Contacts of the helix formed by residues 111 - 121 (chain C) in PDB entry 3QI6
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 TYR 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C MET* 3.7 5.6 - - - -
110C ALA* 1.3 71.5 - - - +
112C GLY* 1.3 73.7 + - - +
113C GLY* 3.0 31.3 + - - -
114C THR* 3.0 18.2 + - - +
115C PHE* 3.0 18.2 + - - +
116C ARG* 5.3 0.9 + - - -
154C GLU* 2.7 20.5 + - - +
158C ASN* 3.6 28.9 - - - +
208C LLP 3.4 71.4 + + + +
368C ARG* 6.0 0.7 - - - -
56D TYR* 4.9 2.8 - - - -
58D ARG* 3.0 22.2 + - - -
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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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110C ALA 3.3 4.8 + - - -
111C TYR* 1.3 80.9 - - - +
113C GLY* 1.3 55.7 - - - +
115C PHE* 3.8 7.6 - - - +
116C ARG* 2.9 33.8 + - - +
158C ASN 5.1 0.8 + - - -
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Residues in contact with GLY 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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87C MET* 3.4 18.9 - - - +
111C TYR* 3.1 26.1 - - - -
112C GLY* 1.3 74.2 - - - +
114C THR* 1.3 59.6 + - - +
116C ARG* 3.5 27.1 + - - +
117C LEU* 3.0 22.2 + - - +
238D GLY* 4.9 0.7 - - - +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C MET* 3.9 12.4 - - - +
90C ALA* 5.0 3.9 - - + +
94C LEU* 5.9 1.1 - - + -
106C ILE* 5.8 0.9 - - + -
107C PRO* 6.0 0.2 - - + -
110C ALA* 4.8 6.7 - - + -
111C TYR* 3.0 31.5 + - - +
113C GLY* 1.3 75.0 - - - +
115C PHE* 1.3 62.7 + - - +
117C LEU* 3.2 3.4 + - - +
118C ILE* 3.1 39.4 + - + +
152C TRP* 3.5 45.4 + - + +
154C GLU* 4.8 1.1 + - - -
183C ASP* 4.8 1.6 + - - -
208C LLP 4.6 5.5 + - - -
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Residues in contact with PHE 115 (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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106C ILE* 3.9 21.8 - - + -
107C PRO 6.0 0.2 - - - -
110C ALA* 5.1 9.8 - - + +
111C TYR 3.0 11.3 + - - +
112C GLY* 3.9 10.3 - - - +
114C THR* 1.3 78.0 - - - +
116C ARG* 1.3 59.4 + - + +
118C ILE* 4.9 2.2 - - - -
119C ASP* 2.8 47.2 + - + +
120C LYS* 3.9 15.9 - - - -
129C TYR* 3.3 36.1 - + - -
131C PRO* 5.5 3.6 - - + -
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Residues in contact with ARG 116 (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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87C MET* 5.4 0.6 - - - +
111C TYR* 5.3 1.0 + - - -
112C GLY 2.9 23.3 + - - +
113C GLY* 3.7 22.3 + - - +
114C THR 3.4 0.2 - - - -
115C PHE* 1.3 76.6 - - - +
117C LEU* 1.3 58.9 + - - +
120C LYS* 2.8 56.0 + - + +
121C VAL* 3.7 1.1 + - - +
58D ARG* 3.6 20.0 - - - +
234D PHE* 4.0 27.1 + - + -
237D ASN* 3.3 33.5 + - - +
238D GLY* 4.5 13.1 + - - -
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Residues in contact with LEU 117 (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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87C MET* 3.4 23.6 - - + -
90C ALA* 4.4 2.0 - - + -
91C ASP* 3.8 36.6 - - + +
94C LEU* 3.9 15.3 - - + -
113C GLY 3.0 18.3 + - - +
114C THR* 3.2 5.6 + - + +
116C ARG* 1.3 78.2 - - - +
118C ILE* 1.3 57.6 + - + +
121C VAL* 3.0 45.5 + - + +
122C PHE* 3.1 28.4 + - + -
95D ARG* 4.7 1.6 - - - +
235D LEU* 5.7 0.7 - - + -
238D GLY* 3.9 20.9 - - - +
239D ALA* 4.7 2.2 - - + +
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Residues in contact with ILE 118 (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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94C LEU* 3.6 36.1 - - + -
104C VAL* 4.2 7.9 - - + -
106C ILE* 3.7 28.3 - - + -
114C THR* 3.1 35.2 + - + +
115C PHE* 4.1 2.9 - - - +
117C LEU* 1.3 75.3 - - - +
119C ASP* 1.3 58.3 + - - +
122C PHE* 3.4 12.6 + - + +
123C THR* 3.1 31.6 + - + +
127C VAL* 5.2 4.0 - - + -
129C TYR* 3.8 33.9 - - + -
152C TRP* 4.9 4.5 - - + -
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Residues in contact with ASP 119 (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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115C PHE* 2.8 42.9 + - + +
118C ILE* 1.3 73.8 - - - +
120C LYS* 1.3 90.6 + - - +
121C VAL 3.6 0.2 - - - -
123C THR* 2.8 30.0 + - - +
129C TYR* 2.6 29.6 + - + +
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Residues in contact with LYS 120 (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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115C PHE* 3.9 17.2 - - - -
116C ARG* 2.8 37.7 + - + +
119C ASP* 1.3 104.4 + - - +
121C VAL* 1.3 60.7 + - - +
123C THR* 4.8 2.1 + - - -
124C GLY* 5.0 2.3 + - - -
234D PHE* 3.7 26.1 - - + -
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Residues in contact with VAL 121 (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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116C ARG 4.7 1.6 - - - +
117C LEU* 3.0 26.4 + - + +
120C LYS* 1.3 81.6 - - + +
122C PHE* 1.3 65.1 + - + +
123C THR 3.2 1.1 - - - -
124C GLY* 2.9 19.6 + - - -
125C TRP* 3.2 30.2 - - + +
95D ARG* 4.1 17.7 - - - +
99D ARG* 5.8 0.2 + - - -
234D PHE* 3.7 29.6 - - + +
235D LEU* 4.0 27.4 - - + -
238D GLY* 6.0 2.0 - - - -
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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