Contacts of the helix formed by residues 67 - 82 (chain B) in PDB entry 3DNJ
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 SER 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ASN 3.8 1.8 + - - -
66B LYS* 1.3 77.6 - - - +
68B ARG* 1.3 65.6 + - - +
69B GLU* 3.6 6.3 + - - +
70B ASP* 3.0 34.3 + - - +
71B ALA* 2.8 22.2 + - - +
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Residues in contact with ARG 68 (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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57B VAL* 5.4 2.0 - - + -
61B GLU* 3.5 23.9 + - - +
67B SER* 1.3 72.9 - - - +
69B GLU* 1.3 61.2 + - - +
71B ALA* 3.4 1.6 + - - +
72B THR* 2.8 41.0 + - - +
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Residues in contact with GLU 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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67B SER* 3.2 6.7 + - - +
68B ARG* 1.3 85.6 - - - +
70B ASP* 1.3 69.0 + - - +
72B THR* 3.3 5.8 + - - -
73B ARG* 3.0 66.5 + - + +
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Residues in contact with ASP 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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66B LYS* 4.4 15.6 + - + +
67B SER* 3.0 29.4 + - - +
69B GLU* 1.3 87.0 - - - +
71B ALA* 1.3 58.3 + - - +
73B ARG* 3.3 10.9 + - - +
74B ILE* 2.9 39.3 + - + +
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Residues in contact with ALA 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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57B VAL* 3.9 11.6 - - + +
60B LEU* 3.4 30.9 - - + +
61B GLU* 3.8 19.3 - - + -
66B LYS* 3.9 9.3 - - + +
67B SER 2.8 18.2 + - - +
68B ARG 3.8 3.6 - - - +
70B ASP* 1.3 75.8 - - - +
72B THR* 1.3 63.6 + - - +
75B MET* 3.0 25.8 + - - +
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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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57B VAL* 4.2 17.9 - - + +
68B ARG* 2.8 30.1 + - - +
69B GLU* 3.6 6.5 - - - -
71B ALA* 1.3 78.6 - - - +
73B ARG* 1.3 57.7 + - + +
75B MET* 3.4 9.8 + - + +
76B LEU* 3.0 45.7 + - + +
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Residues in contact with ARG 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 GLU* 3.0 56.6 + - + +
70B ASP* 3.8 11.2 + - - +
72B THR* 1.3 75.5 - - + +
74B ILE* 1.3 61.3 + - + +
76B LEU* 3.3 9.1 + - + +
77B HIS* 2.9 29.3 + - - +
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Residues in contact with ILE 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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45B ILE* 4.9 2.5 - - + -
60B LEU* 3.9 24.0 - - + -
66B LYS* 3.5 39.5 - - + +
70B ASP* 2.9 24.5 + - + +
73B ARG* 1.3 72.6 - - + +
75B MET* 1.3 67.8 + - - +
77B HIS* 3.1 7.9 + - + +
78B VAL* 2.9 34.1 + - + +
84B GLY* 5.0 1.1 - - - -
85B VAL 3.8 28.3 - - - +
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Residues in contact with MET 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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53B MET* 3.6 52.9 - - + +
56B VAL* 3.7 33.9 - - + -
57B VAL* 3.9 19.1 - - + -
60B LEU* 3.9 1.5 - - + +
71B ALA 3.0 18.3 + - - +
72B THR* 3.6 9.9 - - + +
74B ILE* 1.3 77.4 - - - +
76B LEU* 1.3 82.9 + - + +
78B VAL* 3.3 4.9 + - - +
79B HIS* 3.0 23.3 + - - +
1D TYR* 4.0 8.9 - - + -
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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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53B MET* 4.4 17.3 - - + -
72B THR* 3.0 37.1 + - + +
73B ARG* 3.8 8.7 - - + +
75B MET* 1.3 95.4 - - + +
77B HIS* 1.3 61.6 + - - +
79B HIS* 3.2 7.4 + - + +
80B GLN* 2.9 49.9 + - - +
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Residues in contact with HIS 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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116A MET 5.9 1.2 + - - -
117A GLU* 5.5 5.1 + - - +
73B ARG 2.9 16.8 + - - +
74B ILE* 3.5 10.1 - - + +
76B LEU* 1.3 78.0 - - - +
78B VAL* 1.3 55.9 + - - +
80B GLN* 3.3 6.8 + - - -
81B ASN* 2.9 61.6 + - - +
83B VAL 3.5 18.4 + - - -
84B GLY* 4.2 10.0 - - - -
85B VAL 5.5 0.4 - - - -
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Residues in contact with VAL 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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45B ILE* 3.8 25.8 - - + +
46B LEU 3.8 2.5 - - - -
47B ASN* 3.4 22.1 - - - +
74B ILE* 2.9 22.1 + - + +
75B MET 3.6 6.3 - - - +
77B HIS* 1.3 73.2 - - - +
79B HIS* 1.3 62.7 + - - +
82B GLY* 2.8 27.5 + - - -
83B VAL 3.9 8.5 - - - +
84B GLY* 3.5 27.8 - - - +
1D TYR* 3.2 30.3 - - + +
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Residues in contact with HIS 79 (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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47B ASN* 3.6 19.9 + - - -
53B MET* 3.6 26.6 - - + +
75B MET 3.0 13.9 + - - +
76B LEU* 3.4 14.6 - - + +
78B VAL* 1.3 78.9 - - - +
80B GLN* 1.3 71.3 + - + +
82B GLY 4.5 0.9 + - - -
1D TYR* 2.9 47.1 + - + -
3D PHE 5.4 0.4 - - - -
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Residues in contact with GLN 80 (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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76B LEU* 2.9 35.4 + - + +
77B HIS* 3.8 7.4 + - - +
79B HIS* 1.3 90.6 - - + +
81B ASN* 1.3 70.8 + - - +
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Residues in contact with ASN 81 (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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46A LEU* 3.8 11.7 - - - +
115A THR* 4.1 29.7 + - + +
77B HIS* 2.9 55.1 + - - +
80B GLN* 1.3 90.0 + - - +
82B GLY* 1.3 58.3 + - - +
83B VAL* 3.4 9.4 + - + +
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Residues in contact with GLY 82 (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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46A LEU* 3.7 15.3 - - - +
46B LEU* 3.5 10.0 - - - +
47B ASN* 2.9 32.3 + - - +
78B VAL 2.8 17.0 + - - -
79B HIS 4.5 1.0 + - - -
80B GLN 3.7 0.6 - - - -
81B ASN* 1.3 77.6 - - - +
83B VAL* 1.3 61.5 + - - +
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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