Contacts of the helix formed by residues 68 - 77 (chain B) in PDB entry 3JW8
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 TYR 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 4.6 5.4 - - + -
57B VAL* 3.6 32.8 - - + -
58B SER 4.9 0.7 - - - -
59B HIS* 3.6 22.2 - - + -
63B GLU* 2.5 36.1 + - - -
64B HIS 3.9 7.2 - - - -
65B SER* 3.1 19.7 + - - +
67B ARG* 1.4 81.9 - - + +
69B GLU* 1.3 58.2 + - - +
70B GLU 3.4 2.7 - - - -
71B LEU* 3.3 25.2 + - + +
72B ALA* 2.8 32.3 + - + +
129B LEU* 4.3 13.2 - - + -
131B HIS* 3.2 27.4 - - + +
155B ILE* 5.3 0.2 - - + -
282B HIS* 3.6 24.4 + + - -
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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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43B ARG* 4.5 12.3 + - - -
45B TRP* 3.3 35.9 + - - -
65B SER 4.4 0.4 + - - -
66B GLY 3.5 15.0 + - - +
67B ARG 3.4 3.2 + - - -
68B TYR* 1.3 76.4 - - - +
70B GLU* 1.4 61.0 + - + +
72B ALA* 3.8 1.2 - - - +
73B ARG* 3.1 76.6 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG 5.2 1.0 + - - -
68B TYR 3.4 0.6 - - - -
69B GLU* 1.4 76.2 - - + +
71B LEU* 1.3 67.8 + - - +
73B ARG* 3.0 35.4 + - - +
74B MSE 3.1 18.5 + - - +
283B LYS* 6.1 5.1 - - - +
293B PHE* 3.6 25.2 - - + -
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Residues in contact with LEU 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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68B TYR* 3.3 27.4 + - + +
70B GLU* 1.3 77.8 - - - +
72B ALA* 1.3 58.4 + - - +
74B MSE 3.3 30.8 + - + +
75B LEU* 3.0 35.4 + - + +
129B LEU* 4.6 13.7 - - + -
155B ILE* 4.1 13.9 - - + -
282B HIS* 3.8 37.5 - - + -
293B PHE* 3.6 30.7 - - + -
296B ILE* 4.1 14.8 - - + -
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Residues in contact with ALA 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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45B TRP* 3.3 47.1 - - + +
57B VAL* 5.4 0.9 - - + -
68B TYR* 2.8 19.5 + - + +
69B GLU 3.8 0.2 - - - +
71B LEU* 1.3 74.3 - - - +
73B ARG* 1.3 58.8 + - - +
75B LEU* 3.2 3.5 + - - +
76B MSE 2.8 31.6 + - - +
82B VAL* 3.6 21.0 - - + +
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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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45B TRP* 4.4 5.4 - - + -
69B GLU* 3.1 49.5 + - - +
70B GLU* 3.0 35.8 + - - +
72B ALA* 1.3 73.9 - - - +
74B MSE 1.4 63.4 + - - +
76B MSE 3.3 28.0 + - + +
77B GLY* 3.0 19.8 + - - -
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Residues in contact with MSE 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 GLU 3.1 14.2 + - - +
71B LEU* 3.4 37.9 - - + +
73B ARG* 1.4 75.3 - - - +
75B LEU* 1.3 74.3 + - + +
77B GLY* 3.2 13.1 + - - -
78B LEU* 3.4 17.5 + - - +
293B PHE* 3.5 37.5 - - + +
296B ILE* 3.8 20.4 - - + -
297B ASN* 3.7 35.7 - - + +
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Residues in contact with LEU 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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55B ILE* 4.2 30.7 - - + -
57B VAL* 4.9 4.9 - - + -
71B LEU* 3.0 25.3 + - + +
72B ALA* 3.2 5.6 + - - +
74B MSE 1.3 89.9 - - + +
76B MSE 1.3 62.5 + - - +
78B LEU* 3.0 25.2 + - + +
80B LEU* 3.3 17.6 + - + +
82B VAL* 3.5 21.1 - - + -
129B LEU* 4.4 16.2 - - + -
296B ILE* 4.2 15.7 - - + -
300B VAL* 4.3 25.6 - - + -
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Residues in contact with MSE 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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45B TRP* 3.9 27.8 - - + +
46B LYS 3.7 16.6 - - - +
47B PRO* 3.8 31.1 - - + +
72B ALA 2.8 17.1 + - - +
73B ARG* 3.3 36.3 + - + +
75B LEU* 1.3 71.5 - - - +
77B GLY* 1.3 53.4 + - - +
79B ASP* 2.8 28.8 + - - +
80B LEU 3.4 13.0 + - - +
82B VAL* 3.9 1.0 - - + +
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Residues in contact with GLY 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 ARG 3.0 13.0 + - - -
74B MSE 3.2 8.0 + - - -
76B MSE 1.3 76.2 - - - +
78B LEU* 1.4 59.4 + - - +
79B ASP* 3.2 8.3 + - - +
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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