Contacts of the helix formed by residues 59 - 70 (chain B) in PDB entry 3N6J
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 GLY 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 5.0 0.4 - - - -
40B ASN* 3.5 6.0 + - - +
58B GLY* 1.3 74.6 - - - -
60B ALA* 1.3 64.0 + - - -
61B THR 3.5 2.4 + - - -
62B ILE 3.7 2.3 + - - -
63B GLU* 3.3 22.8 + - - +
415B HIS* 5.3 4.0 - - - -
421B GLY* 3.6 25.1 + - - -
422B ALA* 4.3 8.7 - - - -
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Residues in contact with ALA 60 (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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59B GLY* 1.3 70.3 - - - -
61B THR* 1.3 65.0 + - - +
63B GLU* 4.3 10.5 - - - +
64B ASN* 2.8 45.3 + - - +
420B ASN* 5.8 3.0 + - - +
422B ALA* 5.4 3.2 - - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY 3.5 0.6 - - - -
60B ALA* 1.3 77.1 - - - +
62B ILE* 1.3 58.2 + - - +
64B ASN* 3.8 6.0 - - - +
65B ALA* 2.9 32.2 + - + +
105B TRP* 3.6 38.3 - - + +
109B LEU* 3.8 40.3 - - + +
110B ARG 5.5 0.2 - - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 3.8 17.3 - - - +
56B ALA* 4.3 7.2 - - + -
57B PRO* 3.0 29.6 - - + +
58B GLY 3.8 8.3 - - - +
59B GLY 3.7 3.8 + - - +
60B ALA 3.3 0.2 - - - -
61B THR* 1.3 72.3 - - - +
63B GLU* 1.3 68.0 + - - +
65B ALA* 3.1 8.1 + - - +
66B LEU* 2.9 41.1 + - + +
109B LEU* 3.7 35.4 - - + +
112B ASN* 3.7 26.9 - - + +
113B ALA* 4.1 13.2 - - + -
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Residues in contact with GLU 63 (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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16B VAL* 3.6 25.2 - - + +
18B PRO* 3.2 31.3 - - + +
40B ASN* 3.7 17.4 - - - +
59B GLY 3.3 17.1 + - - +
60B ALA* 3.8 9.5 - - - +
62B ILE* 1.3 79.4 - - - +
64B ASN* 1.3 63.9 + - - +
66B LEU* 3.2 3.7 + - - +
67B THR* 2.9 33.8 + - - +
415B HIS* 4.9 4.2 + - - -
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Residues in contact with ASN 64 (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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60B ALA* 2.8 42.0 + - - +
61B THR* 3.8 6.2 - - - +
63B GLU* 1.3 84.0 - - - +
65B ALA* 1.3 56.3 + - - +
67B THR* 3.3 9.9 + - - -
68B GLU* 2.9 30.7 + - - +
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Residues in contact with ALA 65 (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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61B THR* 2.9 21.2 + - + +
62B ILE* 3.4 6.7 - - - +
64B ASN* 1.3 75.2 - - - +
66B LEU* 1.3 61.9 + - - +
68B GLU* 3.5 15.9 + - - +
69B ALA* 3.3 15.2 + - - +
88B MSE 3.5 12.0 - - + +
105B TRP 6.1 2.0 - - - +
109B LEU 6.1 0.2 - - - -
110B ARG* 4.2 25.5 + - - +
113B ALA* 4.2 13.9 - - + -
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Residues in contact with LEU 66 (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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14B MSE 3.6 24.3 - - + +
16B VAL* 3.5 23.3 - - + -
40B ASN* 4.5 11.7 - - + +
42B VAL* 3.7 22.9 - - + -
56B ALA* 5.2 0.2 - - + -
62B ILE* 2.9 30.9 + - + +
63B GLU 3.4 7.4 - - - +
65B ALA* 1.3 73.5 - - - +
67B THR* 1.3 64.9 + - - +
69B ALA* 3.0 16.3 + - - +
70B ILE* 3.4 9.9 + - - +
88B MSE 3.7 13.9 - - + -
113B ALA* 3.7 28.5 - - + +
116B ALA* 4.7 5.2 - - + -
117B LEU* 4.5 3.6 - - + -
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Residues in contact with THR 67 (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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16B VAL* 3.9 11.7 - - - +
63B GLU* 2.9 20.8 + - - +
64B ASN* 3.5 11.5 + - - -
66B LEU* 1.3 71.2 - - - +
68B GLU* 1.3 67.5 + - - +
70B ILE* 3.0 40.3 + - + +
71B PRO* 3.9 3.5 - - - +
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Residues in contact with GLU 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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64B ASN 2.9 16.3 + - - +
65B ALA* 3.6 11.1 - - - +
67B THR* 1.3 77.5 - - - +
69B ALA* 1.3 56.6 + - - +
71B PRO* 3.2 16.3 - - - +
72B HIS* 3.3 12.4 + - + +
91B GLY 3.9 10.9 - - - +
92B TYR* 3.9 21.0 - - + +
110B ARG* 3.9 22.9 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MSE 4.4 6.1 - - + -
65B ALA 3.3 10.9 + - - +
66B LEU* 3.0 12.6 + - - +
68B GLU* 1.3 80.2 - - - +
70B ILE* 1.3 54.8 + - - +
71B PRO* 3.4 0.7 - - - -
72B HIS* 2.7 25.1 + - - +
73B VAL* 3.2 16.5 + - + +
88B MSE 3.7 24.0 - - + -
92B TYR* 3.9 22.7 - - + +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MSE 3.7 41.3 - - + +
16B VAL* 4.7 7.4 - - + -
66B LEU 3.4 10.9 + - - +
67B THR* 3.0 35.0 - - + +
69B ALA* 1.3 75.6 - - - +
71B PRO* 1.4 63.7 - - + +
73B VAL 3.0 2.6 + - - -
74B VAL* 2.9 51.8 + - + +
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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