Contacts of the helix formed by residues 107 - 120 (chain C) in PDB entry 3LOC
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LEU* 6.3 0.4 - - + -
72C ILE* 3.9 16.2 - - + +
75C ILE* 4.1 35.0 - - + +
103C VAL* 2.8 38.1 + - + +
106C ASP* 1.3 94.5 - - + +
108C PRO* 1.3 64.5 - - - +
109C GLN* 3.2 20.0 - - - +
110C ALA* 3.3 5.6 + - + -
111C SER* 3.2 19.1 + - - -
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Residues in contact with PRO 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 SER 3.6 16.5 - - - +
105C ARG 3.6 12.8 - - - +
106C ASP 3.3 7.4 - - - +
107C TYR* 1.3 90.9 - - - +
109C GLN* 1.3 71.0 + - - +
111C SER* 3.2 3.1 + - - -
112C ARG* 2.9 57.1 + - - +
173C ALA* 4.0 13.7 - - + -
188C ARG* 6.3 1.1 - - - +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.6 33.6 - - + +
28C ASP* 4.7 9.9 - - - +
31C SER* 4.8 11.2 + - - +
106C ASP 4.2 4.3 + - - +
107C TYR* 3.2 32.5 - - - +
108C PRO* 1.3 93.0 - - - +
110C ALA* 1.3 73.2 + - - +
112C ARG* 3.2 21.0 + - - +
113C LEU* 3.0 23.9 + - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.9 24.5 - - + -
68C VAL* 5.7 2.7 - - + +
69C LEU* 4.9 0.2 - - - +
72C ILE* 2.6 43.8 - - + +
107C TYR* 3.3 10.8 + - + +
109C GLN* 1.3 86.0 - - - +
111C SER* 1.3 61.2 + - - +
113C LEU* 3.2 3.9 + - - +
114C PHE* 3.1 21.8 + - - +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 3.4 1.7 - - - +
76C TRP* 3.8 29.0 - - - -
103C VAL* 6.4 0.7 - - - -
104C SER* 5.1 3.5 + - - -
107C TYR 3.2 12.5 + - - -
108C PRO 3.3 9.0 - - - -
109C GLN 3.2 0.2 - - - -
110C ALA* 1.3 75.7 - - - +
112C ARG* 1.3 63.6 + - - +
114C PHE* 3.2 4.7 + - - +
115C CYS* 3.1 18.9 + - - +
170C GLN* 4.1 8.8 - - - +
173C ALA* 4.0 13.9 - - - +
174C ASP* 2.5 29.8 + - - +
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Residues in contact with ARG 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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31C SER* 5.5 1.8 - - - -
108C PRO* 2.9 43.6 + - - +
109C GLN* 3.6 23.4 - - - +
111C SER* 1.3 75.3 - - - +
113C LEU* 1.3 57.5 + - - +
115C CYS* 3.3 2.4 + - - +
116C MSE 2.9 43.2 + - + +
173C ALA 3.6 24.6 + - - -
174C ASP* 3.6 10.3 + - - +
176C ALA* 4.7 8.7 - - - +
177C PRO* 6.0 0.8 - - - +
118D MSE 5.6 0.4 - - - -
119D LEU* 3.6 43.9 + - + +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.6 16.6 - - + -
30C PHE* 3.8 36.1 - - + +
31C SER* 3.8 16.8 - - - +
34C GLY* 5.8 1.3 - - - -
65C TYR* 4.2 20.0 - - + +
68C VAL* 3.4 32.8 - - + -
69C LEU* 4.0 8.7 - - + -
109C GLN 3.0 16.2 + - - +
110C ALA* 3.2 4.7 + - - +
112C ARG* 1.3 76.2 - - - +
114C PHE* 1.3 63.0 + - - +
116C MSE 3.2 17.0 + - + +
117C GLU* 3.0 21.8 + - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.6 16.3 - - + +
72C ILE* 4.6 5.4 - - + -
73C LEU* 3.8 24.9 - - + -
76C TRP* 3.5 29.8 - + + -
110C ALA 3.1 9.9 + - - +
111C SER 3.2 8.3 + - - +
113C LEU* 1.3 76.1 - - - +
115C CYS* 1.3 64.7 + - - +
117C GLU* 3.2 5.6 + - - +
118C MSE 3.1 41.0 + - + +
125C LEU* 3.5 27.6 - - + -
129C LEU* 4.2 7.4 - - + -
212C URA 3.6 16.4 - - - -
175D PHE* 4.0 11.2 - + - -
178D GLN* 3.3 26.7 - - - -
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Residues in contact with CYS 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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111C SER 3.1 9.7 + - - +
112C ARG 3.5 8.1 - - - +
114C PHE* 1.3 77.8 - - - +
116C MSE 1.3 66.0 + - - +
118C MSE 3.0 11.8 + - - +
119C LEU* 3.0 26.8 + - - +
174C ASP* 3.8 15.5 - - - +
175C PHE* 5.8 0.2 - - - -
115D CYS* 3.7 29.8 - - - -
119D LEU* 3.7 16.2 - - + -
175D PHE* 3.8 27.1 - - + -
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Residues in contact with MSE 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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30C PHE 4.7 2.7 - - - +
31C SER* 4.0 36.8 - - - +
34C GLY* 5.6 4.0 - - - -
65C TYR* 5.1 1.6 - - - +
112C ARG* 2.9 49.1 + - + +
113C LEU* 3.2 19.7 + - + +
115C CYS* 1.3 75.3 - - - +
117C GLU* 1.3 63.0 + - - +
119C LEU* 3.2 7.5 + - - +
120C ALA* 3.1 21.8 + - - +
116D MSE 3.7 32.2 - - + +
119D LEU* 3.5 25.4 - - + +
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Residues in contact with GLU 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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65C TYR* 2.6 45.6 + - - +
69C LEU* 4.0 11.4 - - + -
113C LEU 3.0 10.9 + - - +
114C PHE* 3.2 10.3 + - - +
116C MSE 1.3 74.9 - - - +
118C MSE 1.3 61.7 + - - +
120C ALA* 3.2 14.0 + - - +
121C GLY 3.5 0.2 + - - -
122C ALA* 2.8 35.8 + - + -
123C PRO* 3.3 5.7 - - - +
124C LEU* 2.8 33.2 + - - +
125C LEU* 3.0 31.2 + - + -
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Residues in contact with MSE 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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114C PHE* 3.1 34.4 + - + +
115C CYS* 3.0 8.2 + - - +
117C GLU* 1.3 75.9 - - - +
119C LEU* 1.3 60.4 + - + +
121C GLY* 2.9 20.3 + - - -
122C ALA* 4.0 8.1 - - + +
125C LEU* 5.8 0.7 - - - -
129C LEU* 3.9 17.0 - - - -
112D ARG* 5.3 1.6 - - - -
174D ASP 3.5 17.6 - - - +
175D PHE* 3.6 27.1 - - + +
177D PRO* 3.2 52.6 - - + +
178D GLN* 3.2 24.2 - - + +
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Residues in contact with LEU 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 CYS* 3.0 20.3 + - - +
116C MSE 3.6 6.3 - - - +
118C MSE 1.3 75.8 - - - +
120C ALA* 1.3 59.9 + - - +
121C GLY 3.3 1.0 + - - -
112D ARG* 3.7 44.4 + - + +
115D CYS* 3.9 11.2 - - + -
116D MSE 3.6 53.6 - - + +
119D LEU* 3.9 14.6 - - + -
174D ASP* 3.7 35.9 - - + +
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Residues in contact with ALA 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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116C MSE 3.1 11.9 + - - +
117C GLU* 3.6 12.8 - - - +
118C MSE 3.1 1.2 - - - -
119C LEU* 1.3 76.7 - - - +
121C GLY* 1.3 56.6 + - - +
122C ALA 3.5 0.2 - - - -
123C PRO* 3.5 23.1 - - + +
116D MSE 5.4 1.0 - - - +
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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