Contacts of the helix formed by residues 107 - 117 (chain C) in PDB entry 1UU1
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C THR 2.8 8.2 + - - -
106C TYR* 1.3 73.5 - - - +
108C CYS* 1.3 65.5 + - - +
109C TYR 3.2 1.1 + - - -
110C ARG* 3.5 8.8 + - - +
111C ILE* 3.4 31.1 + - - +
310C PHE* 5.1 9.9 - - - -
1336C HSA 3.2 29.5 + - - -
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Residues in contact with CYS 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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106C TYR* 3.1 43.2 + - + -
107C SER* 1.3 81.1 + - - +
109C TYR* 1.3 60.6 + - - +
111C ILE* 3.7 18.6 - - - -
112C PHE* 2.7 62.8 + - + +
1336C HSA 4.1 15.3 - - - -
230D PRO* 5.3 4.7 - - - -
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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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89C ILE* 3.7 34.8 - - + -
93C MET* 3.3 13.8 - - + +
101C PHE* 3.6 38.8 - + + -
105C THR* 3.1 28.7 - - + -
106C TYR* 3.1 29.8 + + + +
108C CYS* 1.3 77.0 - - - +
110C ARG* 1.3 64.1 + - - +
112C PHE* 4.8 0.2 - - - -
113C ALA* 3.0 22.9 + - - +
143C PHE* 3.5 36.5 - + + +
145C PRO* 3.7 13.9 - - + +
173C ASP* 2.8 33.1 + - - +
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Residues in contact with ARG 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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12C TYR* 2.7 38.1 + - + +
101C PHE* 3.8 9.0 - - - -
106C TYR 4.6 0.2 + - - -
107C SER* 3.5 9.0 + - - +
108C CYS 3.3 0.2 - - - -
109C TYR* 1.3 78.7 - - - +
111C ILE* 1.3 63.4 + - + +
113C ALA* 3.8 2.2 - - - +
114C LYS* 2.9 53.6 + - + +
120C PHE* 4.3 14.4 - - + -
122C GLU* 2.9 38.7 + - - +
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Residues in contact with ILE 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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11C ALA* 5.3 1.2 - - - +
12C TYR* 3.7 39.5 - - + +
107C SER* 3.4 26.2 - - - +
108C CYS* 3.7 22.7 - - - +
109C TYR 3.3 0.2 - - - -
110C ARG* 1.3 76.8 - - + +
112C PHE* 1.3 71.7 + - + +
114C LYS* 3.4 2.3 + - - +
115C ALA* 2.9 32.8 + - + +
226D ARG 5.4 4.5 - - - +
230D PRO* 5.7 4.9 - - + -
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Residues in contact with PHE 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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86C ASP* 3.5 47.1 - - - -
89C ILE* 3.6 22.9 - - + -
90C TYR* 4.0 22.4 - + + -
93C MET* 3.8 15.0 - - - -
108C CYS* 2.7 43.9 + - + +
111C ILE* 1.3 77.7 - - + +
113C ALA* 1.3 61.9 + - - +
115C ALA* 3.1 7.0 + - + +
116C VAL* 2.8 33.7 + - - +
228D ARG 5.4 1.3 - - - -
229D LEU* 3.6 19.5 - - + -
230D PRO* 3.8 24.0 - - + -
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Residues in contact with ALA 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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93C MET* 3.5 19.4 - - + -
99C SER* 5.4 0.7 - - - -
101C PHE* 4.6 0.2 - - + -
109C TYR 3.0 20.3 + - - +
110C ARG 3.9 2.2 - - - +
112C PHE* 1.3 76.8 - - - +
114C LYS* 1.3 58.3 + - - +
116C VAL* 3.5 0.4 + - - -
117C GLY 2.8 6.6 + - - -
118C ALA* 2.8 42.1 + - + +
120C PHE* 3.8 33.2 - - + -
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Residues in contact with LYS 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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9C LYS* 5.2 4.8 - - - +
10C ARG* 2.5 72.3 + - - +
11C ALA* 4.1 10.7 - - - +
12C TYR* 3.7 22.1 - - + -
110C ARG* 2.9 46.8 + - + +
111C ILE 3.8 2.7 - - - +
113C ALA* 1.3 75.8 - - - +
115C ALA* 1.3 64.8 + - - +
117C GLY* 3.2 9.8 + - - +
120C PHE* 4.0 21.8 - - + -
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Residues in contact with ALA 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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10C ARG* 4.7 6.6 + - - -
11C ALA* 4.0 12.3 - - + +
90C TYR* 4.9 2.5 - - + -
111C ILE* 2.9 20.2 + - + +
112C PHE* 3.3 10.8 - - + +
114C LYS* 1.3 77.6 - - - +
116C VAL* 1.3 61.0 + - - +
117C GLY 3.5 0.2 + - - -
94D LEU 5.3 1.9 - - - +
226D ARG 3.5 22.9 - - - +
227D VAL* 3.5 38.5 - - - +
228D ARG 5.5 0.7 - - - +
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Residues in contact with VAL 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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10C ARG* 5.7 0.4 - - - -
90C TYR* 4.0 33.9 - - + +
93C MET* 4.9 5.4 - - + +
94C LEU* 3.4 39.7 - - + -
112C PHE 2.8 13.6 + - - +
113C ALA 4.1 0.2 - - - +
115C ALA* 1.3 76.5 - - - +
117C GLY* 1.3 59.4 + - - +
118C ALA* 3.5 27.6 - - + +
119C LYS* 5.3 0.9 - - - +
94D LEU* 4.1 24.3 - - + +
227D VAL* 5.1 1.6 - - + -
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Residues in contact with GLY 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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10C ARG* 4.8 14.1 - - - -
113C ALA 2.8 7.3 + - - -
114C LYS* 3.2 10.2 + - - -
115C ALA 3.2 4.4 + - - -
116C VAL* 1.3 80.1 - - - +
118C ALA* 1.3 64.4 + - - +
119C LYS* 4.0 0.9 + - - +
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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