Contacts of the helix formed by residues 66 - 73 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PHE* 5.4 0.2 - - - -
63A LEU* 4.4 3.4 - - - +
65A ALA* 1.3 87.4 - - + +
67A LYS* 1.3 65.9 + - - +
68A GLY* 4.1 3.1 - - - +
69A TRP* 3.2 29.6 + - + +
70A ASP* 3.6 5.7 + - - +
86A ILE* 4.6 2.5 - - + -
90A LEU 3.7 7.2 - - - +
91A GLY* 3.5 30.1 - - - +
92A TYR* 3.8 30.1 - - + +
106A LEU* 3.9 13.2 - - + -
108A PHE* 3.7 36.6 - - + -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.7 25.4 - - + -
65A ALA 3.8 1.4 + - - +
66A LEU* 1.3 70.6 - - - +
68A GLY* 1.3 62.9 + - - +
70A ASP* 3.1 8.0 + - - +
71A GLN* 3.1 24.5 + - - +
89A ALA 3.9 19.4 + - - +
90A LEU* 3.4 28.0 + - + +
91A GLY 5.2 1.7 + - - +
63B LEU* 4.3 25.5 - - - +
67B LYS* 6.2 1.9 - - - +
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.5 28.1 - - - +
66A LEU 3.2 0.4 - - - -
67A LYS* 1.3 76.1 - - - +
69A TRP* 1.3 56.9 + - - +
71A GLN* 3.7 2.1 - - - -
72A GLY* 2.9 26.7 + - - -
84A LEU* 3.8 4.0 - - - +
86A ILE* 4.0 14.1 - - - -
90A LEU* 2.9 20.5 + - - +
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Residues in contact with TRP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.1 18.4 - - + -
33A TYR* 3.5 34.5 - + - -
56A ILE* 4.3 4.9 - - + -
58A PHE* 3.8 43.7 - + + -
60A LEU* 4.2 0.5 - - - +
65A ALA* 5.0 5.4 - - + -
66A LEU* 3.2 27.3 + - + +
68A GLY* 1.3 75.3 - - - +
70A ASP* 1.3 65.7 + - - +
73A LEU* 3.1 51.9 + - + +
84A LEU* 4.2 6.5 - - + -
86A ILE* 3.8 16.6 - - + -
108A PHE* 3.6 43.1 - + - -
110A ILE* 3.7 18.5 - - + +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.4 16.8 - - - -
59A THR 4.4 0.2 - - - +
60A LEU* 4.1 7.2 - - - +
61A GLY* 3.1 28.2 + - - +
62A ILE 3.5 3.1 + - - -
63A LEU* 2.8 47.4 + - + +
64A GLU 4.8 0.2 + - - -
65A ALA 5.6 0.2 + - - -
66A LEU 3.6 2.9 + - - +
67A LYS 3.1 10.6 + - - +
69A TRP* 1.3 79.3 - - - +
71A GLN* 1.3 62.2 + - + +
72A GLY 3.5 0.2 + - - -
73A LEU 4.2 0.2 + - - -
74A LYS* 3.5 26.2 - - - +
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 6.0 1.6 - - - +
6A PRO 3.9 7.2 + - - -
7A GLU* 3.9 8.3 - - - +
8A VAL* 3.6 30.6 + - + +
10A ILE* 4.0 10.0 - - - +
67A LYS* 3.1 16.1 + - + +
68A GLY 3.8 6.5 - - - +
69A TRP 3.2 0.2 - - - -
70A ASP* 1.3 77.7 - - + +
72A GLY* 1.3 60.5 + - - +
73A LEU 3.6 0.4 + - - -
74A LYS* 4.1 18.4 + - - +
90A LEU* 3.6 32.4 - - - +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.2 3.1 - - - -
10A ILE* 3.7 16.6 - - - +
68A GLY 2.9 17.4 + - - -
69A TRP 3.2 0.4 + - - -
71A GLN* 1.3 79.0 - - - +
73A LEU* 1.3 62.8 + - - +
74A LYS 3.6 1.8 - - - -
82A ARG* 2.8 29.3 + - - -
84A LEU* 3.5 17.3 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR* 2.7 27.7 + - - -
29A MET* 3.9 14.0 - - + +
31A VAL* 5.7 0.4 - - + -
58A PHE* 3.7 12.6 - - + -
60A LEU* 3.7 13.0 - - + +
69A TRP* 3.1 56.6 + - + +
70A ASP 4.2 0.4 + - - -
71A GLN 3.6 0.4 - - - -
72A GLY* 1.3 83.2 - - - +
74A LYS* 1.3 54.6 + - - +
76A MET* 3.7 29.2 - - + +
82A ARG* 3.6 8.1 - - + +
84A LEU* 4.1 7.6 - - + -
110A ILE* 3.9 28.9 - - + -
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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