 1.3 82.2 - - - +
82A GLU* 1.3 70.3 + - + +
83A LYS 3.6 0.4 - - - -
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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 TYR* 3.5 14.9 + - + +
81A LEU* 1.3 90.7 - - + +
83A LYS* 1.3 62.3 + - - +
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Residues in contact with LYS 83 (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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79A CYS* 2.6 51.1 + - + +
81A LEU 3.6 2.0 - - - -
82A GLU* 1.3 82.6 - - - +
84A GLU* 1.3 73.5 + - + +
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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
------------------------------------------------------------
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