Contacts of the helix formed by residues 66 - 81 (chain A) in PDB entry 2CSF
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 ASN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 4.0 8.4 + - - +
61A ASN 5.9 0.4 - - - +
63A SER* 3.3 12.2 + - - +
64A PRO 4.9 0.7 - - - -
65A GLU* 1.3 76.1 - - - +
67A ARG* 1.3 55.1 + - - +
68A THR* 3.7 7.4 + - - -
69A LEU* 3.2 46.6 + - + +
70A TRP* 2.6 44.0 + - - +
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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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65A GLU 3.3 8.9 + - - +
66A ASN* 1.3 68.7 + - - +
68A THR* 1.3 63.0 - - - +
69A LEU 2.7 4.2 + - - -
70A TRP* 4.6 1.6 - - - -
71A GLU* 2.7 66.4 + - + +
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Residues in contact with THR 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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47A LYS* 6.0 3.1 - - - +
51A TRP* 5.1 4.2 + - - +
66A ASN* 3.7 7.0 + - - -
67A ARG* 1.3 79.4 - - - +
69A LEU* 1.3 58.5 + - + +
71A GLU* 4.6 5.8 + - - -
72A ASN* 2.6 43.5 + - - +
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Residues in contact with LEU 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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23A TYR* 4.2 13.0 - - - +
51A TRP* 5.4 6.1 - - + +
55A LEU* 4.6 19.5 - - + -
60A GLU* 3.2 40.4 - - + +
61A ASN 4.4 5.4 - - - +
62A PRO* 4.6 6.5 - - + -
63A SER 5.7 0.2 - - - +
66A ASN* 3.2 28.5 + - + +
67A ARG 2.7 4.9 + - - -
68A THR* 1.3 77.5 - - + +
70A TRP* 1.3 68.7 + - - +
71A GLU 3.0 1.4 + - - -
72A ASN* 3.1 3.7 + - - +
73A LEU* 2.8 40.0 + - + +
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Residues in contact with TRP 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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16A ILE 3.3 23.1 + - - -
17A ASN* 4.3 7.6 - - - -
18A ILE* 3.2 55.0 - - + +
62A PRO* 4.4 0.4 - - + -
63A SER* 2.8 51.5 + - - +
64A PRO* 3.4 29.1 - - + +
66A ASN* 2.6 25.4 + - - +
67A ARG* 4.1 1.8 - - - +
69A LEU* 1.3 73.2 - - - +
71A GLU* 1.3 55.0 + - + +
73A LEU* 3.3 6.6 + - - +
74A CYS* 2.7 49.5 + - + +
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Residues in contact with GLU 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 ARG* 2.7 63.0 + - - +
68A THR* 4.6 5.1 + - - +
70A TRP* 1.3 75.5 - - + +
72A ASN* 1.3 62.9 + - - +
74A CYS* 2.8 29.4 + - - +
75A THR* 3.2 5.9 + - - -
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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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45A ALA* 4.8 9.4 - - + +
47A LYS* 4.2 12.8 - - - +
51A TRP* 3.1 47.4 - - + +
68A THR* 2.6 29.5 + - - +
69A LEU 3.1 2.5 + - - +
71A GLU* 1.3 79.6 - - - +
73A LEU* 1.3 64.9 + - - +
74A CYS 2.9 1.2 + - - -
75A THR* 3.0 23.1 + - - +
76A ILE* 3.1 14.8 + - - +
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Residues in contact with LEU 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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18A ILE* 3.6 16.1 - - + +
22A ILE* 3.2 35.6 - - + +
23A TYR* 3.9 27.1 - - + +
26A ILE* 5.0 2.5 - - + -
51A TRP* 4.9 0.2 - - + -
55A LEU* 4.4 17.5 - - + -
62A PRO* 3.6 31.4 - - + -
69A LEU* 2.8 37.8 + - + +
70A TRP* 3.7 4.9 - - - +
72A ASN* 1.3 74.6 - - + +
74A CYS* 1.3 56.4 + - - +
76A ILE* 3.9 10.3 - - + -
77A ARG* 3.0 24.1 + - - +
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Residues in contact with CYS 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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16A ILE* 4.0 29.5 - - - +
18A ILE* 3.9 8.5 - - + -
70A TRP* 2.7 33.3 + - + +
71A GLU* 2.8 17.8 + - - +
73A LEU* 1.3 72.8 - - - +
75A THR* 1.3 61.4 + - - +
77A ARG* 3.3 11.8 + - - +
78A ARG* 3.4 20.9 + - - +
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Residues in contact with THR 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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44A ALA 3.2 24.2 + - - +
45A ALA* 3.6 18.4 - - + -
71A GLU 3.2 4.1 + - - -
72A ASN* 3.0 17.0 + - - +
74A CYS* 1.3 79.7 - - - +
76A ILE* 1.3 65.5 + - + +
78A ARG* 3.5 12.8 + - - +
79A PHE* 3.4 18.2 + - - +
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Residues in contact with ILE 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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22A ILE* 4.6 3.4 - - + -
26A ILE* 4.1 13.7 - - + -
40A PHE* 3.4 37.0 - - + -
41A ALA* 5.8 0.4 - - - -
44A ALA* 3.9 13.0 - - + -
45A ALA* 3.7 17.5 - - + +
51A TRP* 3.4 39.5 - - + -
52A LEU* 4.8 3.6 - - + -
55A LEU* 4.7 2.0 - - + -
72A ASN 3.1 14.9 + - - +
73A LEU* 4.0 13.2 - - + +
75A THR* 1.3 75.2 - - + +
77A ARG* 1.3 64.8 + - - +
79A PHE* 3.4 7.2 + - - +
80A LEU* 3.3 18.9 + - + +
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Residues in contact with ARG 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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9A ILE* 4.0 29.7 - - - +
16A ILE* 3.4 26.5 - - + +
17A ASN* 3.0 30.6 + - - +
18A ILE* 3.4 14.6 - - + +
19A THR 6.0 0.4 - - - +
22A ILE* 3.8 15.2 - - + +
25A GLU* 4.7 14.5 + - - -
73A LEU 3.0 19.2 + - - +
74A CYS 3.5 4.9 - - - +
75A THR 3.2 0.4 - - - -
76A ILE* 1.3 77.5 - - - +
78A ARG* 1.3 57.6 + - - +
80A LEU* 3.6 7.8 + - - +
81A ASN* 2.7 53.5 + - - +
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Residues in contact with ARG 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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14A ALA* 5.9 7.1 - - - +
16A ILE* 3.3 34.7 - - + +
74A CYS* 3.4 13.2 + - - +
75A THR* 3.8 12.8 - - - +
76A ILE 3.3 0.2 - - - -
77A ARG* 1.3 75.3 - - - +
79A PHE* 1.3 66.2 + - - +
81A ASN* 3.2 22.9 + - + +
82A LEU* 3.6 11.1 + - - +
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Residues in contact with PHE 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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40A PHE* 5.3 1.3 - + + -
43A VAL* 3.1 35.0 - - + -
44A ALA* 3.6 15.7 - - + -
75A THR 3.4 9.7 + - - +
76A ILE* 3.4 13.4 + - + +
77A ARG 3.3 0.6 - - - -
78A ARG* 1.3 78.5 - - - +
80A LEU* 1.3 63.1 + - + +
82A LEU* 2.8 38.0 + - + +
87A ARG* 3.7 16.6 - - + -
90A ILE* 3.3 38.4 - - + -
91A TYR* 2.8 47.1 - + - -
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Residues in contact with LEU 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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22A ILE* 4.3 20.2 - - + +
25A GLU* 3.5 44.6 - - + +
26A ILE* 4.5 3.8 - - + -
29A GLU* 3.8 21.3 - - + +
40A PHE* 3.5 33.4 - - + -
76A ILE 3.3 16.3 + - - +
77A ARG* 3.6 9.6 + - - +
79A PHE* 1.3 78.0 - - + +
81A ASN* 1.3 61.1 + - - +
82A LEU 3.0 2.0 - - - +
87A ARG* 2.9 31.2 + - - +
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Residues in contact with ASN 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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8A PRO* 6.0 1.9 - - - +
9A ILE* 3.7 31.5 + - - +
16A ILE* 5.7 2.0 - - - +
77A ARG* 2.7 48.1 + - - +
78A ARG* 3.2 17.9 + - - +
79A PHE 3.1 0.6 - - - -
80A LEU* 1.3 77.7 - - - +
82A LEU* 1.3 61.6 + - + +
83A PRO* 3.9 1.6 - - - +
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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