Contacts of the helix formed by residues 64 - 80 (chain C) in PDB entry 5F1B
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR* 3.7 21.6 - - + +
44C ASP 5.0 1.9 - - - +
46C HIS* 4.2 14.2 + - + +
60C GLY 3.8 3.0 + - - -
61C PRO 3.2 15.9 + - - +
62C PRO 3.3 0.2 - - - -
63C LEU* 1.3 81.7 - - - +
65C ILE* 1.3 66.7 + - - +
66C GLN* 2.7 37.1 + - - +
67C ILE* 3.2 14.8 + - + +
68C LEU* 3.1 19.9 + - - +
137C TYR* 4.0 2.2 - - - -
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU 4.4 0.2 - - - -
64C ASP* 1.3 76.3 + - - +
66C GLN* 1.3 75.1 + - + +
68C LEU* 3.3 3.5 + - + +
69C HIS* 3.2 37.6 + - + +
123C LEU* 3.8 36.3 - - + +
124C ASP* 4.2 4.9 - - - +
137C TYR* 3.4 43.7 + - + +
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Residues in contact with GLN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASP* 2.7 19.2 + - - +
65C ILE* 1.3 80.0 - - + +
67C ILE* 1.3 63.3 + - + +
69C HIS* 3.4 9.6 + - - +
70C GLN* 3.0 37.7 + - - +
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 5.6 0.7 - - + -
40C ALA* 3.9 17.0 - - + -
43C THR* 3.3 27.1 - - - +
61C PRO 4.0 1.1 - - - +
62C PRO* 3.8 27.1 - - + +
64C ASP* 3.2 24.9 + - + +
66C GLN* 1.3 78.8 - - + +
68C LEU* 1.3 57.3 + - - +
70C GLN* 3.1 18.4 + - - +
71C VAL* 2.8 33.9 + - + +
226C ASN* 4.0 19.5 - - + +
227C LEU* 4.0 16.2 - - + -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO 3.6 17.5 - - - +
63C LEU* 3.6 33.9 - - + +
64C ASP 3.1 11.4 + - - +
65C ILE* 3.7 7.4 - - - +
66C GLN 3.3 0.2 - - - -
67C ILE* 1.3 77.1 - - - +
69C HIS* 1.3 57.2 + - - +
71C VAL* 3.9 2.9 - - - +
72C LEU* 2.9 30.0 + - - +
112C VAL* 4.0 28.9 - - + -
113C LEU* 3.6 16.6 - - + +
116C PHE* 5.6 3.6 - - + -
123C LEU* 3.8 21.5 - - + -
137C TYR* 3.7 23.8 - - + -
189C LEU* 4.0 7.4 - - + -
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Residues in contact with HIS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.2 35.2 + - + +
66C GLN* 3.8 9.6 - - - +
67C ILE 3.3 0.2 - - - -
68C LEU* 1.3 76.1 - - - +
70C GLN* 1.3 59.6 + - + +
72C LEU* 4.4 0.2 - - - -
73C ASP* 3.0 25.8 + - - +
120C HIS* 2.9 60.1 + - + +
123C LEU* 3.7 15.8 - - + +
124C ASP* 2.6 37.0 + - - -
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLN* 3.0 31.3 + - - +
67C ILE* 3.1 18.8 + - - +
69C HIS* 1.3 75.8 - - + +
71C VAL* 1.3 65.6 + - - +
73C ASP* 3.2 14.6 + - - +
74C LEU* 3.0 21.7 + - - +
222C TYR* 4.7 1.7 + - - -
224C ASN* 2.8 30.6 + - - +
226C ASN* 2.8 36.5 + - - +
227C LEU* 4.2 9.5 - - + +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 3.8 32.1 - - + -
67C ILE* 2.8 23.8 + - + +
68C LEU* 3.9 4.9 - - - +
70C GLN* 1.3 75.6 - - - +
72C LEU* 1.3 57.4 + - - +
74C LEU* 3.1 11.7 + - + +
75C GLN* 2.9 25.3 + - - +
113C LEU* 3.6 22.2 - - + -
189C LEU* 4.0 20.6 - - + -
191C ILE* 3.6 22.7 - - + -
227C LEU* 3.8 12.6 - - + -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU 2.9 18.7 + - - +
69C HIS 3.7 4.3 - - - +
71C VAL* 1.3 74.8 - - - +
73C ASP* 1.3 58.5 + - - +
75C GLN* 4.0 16.8 - - - +
76C ILE* 2.9 44.3 + - + +
113C LEU* 3.8 20.8 - - + +
118C ASN* 3.6 31.0 - - + +
119C SER 3.6 9.2 - - - +
120C HIS* 3.5 48.0 - - + +
123C LEU* 4.8 3.6 - - + -
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C HIS* 3.0 19.7 + - - +
70C GLN* 3.2 18.0 + - - +
72C LEU* 1.3 76.0 - - - +
74C LEU* 1.3 62.3 + - - +
76C ILE* 3.9 4.7 - - - +
77C ALA* 3.0 24.3 + - - +
120C HIS* 3.1 23.5 + - - -
222C TYR* 4.2 10.7 + - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.4 12.3 - - + -
38C ILE* 4.4 18.2 - - + -
70C GLN 3.0 11.0 + - - +
71C VAL* 3.3 13.2 - - + +
73C ASP* 1.3 76.0 - - - +
75C GLN* 1.3 57.3 + - - +
77C ALA* 3.2 4.4 + - - +
78C ILE* 3.0 45.1 + - + +
191C ILE* 5.3 2.5 - - + -
218C PHE* 4.3 7.2 - - + -
219C VAL* 4.8 6.5 - - + -
222C TYR* 3.6 52.4 + - + -
227C LEU* 4.7 6.5 - - + -
229C ILE* 3.8 26.7 - - + -
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Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL 2.9 15.3 + - - +
72C LEU* 3.8 13.2 - - + +
73C ASP 3.3 0.4 - - - -
74C LEU* 1.3 80.5 - - - +
76C ILE* 1.3 56.9 + - - +
78C ILE* 3.4 10.5 + - - +
79C GLU* 3.1 34.5 + - - +
109C ILE* 3.8 13.8 - - + +
111C SER* 2.7 30.0 + - - -
113C LEU* 4.0 5.7 - - - +
118C ASN* 2.8 43.2 + - - +
191C ILE* 3.6 15.5 - - + +
193C PHE* 4.2 17.4 - - + -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 2.9 46.5 + - + +
73C ASP* 3.9 4.7 - - - +
75C GLN* 1.3 72.8 - - - +
77C ALA* 1.3 65.7 + - - +
79C GLU* 3.3 19.3 + - + +
80C ASN* 3.1 42.4 + - - +
118C ASN* 4.2 10.1 - - + +
120C HIS* 3.9 19.5 - - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASP 3.0 19.4 + - - +
74C LEU* 3.5 6.5 - - - +
76C ILE* 1.3 73.8 - - - +
78C ILE* 1.3 65.1 + - - +
80C ASN* 3.1 18.5 + - - +
81C ILE* 3.1 17.7 + - - +
218C PHE* 3.7 24.9 - - + -
222C TYR* 4.9 3.1 - - + +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.6 30.5 - - + -
74C LEU* 3.0 27.0 + - + +
75C GLN* 3.5 8.7 - - - +
77C ALA* 1.3 76.1 - - - +
79C GLU* 1.3 61.8 + - - +
81C ILE* 3.2 23.7 + - + +
191C ILE* 6.5 0.4 - - + -
193C PHE* 3.4 32.5 - - + -
211C TRP* 3.6 16.7 - - + -
215C PHE* 3.7 23.1 - - + -
218C PHE* 4.3 9.2 - - + -
219C VAL* 3.7 21.8 - - + -
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLN* 3.1 27.5 + - - +
76C ILE* 3.5 21.8 - - + +
77C ALA 3.3 0.4 - - - -
78C ILE* 1.3 75.4 - - - +
80C ASN* 1.3 64.0 + - - +
81C ILE 3.7 2.3 + - - +
91C THR* 5.5 0.3 - - - -
92C LEU* 4.2 18.1 + - + +
93C GLN* 3.3 33.6 + - - +
107C CYS* 5.7 3.7 + - + +
109C ILE* 4.5 25.5 - - + +
118C ASN* 4.2 18.7 + - - +
164C THR* 5.9 2.4 - - - +
193C PHE* 4.5 4.0 - - + -
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Residues in contact with ASN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.1 33.0 + - - +
77C ALA* 3.1 11.1 + - - +
79C GLU* 1.3 81.0 - - - +
81C ILE* 1.3 65.1 + - - +
82C THR* 3.3 14.3 + - - +
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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
------------------------------------------------------------
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