Contacts of the helix formed by residues 68 - 78 (chain C) in PDB entry 3J41
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 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C TYR* 5.3 1.2 + - - -
66C HIS* 2.6 14.1 + - - +
67C VAL* 1.3 78.5 - - - +
69C PRO* 1.3 70.5 - - - +
70C ALA* 2.8 23.5 + - - +
71C VAL* 2.9 28.0 + - + +
72C THR* 2.8 22.5 + - - -
93C GLN* 3.3 7.0 - - - -
138C THR* 5.6 0.2 - - - +
141C PHE* 3.9 10.1 - - + -
183C MET 2.6 27.3 + - - -
184C ASN* 3.3 16.8 - - - +
185C PRO* 3.4 6.2 - - - +
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Residues in contact with PRO 69 (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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68C ASN* 1.3 82.9 - - - +
70C ALA* 1.3 52.0 + - - +
72C THR* 3.1 2.8 + - - -
73C PHE* 2.7 37.2 + - - +
90C MET* 3.5 33.7 - - + +
93C GLN* 3.0 24.0 - - + +
94C LEU* 4.5 9.2 - - + -
184C ASN* 3.4 17.0 - - - +
185C PRO* 4.1 13.9 - - + -
186C ALA* 3.4 26.2 - - + +
205C TRP* 4.6 1.3 - - + -
209C VAL* 5.8 0.9 - - + -
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Residues in contact with ALA 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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68C ASN* 2.8 18.0 + - - +
69C PRO* 1.3 75.4 - - - +
71C VAL* 1.3 58.0 + - - +
73C PHE* 3.4 7.3 + - - +
74C ALA 2.9 21.3 + - - -
138C THR* 4.3 5.4 - - + -
185C PRO* 3.7 7.6 - - + +
208C PRO* 3.6 43.1 - - + +
209C VAL* 4.1 6.1 - - - +
212C ALA* 3.0 16.9 - - + +
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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
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65C ALA 5.3 0.9 - - - +
66C HIS* 4.1 17.7 - - - +
68C ASN* 2.9 37.8 + - + +
70C ALA* 1.3 74.6 - - + +
72C THR* 1.3 65.9 + - - +
74C ALA* 3.1 10.5 + - + +
75C PHE* 3.0 44.5 + - + -
138C THR* 5.9 0.4 - - + -
141C PHE* 3.8 11.0 - - + -
142C VAL* 4.6 7.2 - - + -
145C ILE* 3.7 33.2 - - + -
146C PHE* 6.1 0.4 - - + -
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Residues in contact with THR 72 (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 HIS* 2.9 24.3 - - - +
68C ASN 2.8 8.0 + - - -
69C PRO 3.5 8.1 - - - -
71C VAL* 1.3 73.5 - - - +
73C PHE* 1.3 66.6 + - - +
75C PHE 3.0 2.3 + - - +
76C LEU* 2.9 19.1 + - - +
81C MET* 3.5 13.7 - - + +
86C ALA* 3.5 43.7 - - + +
89C TYR* 3.7 2.3 - - + -
90C MET* 4.0 8.5 - - + -
93C GLN* 2.9 25.1 + - - -
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Residues in contact with PHE 73 (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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69C PRO 2.7 20.2 + - - +
70C ALA* 3.5 9.6 - - - +
72C THR* 1.3 74.8 - - - +
74C ALA* 1.3 67.9 + - - +
76C LEU* 3.0 27.6 + - + +
77C VAL* 3.1 42.2 + - + +
86C ALA* 6.0 0.2 - - - -
90C MET* 5.2 8.0 - - + -
209C VAL* 3.6 48.2 - - + -
212C ALA* 4.5 0.4 - - + -
213C GLY* 4.1 13.0 - - - -
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Residues in contact with ALA 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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70C ALA 2.9 13.6 + - - +
71C VAL* 3.1 14.1 - - + +
73C PHE* 1.3 80.3 - - - +
75C PHE* 1.3 56.0 + - - +
77C VAL* 3.3 5.1 - - - +
78C GLY 3.1 12.3 + - - -
142C VAL* 3.8 20.4 - - + -
146C PHE* 3.3 9.6 - - + -
212C ALA* 3.7 26.0 - - + +
216C SER* 3.0 21.8 + - - -
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Residues in contact with PHE 75 (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 HIS* 3.2 33.9 - + - +
71C VAL* 3.0 36.1 + - + -
72C THR 3.0 7.7 + - - +
74C ALA* 1.3 74.9 - - - +
76C LEU* 1.3 61.7 + - - +
78C GLY* 3.5 1.2 + - - -
79C SER 3.3 1.9 + - - -
80C GLN* 2.9 63.5 + - + +
81C MET* 3.7 17.5 + - + -
145C ILE* 3.5 25.1 - - + -
146C PHE* 3.7 26.2 - + - -
149C TYR* 3.5 25.6 - + + -
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Residues in contact with LEU 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 THR 2.9 11.6 + - - +
73C PHE* 3.0 25.1 + - + +
75C PHE* 1.3 73.3 - - - +
77C VAL* 1.3 57.7 + - + +
78C GLY 2.8 3.6 - - - -
79C SER* 2.6 29.1 + - - -
81C MET* 3.7 23.4 - - + +
82C SER 3.8 4.3 - - - +
83C LEU* 3.8 44.4 - - + +
86C ALA* 3.9 14.8 - - + -
90C MET* 6.6 0.2 - - - -
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Residues in contact with VAL 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 PHE* 3.1 47.6 + - + +
74C ALA* 3.3 15.3 - - - +
76C LEU* 1.3 77.2 - - + +
78C GLY* 1.3 59.9 + - - +
79C SER* 3.1 6.9 + - - -
213C GLY* 4.7 3.6 - - - -
216C SER* 3.5 17.8 + - - +
217C LEU* 4.6 14.4 - - + +
221C PHE* 4.8 15.4 - - - -
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Residues in contact with GLY 78 (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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74C ALA 3.1 11.3 + - - -
75C PHE* 3.7 2.7 - - - -
76C LEU 2.8 1.4 - - - -
77C VAL* 1.3 77.2 - - - +
79C SER* 1.3 71.1 + - - +
80C GLN* 3.4 12.3 + - - +
146C PHE* 4.6 8.3 - - - -
216C SER* 3.5 16.8 - - - -
220C ASP* 5.4 8.7 - - - +
221C PHE* 6.4 0.4 - - - -
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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