Contacts of the helix formed by residues 68 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 5.3 1.2 + - - -
66A HIS 2.6 14.4 + - - +
67A VAL* 1.3 78.7 - - - +
69A PRO* 1.3 70.4 - - - +
70A ALA* 2.8 23.2 + - - +
71A VAL* 2.9 27.7 + - + +
72A THR* 2.8 22.5 + - - -
93A GLN* 3.3 7.2 - - - -
141A PHE* 3.9 10.0 - - + -
168A LEU* 6.1 0.2 - - - +
183A MET 2.6 27.7 + - - -
184A ASN* 3.3 17.0 - - - +
185A PRO* 3.4 6.6 - - - +
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Residues in contact with PRO 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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68A ASN* 1.3 84.8 - - - +
70A ALA* 1.3 50.6 - - - +
72A THR* 3.1 2.9 + - - -
73A PHE* 2.7 37.1 + - - +
90A MET* 3.5 34.1 - - + +
93A GLN* 3.0 22.4 - - + +
94A LEU* 4.5 9.4 - - + -
184A ASN* 3.4 16.4 - - - +
185A PRO* 4.1 13.5 - - + -
186A ALA* 3.4 27.1 - - + +
205A TRP* 4.6 1.8 - - + -
209A VAL* 5.8 1.3 - - + -
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Residues in contact with ALA 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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68A ASN* 2.8 17.9 + - - +
69A PRO* 1.3 74.8 - - - +
71A VAL* 1.3 56.3 + - - +
73A PHE* 3.4 6.5 + - - +
74A ALA 2.9 21.8 + - - -
138A THR* 4.3 4.9 - - + -
185A PRO* 3.7 7.6 - - + +
208A PRO* 3.6 43.7 - - + +
209A VAL* 4.1 6.0 - - - +
212A ALA* 3.0 17.8 - - + +
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Residues in contact with VAL 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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65A ALA 5.3 0.7 - - - +
66A HIS* 4.1 19.5 - - - +
68A ASN* 2.9 36.8 + - + +
70A ALA* 1.3 73.6 - - + +
72A THR* 1.3 67.5 + - - +
74A ALA* 3.1 10.4 + - + +
75A PHE* 3.0 44.2 + - + -
138A THR* 5.9 0.2 - - + -
141A PHE* 3.8 11.4 - - + -
142A VAL* 4.6 7.4 - - + -
145A ILE* 3.7 32.8 - - + -
146A PHE* 6.1 0.2 - - + -
149A TYR* 6.2 0.2 - - - +
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Residues in contact with THR 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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66A HIS* 2.9 24.4 - - - +
68A ASN 2.8 7.5 + - - -
69A PRO 3.5 8.1 - - - -
71A VAL* 1.3 73.1 - - - +
73A PHE* 1.3 66.7 + - - +
75A PHE 3.0 2.1 + - - -
76A LEU* 2.9 18.9 + - - +
81A MET* 3.5 14.9 - - + +
86A ALA* 3.5 44.2 - - + +
89A TYR* 3.7 2.3 - - + -
90A MET* 4.0 6.7 - - + -
93A GLN* 2.9 24.8 + - - -
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Residues in contact with PHE 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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69A PRO 2.7 22.0 + - - +
70A ALA* 3.5 9.9 - - - +
72A THR* 1.3 73.3 - - - +
74A ALA* 1.3 67.7 + - - +
76A LEU* 3.0 29.6 + - + +
77A VAL* 3.1 40.2 + - + +
90A MET* 5.4 8.3 - - + -
209A VAL* 3.6 47.1 - - + -
212A ALA* 4.5 0.2 - - + -
213A GLY* 4.1 13.7 - - - -
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Residues in contact with ALA 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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70A ALA 2.9 14.9 + - - +
71A VAL* 3.1 13.9 - - + +
73A PHE* 1.3 80.3 - - - +
75A PHE* 1.3 56.8 + - - +
77A VAL* 3.3 5.6 - - - +
78A GLY 3.1 12.1 + - - -
142A VAL* 3.8 20.6 - - + -
146A PHE* 3.3 9.2 - - + -
212A ALA* 3.7 24.7 - - + +
216A SER* 3.0 22.0 + - - -
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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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66A HIS* 3.2 33.4 - + - +
71A VAL* 3.0 37.4 + - + -
72A THR 3.0 8.3 + - - +
74A ALA* 1.3 74.0 - - - +
76A LEU* 1.3 62.0 + - - +
78A GLY* 3.7 0.8 - - - -
79A SER 3.3 2.1 + - - -
80A GLN* 2.9 65.0 + - + +
81A MET* 3.7 17.8 + - + -
145A ILE* 3.5 24.9 - - + -
146A PHE* 3.7 26.2 - + - -
149A TYR* 3.5 25.8 - + + -
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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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72A THR 2.9 12.4 + - - +
73A PHE* 3.0 25.5 + - + +
75A PHE* 1.3 72.4 - - - +
77A VAL* 1.3 56.9 + - + +
78A GLY 2.8 3.8 - - - -
79A SER* 2.6 28.9 + - - -
81A MET* 3.7 22.7 - - + +
82A SER 3.8 4.9 - - - +
83A LEU* 3.8 43.7 - - + +
86A ALA* 3.9 14.1 - - + -
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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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73A PHE* 3.1 48.5 + - + +
74A ALA* 3.3 13.9 - - - +
76A LEU* 1.3 77.9 - - + +
78A GLY* 1.3 60.6 + - - +
79A SER* 3.1 6.6 + - - -
213A GLY* 4.7 4.5 - - - -
216A SER* 3.5 17.7 + - - +
217A LEU* 4.6 14.2 - - + +
221A PHE* 4.9 14.6 - - - -
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Residues in contact with GLY 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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74A ALA 3.1 11.2 + - - -
75A PHE 3.7 2.0 - - - -
76A LEU 2.8 1.8 - - - -
77A VAL* 1.3 77.7 - - - +
79A SER* 1.3 72.0 + - - +
80A GLN* 3.4 13.6 + - - +
146A PHE* 4.6 8.7 - - - -
216A SER* 3.5 16.6 - - - -
220A ASP* 5.4 9.7 - - - +
221A PHE* 6.5 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