Contacts of the helix formed by residues 104 - 114 (chain C) in PDB entry 5EWL
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 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C VAL* 3.9 22.4 - - + +
94C HIS* 4.3 6.7 - - + +
95C PRO* 4.7 5.6 - - + -
103C THR* 1.4 82.1 - - + +
105C THR* 1.3 49.5 + - - -
106C PRO* 3.6 0.9 - - - -
107C ILE* 3.0 18.8 + - + +
108C SER* 2.8 32.5 + - - -
118C VAL* 5.7 0.2 - - - +
120C GLY* 6.2 0.4 - - - -
123C THR* 3.2 36.1 - - + +
128C TYR* 3.2 26.0 - - + +
137C PHE* 4.3 14.6 - - + -
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Residues in contact with THR 105 (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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103C THR* 3.0 12.1 + - - -
104C PRO* 1.3 75.5 - - - +
106C PRO* 1.4 63.3 - - + +
108C SER* 3.0 7.1 + - - -
109C TYR* 2.8 69.0 + - + +
128C TYR* 3.1 25.5 + - - -
134C HIS* 3.5 6.1 + - + -
114D PHE* 5.9 2.7 - - + -
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Residues in contact with PRO 106 (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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71C ALA* 3.6 45.5 - - + +
74C MET* 4.5 7.9 - - + -
75C ALA* 4.2 12.3 - - + +
103C THR* 3.1 31.0 - - - +
105C THR* 1.4 82.4 - - + +
107C ILE* 1.4 53.8 + - + +
109C TYR* 4.1 3.9 - - + +
110C THR* 2.7 38.0 + - - -
114D PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 107 (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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32C VAL* 4.0 20.4 - - + -
67C HIS* 4.8 4.9 - - + -
74C MET* 4.0 17.9 - - + -
78C VAL* 3.9 27.4 - - + +
90C ILE* 3.9 20.0 - - + -
92C VAL* 3.4 48.9 - - + -
103C THR 4.5 2.7 - - - +
104C PRO* 3.0 16.5 + - + +
106C PRO* 1.4 73.3 - - - +
108C SER* 1.3 58.8 + - - +
110C THR* 3.4 1.4 + - - -
111C ALA* 2.9 34.4 + - - +
118C VAL* 4.3 6.7 - - + -
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Residues in contact with SER 108 (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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104C PRO 2.8 16.0 + - - -
105C THR* 3.4 9.0 - - - -
107C ILE* 1.3 72.4 - - - +
109C TYR* 1.3 58.0 + - - +
111C ALA* 4.2 0.3 - - - +
112C GLY* 2.8 28.8 + - - -
118C VAL* 4.4 12.9 - - - +
128C TYR* 5.2 0.2 - - - -
133C ILE 4.7 0.9 + - - +
134C HIS* 2.8 43.3 + - - +
136C SER 5.6 0.7 + - - +
137C PHE* 4.0 17.9 - - - +
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Residues in contact with TYR 109 (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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105C THR* 2.8 46.8 + - + +
106C PRO* 4.1 4.0 - - + +
108C SER* 1.3 74.1 - - - +
110C THR* 1.4 60.0 + - - +
112C GLY* 3.7 1.0 - - - -
113C PHE* 2.9 31.2 + - - +
133C ILE* 3.7 43.9 - - + +
134C HIS* 4.1 10.3 + + - -
110D GLN* 4.2 40.0 + - + -
114D PHE* 4.9 20.2 - + + -
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Residues in contact with THR 110 (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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75C ALA* 3.8 21.7 - - + +
78C VAL* 3.9 21.5 - - + -
79C CYS* 3.6 31.0 - - - -
83C ILE* 4.0 5.2 - - + -
106C PRO 2.7 23.8 + - - -
107C ILE 4.0 1.8 - - - -
109C TYR* 1.4 74.2 - - - +
111C ALA* 1.3 61.4 + - - +
113C PHE* 3.3 19.4 - - - +
114C TYR* 3.4 15.4 - - - -
329C CYS* 4.2 2.0 - - - -
78D PRO* 4.6 16.2 - - + +
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Residues in contact with ALA 111 (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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78C VAL* 4.8 0.6 - - - +
83C ILE* 4.6 7.8 - - - +
90C ILE* 3.9 19.3 - - + -
107C ILE 2.9 17.3 + - - +
110C THR* 1.3 75.3 - - - +
112C GLY* 1.3 59.5 + - - +
114C TYR* 3.1 4.9 + - - +
115C ARG 3.0 7.4 + - - -
116C ILE* 2.9 47.5 + - + +
118C VAL* 3.5 17.9 - - + -
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Residues in contact with GLY 112 (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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108C SER 2.8 23.8 + - - -
109C TYR* 3.7 1.8 - - - -
111C ALA* 1.3 70.6 - - - +
113C PHE* 1.3 63.8 + - - +
115C ARG* 3.0 29.0 + - - -
116C ILE 4.3 2.9 + - - -
135C LEU* 3.4 26.8 - - - +
136C SER* 4.9 3.4 - - - -
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Residues in contact with PHE 113 (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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109C TYR 2.9 13.1 + - - +
110C THR 3.3 13.0 - - - +
112C GLY* 1.3 74.9 - - - +
114C TYR* 1.4 89.6 + + - +
115C ARG* 3.9 5.1 + - - +
332C ASN 3.7 6.1 - - - -
333C THR* 4.0 17.8 - - - +
335C ILE* 3.5 20.8 + - - +
77D ASP* 4.1 3.1 - - - -
78D PRO* 3.5 35.4 - - + -
105D GLN* 3.8 24.7 - - + -
107D ALA* 3.9 30.7 - - + -
111D ILE* 4.1 9.6 - - + -
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Residues in contact with TYR 114 (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 ILE* 3.8 14.4 - - + -
110C THR 3.4 20.9 - - - -
111C ALA 3.1 3.2 + - - +
113C PHE* 1.4 95.5 - + - +
115C ARG* 1.3 64.5 + - - +
116C ILE* 3.3 19.1 - - + -
326C PRO* 3.5 21.8 - - + -
328C GLY 4.5 0.9 - - - -
329C CYS* 3.1 48.5 + - - +
332C ASN* 2.8 42.4 + - + -
334C ASN 3.6 13.5 - - - -
335C ILE* 4.2 3.8 - - - +
336C TRP* 2.8 33.9 + - - +
77D ASP* 3.6 6.1 - - - +
78D PRO* 3.7 3.4 - - + +
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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