Contacts of the helix formed by residues 84 - 94 (chain C) in PDB entry 5UHE
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 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C TRP* 3.5 10.8 - - - -
64C LEU 4.5 1.6 - - - -
65C ILE 5.5 0.4 - - - -
66C GLY* 4.6 4.7 - - - -
70C TRP* 3.3 15.7 - - - -
83C VAL* 1.3 77.2 - - - +
85C GLY* 1.3 61.8 + - - -
86C LEU 3.2 3.1 - - - -
87C GLU* 3.0 23.6 + - - -
88C GLU* 3.0 27.5 + - - +
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TRP* 2.8 49.7 + - - -
64C LEU* 3.3 10.1 + - - -
84C GLY* 1.3 72.2 - - - +
86C LEU* 1.3 61.8 + - - +
88C GLU* 3.5 0.7 - - - +
89C VAL* 3.4 25.5 + - - +
386C GLN* 3.4 9.4 + - - -
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.0 26.7 + - + +
65C ILE* 4.6 5.4 - - - +
84C GLY 3.2 0.2 - - - -
85C GLY* 1.3 75.6 - - - +
87C GLU* 1.3 65.3 + - + +
88C GLU 3.1 1.3 - - - -
89C VAL* 3.2 16.7 + - + +
90C LEU* 3.3 18.7 + - + +
110C PRO* 4.4 15.9 - - + -
112C PHE* 3.9 33.2 - - + -
133C LEU* 4.4 20.6 - - + -
157C PHE* 4.6 7.9 - - + -
386C GLN* 6.1 0.4 - - - -
389C ILE* 3.6 39.3 - - + -
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE 6.0 1.8 - - - +
66C GLY* 5.9 1.5 - - - -
71C ARG* 3.6 25.3 + - - -
82C PRO 4.1 4.5 - - - +
83C VAL* 3.6 21.0 - - + +
84C GLY* 3.0 26.8 + - - +
86C LEU* 1.3 77.2 - - + +
88C GLU* 1.3 62.5 - - - +
90C LEU* 3.2 7.7 + - - +
91C TYR* 3.2 37.2 + - + -
110C PRO* 4.1 28.6 - - + +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TRP* 3.6 15.8 + - - -
83C VAL* 3.5 14.2 - - + +
84C GLY 3.0 16.5 + - - +
85C GLY 3.5 3.1 - - - +
87C GLU* 1.3 75.4 - - - +
89C VAL* 1.3 65.4 - - - +
91C TYR* 3.0 16.4 + - - +
92C GLU* 3.0 35.0 + - + +
310C ARG* 2.8 39.4 + - - +
386C GLN* 3.1 26.7 + - - +
390C ARG* 3.5 6.3 + - - -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLY 3.4 15.7 + - - +
86C LEU* 3.2 13.1 + - + +
88C GLU* 1.3 76.2 - - - +
90C LEU* 1.3 68.4 + - + +
92C GLU* 4.1 7.6 - - - +
93C LEU* 3.3 22.2 + - - +
386C GLN* 3.8 28.7 - - + +
389C ILE* 4.6 12.1 - - + -
390C ARG* 3.9 22.4 - - + +
393C MET* 3.8 30.5 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LEU* 3.4 14.6 - - + +
87C GLU* 3.2 7.6 + - - +
88C GLU 3.1 0.8 - - - -
89C VAL* 1.3 86.6 - - + +
91C TYR* 1.3 62.6 + - + +
93C LEU* 3.8 5.2 - - + +
94C SER* 3.0 33.0 + - - -
107C PHE* 4.1 34.2 - - + +
108C SER* 4.4 8.1 - - - +
110C PRO* 4.3 23.1 - - + -
135C VAL* 4.2 22.4 - - + -
393C MET* 4.3 24.0 - - + -
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 4.9 23.8 - - + -
87C GLU* 3.2 22.5 + - + +
88C GLU* 3.0 9.4 + - - +
90C LEU* 1.3 83.5 - - + +
92C GLU* 1.3 65.5 + - + +
94C SER* 3.0 20.8 - - - +
107C PHE 4.8 10.1 - - - -
108C SER* 5.2 11.0 - - - -
109C ASP 6.1 0.2 - - - -
310C ARG* 6.4 0.2 - - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 3.0 43.7 + - + +
89C VAL* 4.1 4.9 - - - +
91C TYR* 1.3 77.8 - - + +
93C LEU* 1.3 67.7 + - - +
94C SER 3.6 3.1 - - - +
208C ARG* 5.6 3.6 + - - -
303C GLU* 5.3 4.2 - - - +
307C ASP* 5.5 3.8 - - - +
310C ARG* 4.2 7.3 + - - +
390C ARG* 3.3 31.0 + - - -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 3.3 18.2 + - + +
90C LEU* 3.8 6.7 - - + +
92C GLU* 1.3 82.6 - - - +
94C SER* 1.3 61.6 + - - +
95C PRO 3.6 11.7 - - - +
96C ILE* 4.2 15.4 + - + +
107C PHE* 3.6 33.4 - - + -
393C MET* 3.6 38.1 - - + +
394C SER* 5.2 1.3 - - - +
396C MET* 6.2 0.9 - - + -
397C GLU* 3.8 38.2 - - + +
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU 3.0 21.2 + - - -
91C TYR* 3.0 21.2 - - - +
92C GLU 3.5 3.5 - - - +
93C LEU* 1.3 80.7 - - - +
95C PRO* 1.3 67.7 - - - +
96C ILE* 4.2 1.1 - - - +
105C LEU 4.7 0.4 - - - -
106C SER* 3.4 10.2 - - - -
107C PHE* 3.0 37.2 + - - -
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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