Contacts of the helix formed by residues 55 - 68 (chain A) in PDB entry 1CF7
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 LYS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.8 33.8 + - - +
44A LYS* 4.6 16.7 - - - +
47A ALA* 4.3 17.7 - - + +
54A GLN* 1.3 73.3 - - - +
56A ARG* 1.3 67.4 + - - +
58A ILE* 2.6 34.3 + - + +
59A TYR* 3.2 39.2 + - + +
77A ASN* 4.1 7.3 - - - +
604D A 5.4 0.4 - - - -
605D C 3.5 10.9 + - - -
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Residues in contact with ARG 56 (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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54A GLN* 3.1 5.5 + - + +
55A LYS* 1.3 76.4 - - - +
57A ARG* 1.3 82.5 + - - +
59A TYR* 3.0 21.7 + - - +
60A ASP* 3.0 32.2 + - - +
63A ASN* 5.2 3.2 - - - +
71B LEU* 6.3 0.2 - - - +
122B ARG* 5.9 1.2 - - - +
508C G 3.4 26.4 + - + +
509C C 4.4 4.3 - - - +
606D C 3.7 42.2 + - - +
607D G 3.0 48.4 + - - -
608D C 3.4 11.1 - - - +
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Residues in contact with ARG 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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22A LEU* 4.4 11.1 - - + +
25A LEU* 3.9 29.2 - - + -
53A ARG* 5.1 9.0 - - + -
54A GLN* 3.1 17.5 + - + +
55A LYS 2.8 4.0 + - - -
56A ARG* 1.3 94.3 - - - +
58A ILE* 1.3 68.4 + - + +
60A ASP* 2.4 49.1 + - - +
61A ILE* 3.3 9.0 + - - +
506C G 5.7 5.6 - - - -
507C C 3.2 34.9 - - - +
508C G 2.7 49.1 + - - -
608D C 4.6 0.4 - - - +
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Residues in contact with ILE 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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25A LEU* 6.2 2.7 - - + -
29A PHE* 4.1 33.9 - - + -
43A LEU* 4.6 22.0 - - + +
46A ALA* 4.4 7.2 - - + -
47A ALA* 4.4 17.9 - - + +
50A LEU* 4.4 23.1 - - + -
54A GLN 5.1 1.3 - - - +
55A LYS* 2.6 32.6 + - + +
57A ARG* 1.3 73.7 - - + +
59A TYR* 1.3 66.9 + - + +
61A ILE* 2.9 22.5 + - + +
62A THR* 3.0 20.4 + - + -
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Residues in contact with TYR 59 (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 LEU* 4.3 13.7 - - + -
55A LYS* 3.2 40.1 + - + +
56A ARG* 3.0 22.9 + - - +
58A ILE* 1.3 79.7 - - + +
60A ASP* 1.3 57.0 + - - +
62A THR* 3.4 9.2 - - - -
63A ASN* 2.9 46.3 + - - +
604D A 3.7 6.9 - - - +
605D C 2.6 57.3 + + - -
606D C 3.6 51.8 - + + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 27.3 - - + +
56A ARG* 3.0 26.6 + - - +
57A ARG* 2.4 49.9 + - - +
59A TYR* 1.3 77.4 - - - +
61A ILE* 1.3 64.9 + - - +
63A ASN* 4.7 0.4 + - - +
64A VAL* 3.0 22.3 + - - +
71B LEU* 3.3 19.3 - - + +
122B ARG* 5.4 1.0 + - - -
125B ASP* 4.2 13.4 - - - +
129B VAL* 4.6 1.0 - - - +
507C C 5.4 0.3 + - - -
608D C 5.3 1.0 + - - -
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Residues in contact with ILE 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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22A LEU* 3.7 19.7 - - + -
25A LEU* 3.9 14.6 - - + +
26A THR* 3.9 30.1 - - + +
29A PHE* 3.8 47.6 - - + -
50A LEU* 5.3 0.4 - - + -
57A ARG 3.3 7.4 + - - +
58A ILE* 2.9 16.0 + - + +
60A ASP* 1.3 80.8 - - - +
62A THR* 1.3 65.5 + - - +
64A VAL* 3.2 7.0 + - - +
65A LEU* 3.1 40.3 + - + +
129B VAL* 4.7 4.5 - - + -
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Residues in contact with THR 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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29A PHE* 4.1 23.3 - - + -
43A LEU* 4.3 22.8 - - + +
58A ILE* 3.0 17.9 + - + +
59A TYR* 3.3 24.3 + - - -
61A ILE* 1.3 77.8 - - - +
63A ASN* 1.3 69.4 + - - +
64A VAL 3.2 0.2 + - - -
65A LEU* 3.2 6.7 + - - +
66A GLU* 2.9 43.9 + - - +
71A ILE* 5.4 4.5 - - + -
79A ILE* 4.8 10.5 - - + -
606D C 4.4 1.9 + - - -
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Residues in contact with ASN 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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56A ARG* 5.2 3.2 - - - +
59A TYR* 2.9 33.2 + - - +
60A ASP* 4.7 0.4 - - - +
61A ILE 3.2 0.2 + - - -
62A THR* 1.3 72.4 + - - +
64A VAL* 1.3 57.9 + - - +
66A GLU* 3.3 6.7 - - - +
67A GLY 3.0 21.5 + - - -
71B LEU* 3.7 32.6 - - + +
72B ARG* 3.0 42.3 + - - +
606D C 3.2 45.8 + - - +
607D G 4.5 1.5 + - - -
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Residues in contact with VAL 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 ASP 3.0 22.0 - - - +
61A ILE 3.2 5.6 + - - +
63A ASN* 1.3 74.0 - - - +
65A LEU* 1.3 65.7 + - + +
67A GLY* 3.3 1.0 + - - -
68A ILE* 3.2 22.6 + - + +
71B LEU* 4.0 10.1 - - + -
75B SER* 3.1 30.6 - - - +
125B ASP 4.9 2.2 - - - +
126B ALA* 4.6 5.8 - - - +
129B VAL* 3.0 44.6 - - + -
130B LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 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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26A THR* 6.1 1.1 - - + -
29A PHE* 4.6 10.8 - - + -
30A VAL* 5.4 2.0 - - + -
33A LEU* 5.0 7.9 - - + -
61A ILE* 3.1 34.7 + - + +
62A THR* 3.9 4.9 - - - +
64A VAL* 1.3 79.6 - - + +
66A GLU* 1.3 57.4 + - - +
68A ILE* 3.6 5.1 + - + +
69A GLY 3.2 5.0 + - - -
70A LEU* 3.0 41.8 + - + -
71A ILE* 3.6 30.5 + - + -
81A TRP* 5.1 3.4 - - + -
129B VAL* 5.1 7.4 - - + -
130B LEU* 6.2 1.3 - - + -
133B MET* 4.0 42.0 - - + -
135B ILE* 5.8 1.1 - - + -
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Residues in contact with GLU 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 THR* 2.9 42.1 + - - +
63A ASN* 3.3 4.0 + - - +
65A LEU* 1.3 73.2 - - - +
67A GLY* 1.3 66.2 + - - +
68A ILE 3.1 0.2 - - - -
69A GLY* 3.1 13.2 + - - -
71A ILE* 3.5 30.4 - - + +
72A GLU* 4.7 2.9 - - - -
73A LYS* 3.3 34.6 + - - +
79A ILE* 4.7 5.5 - - - +
72B ARG* 2.5 43.7 + - - -
606D C 4.7 1.1 + - - -
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Residues in contact with GLY 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 ASN 3.0 13.1 + - - -
64A VAL* 3.3 3.7 + - - -
66A GLU* 1.3 77.1 - - - +
68A ILE* 1.3 63.2 + - - +
69A GLY 3.7 0.2 + - - -
72B ARG* 3.6 31.6 - - - +
75B SER* 5.0 1.3 - - - -
76B MET* 3.8 26.1 - - - +
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Residues in contact with ILE 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 VAL* 3.3 16.4 - - + +
65A LEU* 3.8 7.4 - - + +
66A GLU 3.1 0.4 - - - -
67A GLY* 1.3 80.5 - - - +
69A GLY* 1.3 59.7 + - - +
70A LEU* 3.7 21.3 - - + +
75B SER 3.7 14.1 - - - +
76B MET* 4.4 3.4 - - + -
79B CYS* 3.4 36.6 - - + -
130B LEU* 4.0 18.4 - - + -
135B ILE* 5.1 2.7 - - + -
148B LEU* 3.6 33.6 - - + +
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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