Contacts of the helix formed by residues 68 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TYR* 5.3 1.4 + - - -
66B HIS 2.6 14.8 + - - +
67B VAL* 1.3 79.1 - - - +
69B PRO* 1.3 70.0 - - - +
70B ALA* 2.8 23.9 + - - +
71B VAL* 2.9 27.2 + - + +
72B THR* 2.8 22.9 + - - -
93B GLN* 3.3 7.1 - - - -
138B THR* 5.6 0.2 - - - +
141B PHE* 3.9 10.6 - - + -
168B LEU* 6.1 0.2 - - - +
183B MET 2.6 27.5 + - - -
184B ASN* 3.3 16.2 - - - +
185B PRO* 3.4 6.4 - - - +
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 1.3 84.2 - - - +
70B ALA* 1.3 50.6 + - - +
72B THR* 3.1 3.0 + - - -
73B PHE* 2.7 37.3 + - - +
90B MET* 3.5 36.4 - - + +
93B GLN* 3.0 22.4 - - + +
94B LEU* 4.5 9.2 - - + -
184B ASN* 3.4 16.4 - - - +
185B PRO* 4.1 13.9 - - + -
186B ALA* 3.4 27.8 - - + +
205B TRP* 4.6 2.2 - - + -
209B VAL* 5.8 1.6 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 2.8 18.8 + - - +
69B PRO* 1.3 75.9 - - - +
71B VAL* 1.3 56.2 + - - +
73B PHE* 3.4 6.6 + - - +
74B ALA 2.9 21.8 + - - -
138B THR* 4.3 5.2 - - + -
142B VAL* 5.2 0.2 - - - -
185B PRO* 3.7 7.6 - - + +
208B PRO* 3.6 43.1 - - + +
209B VAL* 4.1 6.5 - - - +
212B ALA* 3.0 17.2 - - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 5.3 1.1 - - - +
66B HIS* 4.1 18.4 - - - +
68B ASN* 2.9 37.4 + - + +
70B ALA* 1.3 73.9 - - + +
72B THR* 1.3 66.4 + - - +
74B ALA* 3.1 10.7 + - + +
75B PHE* 3.0 44.6 + - + -
138B THR* 5.9 0.7 - - + -
141B PHE* 3.8 11.2 - - + -
142B VAL* 4.6 6.3 - - + -
145B ILE* 3.7 31.9 - - + -
146B PHE* 6.1 0.4 - - + -
149B TYR* 6.2 0.2 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B HIS* 2.9 25.4 - - - +
68B ASN 2.8 7.7 + - - -
69B PRO 3.5 7.4 - - - -
71B VAL* 1.3 72.9 - - - +
73B PHE* 1.3 66.8 + - - +
75B PHE 3.0 2.3 + - - -
76B LEU* 2.9 19.4 + - - +
81B MET* 3.5 14.3 - - + +
86B ALA* 3.5 44.0 - - + +
89B TYR* 3.7 3.1 - - + -
90B MET* 4.0 8.5 - - + -
93B GLN* 2.9 24.6 + - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO 2.7 20.7 + - - +
70B ALA* 3.5 10.1 - - - +
72B THR* 1.3 73.5 - - - +
74B ALA* 1.3 68.1 + - - +
76B LEU* 3.0 27.7 + - + +
77B VAL* 3.1 39.7 + - + +
86B ALA* 6.0 0.2 - - - -
90B MET* 5.4 8.5 - - + -
209B VAL* 3.6 48.0 - - + -
212B ALA* 4.5 0.4 - - + -
213B GLY* 4.1 13.2 - - - -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA 2.9 14.5 + - - +
71B VAL* 3.1 13.7 + - + +
73B PHE* 1.3 78.4 - - - +
75B PHE* 1.3 56.6 + - - +
77B VAL* 3.3 5.4 - - - +
78B GLY 3.1 12.1 + - - -
142B VAL* 3.8 20.2 - - + -
146B PHE* 3.3 10.0 - - + -
212B ALA* 3.7 25.6 - - + +
216B SER* 3.0 21.7 + - - -
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B HIS* 3.2 34.5 - + - +
71B VAL* 3.0 37.8 + - + -
72B THR 3.0 7.5 + - - +
74B ALA* 1.3 73.4 - - - +
76B LEU* 1.3 61.9 + - - +
78B GLY* 3.7 0.9 - - - -
79B SER 3.3 2.1 + - - -
80B GLN* 2.9 63.1 + - + +
81B MET* 3.7 17.3 + - + -
145B ILE* 3.5 24.9 - - + -
146B PHE* 3.7 27.1 - + - -
149B TYR* 3.5 25.6 - + + -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR 2.9 11.1 + - - +
73B PHE* 3.0 25.3 + - + +
75B PHE* 1.3 74.8 - - - +
77B VAL* 1.3 57.6 + - + +
78B GLY 2.8 4.0 - - - -
79B SER* 2.6 28.9 + - - -
81B MET* 3.7 23.3 - - + +
82B SER 3.8 4.5 - - - +
83B LEU* 3.8 42.6 - - + +
86B ALA* 3.9 15.3 - - + -
87B ILE* 6.3 0.2 - - + -
90B MET* 6.6 0.2 - - - -
42E ASN 5.5 0.9 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.1 48.7 + - + +
74B ALA* 3.3 15.0 - - - +
76B LEU* 1.3 77.5 - - + +
78B GLY* 1.3 59.8 + - - +
79B SER* 3.1 6.9 + - - -
213B GLY* 4.7 4.5 - - - -
216B SER* 3.5 17.2 + - - +
217B LEU* 4.6 16.4 - - + +
220B ASP* 4.7 1.6 - - - +
221B PHE* 4.8 9.0 - - - -
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA 3.1 11.2 + - - -
75B PHE 3.7 2.5 - - - -
76B LEU 2.8 1.8 - - - -
77B VAL* 1.3 77.0 - - - +
79B SER* 1.3 71.6 + - - +
80B GLN* 3.4 13.5 + - - +
146B PHE* 4.6 5.4 - - - -
216B SER* 3.5 10.8 - - - -
220B ASP* 3.5 25.0 - - - +
221B PHE* 5.0 1.6 - - - -
222B LEU* 5.7 2.6 - - - +
44E THR* 4.8 4.1 - - - +
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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