Contacts of the helix formed by residues 85 - 95 (chain E) in PDB entry 3PHW
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 SER 85 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E TYR* 4.1 0.4 - - - -
83E GLY 3.8 0.8 + - - -
84E LEU* 1.3 77.0 - - - +
86E LEU* 1.3 66.6 + - - +
87E GLU* 4.2 3.4 + - - +
88E ASP* 3.0 33.8 + - - +
89E TYR* 2.7 20.4 + - - +
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Residues in contact with LEU 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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69E ALA* 4.2 1.8 - - + -
70E ARG* 4.2 38.4 - - + +
73E TYR* 3.6 44.4 - - + -
74E GLN* 3.5 31.4 - - + +
85E SER* 1.3 70.9 - - - +
87E GLU* 1.3 68.0 + - + +
89E TYR* 3.0 13.1 + - + +
90E LEU* 3.1 34.0 + - + +
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Residues in contact with GLU 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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70E ARG* 4.6 20.5 + - - +
85E SER* 3.3 3.2 + - - +
86E LEU* 1.3 80.1 - - + +
88E ASP* 1.3 67.4 + - - +
90E LEU* 3.7 9.5 + - - +
91E LYS* 3.6 18.9 + - - +
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Residues in contact with ASP 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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84E LEU* 3.8 23.4 - - + +
85E SER* 3.0 29.0 + - - +
87E GLU* 1.3 80.9 - - - +
89E TYR* 1.3 65.3 + - - +
91E LYS* 3.9 6.6 + - - +
92E ARG* 3.6 15.7 + - - +
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Residues in contact with TYR 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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65E THR* 4.3 0.7 - - - +
69E ALA* 3.9 18.8 - - + -
73E TYR* 3.5 44.0 - + + +
82E VAL* 4.2 15.3 - - + -
84E LEU* 4.1 8.9 - - + +
85E SER 2.7 11.8 + - - +
86E LEU 3.0 10.1 + - - +
88E ASP* 1.3 76.7 - - - +
90E LEU* 1.3 70.7 + - + +
92E ARG* 3.3 4.8 + - + +
93E MET* 2.9 46.1 + - + +
103E LEU* 4.0 12.3 - - + +
104E GLU* 2.6 35.2 + - - +
107E MET* 3.3 19.0 - - + +
72F ARG* 6.3 0.2 - - - -
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Residues in contact with LEU 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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66E GLU* 3.7 28.5 - - + +
69E ALA* 3.5 30.1 - - + -
70E ARG* 3.4 45.1 - - + +
86E LEU* 3.1 30.1 + - + +
87E GLU* 4.1 7.0 - - - +
88E ASP 3.5 0.2 - - - -
89E TYR* 1.3 79.9 - - + +
91E LYS* 1.3 62.5 + - - +
93E MET* 3.9 8.7 - - + +
94E LEU* 3.1 38.7 + - + +
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Residues in contact with LYS 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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87E GLU 3.6 14.6 + - - +
88E ASP* 4.2 6.3 - - - +
89E TYR 3.3 0.6 - - - -
90E LEU* 1.3 80.1 - - - +
92E ARG* 1.3 61.9 + - - +
94E LEU* 4.0 6.4 - - + +
95E SER* 2.9 26.1 + - - +
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Residues in contact with ARG 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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92C ARG* 5.9 5.1 - - + +
95C SER* 3.5 25.4 + - - -
96C ASP* 2.9 32.9 + - - +
97C ASN* 4.3 7.9 + - - +
98C GLU* 3.7 19.6 + - - -
84E LEU* 3.5 36.7 - - + +
88E ASP* 3.6 10.3 + - - +
89E TYR* 3.3 8.1 + - + +
91E LYS* 1.3 76.0 - - - +
93E MET* 1.3 65.9 + - - +
95E SER* 3.2 17.9 + - - +
98E GLU* 3.0 43.9 - - + +
74F ARG* 6.3 0.4 - - - +
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Residues in contact with MET 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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42E TYR* 3.6 21.9 + - - +
62E LYS* 3.1 30.2 + - - +
65E THR* 3.4 33.9 - - + +
66E GLU* 3.6 24.5 - - + +
89E TYR* 2.9 44.0 + - + +
90E LEU* 3.9 12.8 - - + +
91E LYS 3.3 0.2 - - - -
92E ARG* 1.3 77.7 - - - +
94E LEU* 1.3 80.3 + - + +
95E SER 3.6 0.2 + - - -
98E GLU* 3.7 15.2 - - + +
99E TRP 6.1 0.4 - - - +
104E GLU* 4.5 3.1 - - - +
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Residues in contact with LEU 94 (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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62E LYS* 3.4 32.8 + - + +
63E ARG* 5.2 5.4 - - - +
66E GLU* 3.9 34.1 - - + +
90E LEU* 3.1 23.5 + - + +
91E LYS* 4.1 7.9 - - + +
92E ARG 3.2 0.2 - - - -
93E MET* 1.3 100.1 - - + +
95E SER* 1.3 66.8 + - - +
96E ASP* 3.3 2.4 + - - -
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Residues in contact with SER 95 (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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92C ARG* 3.4 26.9 + - - -
62E LYS* 3.3 4.0 + - - -
91E LYS* 2.9 19.5 + - - +
92E ARG* 3.2 14.9 + - - +
94E LEU* 1.3 77.3 - - - +
96E ASP* 1.3 67.4 + - - +
98E GLU* 3.1 18.7 + - - +
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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