Contacts of the helix formed by residues 83 - 93 (chain E) in PDB entry 2NYM
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 PRO 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E ILE* 4.5 1.8 - - + -
82E TYR* 1.4 84.0 - - - +
84E GLU* 1.3 62.5 + - + +
85E VAL* 3.0 8.7 + - + +
86E VAL* 4.0 11.7 - - + +
87E HIS* 3.6 18.4 + - - +
134E PHE* 6.4 0.4 - - + -
144E ILE 5.1 3.8 - - - +
148E TYR* 3.1 61.9 - - + +
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Residues in contact with GLU 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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36E LEU* 3.8 28.6 - - + +
39E CYS* 4.6 16.4 - - + +
40E CYS* 4.1 16.5 - - - +
82E TYR* 3.4 23.3 + - + -
83E PRO* 1.3 81.6 - - + +
85E VAL* 1.3 61.4 + - - +
87E HIS* 4.1 14.5 - - - +
88E MSE 2.9 30.7 + - - +
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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
----------------------------------------------------------
39E CYS* 5.6 2.2 - - + -
66E MSE 5.6 2.2 - - + -
82E TYR* 4.0 32.8 - - + +
83E PRO* 4.8 1.1 - - + -
84E GLU* 1.3 76.2 - - - +
86E VAL* 1.3 72.0 + - - +
88E MSE 3.0 9.3 + - - +
89E PHE* 2.8 17.8 + - + +
130E PHE* 3.3 37.7 - - + -
131E PHE* 4.3 7.9 - - + -
134E PHE* 3.2 46.4 - - + -
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E PRO* 3.9 15.0 + - + +
85E VAL* 1.3 76.6 - - - +
87E HIS* 1.3 70.9 + - - +
89E PHE* 2.5 22.4 + - - +
90E ALA* 2.9 12.9 + - + -
131E PHE* 4.4 13.9 - - + -
134E PHE* 5.0 7.4 - - + -
144E ILE 5.9 1.3 - - - +
145E ALA* 5.8 2.2 - - + -
148E TYR* 3.4 35.2 - - + +
149E ILE* 3.9 18.4 - - + -
153E PHE* 4.1 21.1 - - + -
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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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43E PHE* 4.8 12.7 - - + +
44E ASP* 5.7 4.2 + - - +
83E PRO 3.6 14.4 + - - +
84E GLU* 4.1 15.3 - - - +
85E VAL 3.5 0.2 - - - -
86E VAL* 1.3 83.0 - - - +
88E MSE 1.3 69.2 + - - +
90E ALA* 3.3 9.5 + - - +
91E VAL* 3.0 40.8 - - + +
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Residues in contact with MSE 88 (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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39E CYS* 4.2 13.7 - - + +
42E LEU* 3.4 18.2 - - + +
43E PHE* 3.8 31.8 - - + +
59E LYS* 4.5 0.2 - - - -
63E LEU* 4.0 16.2 - - + -
66E MSE 6.2 0.9 - - - +
84E GLU 2.9 19.1 + - - +
85E VAL* 3.0 10.0 + - - +
86E VAL 2.8 3.2 + - - -
87E HIS* 1.3 79.3 - - - +
89E PHE* 1.3 60.4 + - - +
91E VAL* 3.3 8.9 + - - +
92E ASN* 2.8 52.6 + - - +
127E VAL* 3.7 28.9 - - + -
130E PHE* 4.7 19.3 - - + -
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Residues in contact with PHE 89 (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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85E VAL* 2.8 9.3 + - + +
86E VAL* 2.5 14.2 + - - +
88E MSE 1.3 74.8 - - - +
90E ALA* 1.3 54.9 + - - +
91E VAL 2.5 19.0 + - - -
92E ASN* 2.9 11.4 + - - -
93E MSE 3.0 39.2 + - + +
94E PHE* 3.7 19.1 - + - -
127E VAL* 3.7 13.0 - - + -
128E TYR* 3.7 25.6 - + - -
131E PHE* 3.6 45.8 - + + -
153E PHE* 3.5 33.0 - + - -
157E LEU* 3.9 19.7 - - + -
175E THR* 5.1 0.9 - - + -
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Residues in contact with ALA 90 (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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86E VAL* 2.9 18.2 + - + +
87E HIS* 4.0 5.4 - - - +
89E PHE* 1.3 73.1 - - - +
91E VAL* 1.3 66.2 + - - +
94E PHE* 3.2 52.1 - - + +
153E PHE* 4.0 11.4 - - + -
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Residues in contact with VAL 91 (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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43E PHE* 5.3 0.9 - - + -
44E ASP* 4.9 20.0 - - - +
46E VAL* 6.4 2.0 - - + -
87E HIS* 3.0 46.0 - - + +
88E MSE 3.5 8.3 - - - +
89E PHE 2.5 9.5 + - - -
90E ALA* 1.3 77.9 - - - +
92E ASN* 1.3 62.8 + - - +
93E MSE 3.3 1.1 - - - +
94E PHE 4.5 10.2 - - - +
95E ARG* 5.8 1.2 - - - +
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Residues in contact with ASN 92 (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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42E LEU 4.0 3.7 + - - +
43E PHE* 4.3 7.2 + - - +
46E VAL* 5.0 3.5 + - - -
59E LYS* 3.0 25.7 + - - -
88E MSE 2.8 54.8 + - - +
89E PHE 2.9 1.2 + - - -
91E VAL* 1.3 79.8 - - - +
93E MSE 1.3 63.4 + - - +
95E ARG* 4.5 7.7 + - - +
123E HIS* 5.4 0.3 - - - -
124E LEU* 3.1 31.2 - - + +
127E VAL* 3.8 20.0 - - + +
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Residues in contact with MSE 93 (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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89E PHE* 3.0 44.8 + - + +
92E ASN* 1.3 87.7 - - - +
94E PHE* 1.3 72.7 + - + +
95E ARG* 3.0 37.6 + - - +
124E LEU* 3.7 21.8 - - + -
127E VAL* 4.4 9.0 - - + -
128E TYR* 2.9 46.2 - - + +
160E LEU* 3.2 16.3 - - + +
168E GLU* 3.1 15.5 - - - +
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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