Contacts of the strand formed by residues 80 - 87 (chain E) in PDB entry 4MNE
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 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E ALA* 3.6 4.2 - - - +
77E GLY 3.3 23.9 + - - +
78E ASN 3.6 2.0 - - - -
79E GLY* 1.3 80.9 - - - +
81E VAL* 1.3 63.6 + - - +
97E LYS* 5.0 2.9 - - - -
98E LEU 3.3 12.8 - - - -
99E ILE* 4.5 2.0 - - - -
100E HIS* 4.0 7.0 + - - -
901E ACP 3.9 12.0 + - - -
903E 573 3.7 9.8 + - - -
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Residues in contact with VAL 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLU* 3.8 19.1 - - + +
75E GLY 3.5 14.8 - - - +
76E ALA* 3.9 8.5 - - + +
80E GLY* 1.3 74.8 - - - +
82E VAL* 1.3 67.0 + - - +
83E PHE* 3.8 32.7 + - + -
96E ARG 4.0 0.5 - - - +
97E LYS* 3.5 2.4 - - - +
98E LEU* 2.9 41.5 + - + +
100E HIS* 3.9 19.5 - - + +
138E GLU* 5.3 0.2 - - - +
901E ACP 4.3 0.6 + - - -
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Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLU* 3.7 3.5 - - - +
74E LEU* 2.8 52.3 + - + +
75E GLY 2.9 14.1 + - - +
81E VAL* 1.3 77.2 - - - +
83E PHE* 1.3 59.5 + - - +
95E ALA* 4.2 9.6 - - + -
96E ARG 3.4 9.4 - - - +
97E LYS* 3.5 31.0 - - + +
143E MET* 4.5 1.1 - - + -
901E ACP 3.6 52.7 - - + +
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Residues in contact with PHE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LYS* 3.4 48.9 - - + -
72E SER 3.6 2.5 - - - +
73E GLU* 3.7 31.4 - - + -
74E LEU* 4.1 4.5 - - - -
81E VAL* 3.8 35.7 - - + -
82E VAL* 1.3 73.7 - - - +
84E LYS* 1.3 61.7 + - - +
85E VAL* 3.4 19.9 + - + +
95E ALA* 3.6 3.3 - - - -
96E ARG* 2.7 46.6 + - + +
98E LEU* 4.4 18.4 - - + -
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LYS* 4.2 0.3 - - - -
71E ILE* 2.9 45.7 + - + +
72E SER* 2.8 35.7 + - - +
74E LEU* 3.7 22.2 - - + +
83E PHE* 1.3 71.5 - - - +
85E VAL* 1.3 61.6 + - - +
93E VAL* 3.8 30.1 - - + -
94E MET 3.7 5.6 - - - +
145E HIS* 4.1 25.8 - - + +
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 3.5 36.8 - - + -
69E GLU 3.6 10.5 - - - +
70E LYS* 4.7 9.4 - - + -
71E ILE* 3.4 8.3 - - - +
83E PHE* 3.4 28.0 - - + +
84E LYS* 1.3 78.7 - - - +
86E SER* 1.3 61.7 + - - +
87E HIS 4.6 0.7 - - - +
93E VAL* 3.4 5.5 - - - +
94E MET* 3.1 39.9 + - + +
96E ARG* 3.7 26.5 - - + +
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 3.4 3.8 - - - -
69E GLU* 3.0 37.2 + - - -
71E ILE* 3.5 16.5 - - - +
85E VAL* 1.3 72.6 - - - +
87E HIS* 1.3 72.0 + - - +
88E LYS* 3.2 10.1 + - - +
91E GLY* 4.5 8.1 + - - -
92E LEU 3.8 5.7 + - - -
93E VAL* 4.7 3.6 - - - +
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Residues in contact with HIS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 3.4 27.3 - - + +
67E ASP* 3.7 24.2 + - + -
68E PHE* 4.0 18.3 - + + -
85E VAL* 4.0 2.4 + - - +
86E SER* 1.3 71.6 + - - +
88E LYS* 1.3 65.6 + - - +
89E PRO* 3.5 28.7 - - + +
90E SER* 2.7 31.8 + - - +
91E GLY* 3.1 20.6 + - - -
92E LEU* 3.1 15.6 + - - +
94E MET* 4.1 19.9 - - - +
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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