Contacts of the helix formed by residues 66 - 73 (chain B) in PDB entry 4MSP
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 LEU 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.6 0.4 - - - -
65B ALA* 1.3 86.0 - - + +
67B LYS* 1.3 66.1 + - - +
68B GLY* 4.0 3.1 - - - +
69B TRP* 3.1 27.4 + - + +
70B ASP* 3.4 12.0 + - - +
86B ILE* 4.7 2.5 - - + -
90B LEU 3.7 7.9 - - - +
91B GLY* 3.7 23.1 - - - +
92B TYR* 3.4 40.2 - - + +
106B LEU* 3.9 16.2 - - + -
108B PHE* 3.8 35.4 - - + -
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Residues in contact with LYS 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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67A LYS* 6.2 1.6 - - - +
63B LEU* 3.7 35.0 - - + -
65B ALA 3.7 1.4 + - - +
66B LEU* 1.3 72.2 - - - +
68B GLY* 1.3 58.0 + - - +
70B ASP* 3.1 7.0 + - - +
71B GLN* 3.0 31.1 + - + +
89B ALA 3.9 14.0 + - - +
90B LEU* 3.5 34.0 + - + +
91B GLY 5.2 7.2 + - - +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.7 27.0 - - - +
66B LEU* 3.1 0.4 - - - -
67B LYS* 1.3 78.6 - - - +
69B TRP* 1.3 56.2 + - - +
71B GLN* 3.4 2.3 + - - -
72B GLY* 2.9 26.5 + - - -
84B LEU* 4.0 3.8 - - - +
86B ILE* 3.9 14.1 - - - -
90B LEU* 3.0 20.4 + - - +
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Residues in contact with TRP 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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31B VAL* 4.2 15.7 - - + -
33B TYR* 3.5 36.3 - + + -
56B ILE* 4.7 4.5 - - + -
58B PHE* 3.9 42.0 - + + -
60B LEU* 4.0 0.7 - - - +
65B ALA* 5.0 6.1 - - + -
66B LEU* 3.1 26.2 + - + +
68B GLY* 1.3 73.0 - - - +
70B ASP* 1.3 66.1 + - - +
73B LEU* 3.1 52.3 + - + +
84B LEU* 4.1 6.5 - - + -
86B ILE* 3.8 15.7 - - + -
108B PHE* 3.5 43.8 - + - -
110B ILE* 3.7 18.7 - - + +
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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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58B PHE* 3.5 17.3 - - - -
59B THR 4.4 0.3 - - - +
60B LEU* 3.8 7.8 - - - +
61B GLY* 3.1 27.7 + - - -
62B ILE 3.4 5.5 + - - -
63B LEU* 2.9 44.6 + - + +
65B ALA 5.4 0.2 + - - -
66B LEU 3.4 4.0 + - - +
67B LYS* 3.1 13.0 + - - +
69B TRP* 1.3 80.5 - - - +
71B GLN* 1.3 61.4 + - + +
73B LEU 4.2 0.2 + - - -
74B LYS* 3.3 27.2 - - - +
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Residues in contact with GLN 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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6B PRO* 5.1 1.9 - - - +
7B GLU* 3.0 42.5 + - - +
8B VAL* 4.1 12.5 + - + +
10B ILE* 3.8 10.2 - - - +
67B LYS* 3.0 17.2 + - + +
68B GLY 3.4 4.0 + - - +
69B TRP 3.3 0.2 - - - -
70B ASP* 1.3 78.4 - - + +
72B GLY* 1.3 60.7 + - - +
73B LEU 3.6 0.6 + - - -
74B LYS* 4.4 22.7 + - - +
90B LEU* 3.7 30.6 - - - +
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Residues in contact with GLY 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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8B VAL* 4.0 2.2 - - - -
10B ILE* 3.6 17.8 - - - +
68B GLY 2.9 17.9 + - - -
69B TRP 3.2 0.4 + - - -
71B GLN* 1.3 78.5 - - - +
73B LEU* 1.3 62.5 + - - +
74B LYS 3.6 1.1 - - - -
82B ARG* 2.8 22.3 + - - -
84B LEU* 3.5 24.2 - - - +
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Residues in contact with LEU 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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23B THR* 2.8 24.8 + - - -
29B MET* 3.8 13.2 - - + +
31B VAL* 5.7 0.7 - - + -
58B PHE* 3.8 13.7 - - + -
60B LEU* 3.7 14.2 - - + +
69B TRP* 3.1 55.5 + - + +
70B ASP 4.2 0.2 + - - -
71B GLN 3.6 0.6 - - - -
72B GLY* 1.3 84.4 - - - +
74B LYS* 1.3 54.7 + - - +
76B MET* 3.8 27.8 - - + +
82B ARG* 3.7 9.0 - - + +
84B LEU* 4.2 7.9 - - + -
110B ILE* 3.9 30.1 - - + -
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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