Contacts of the helix formed by residues 109 - 121 (chain F) in PDB entry 4S0H
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 109 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107F LEU 3.8 1.6 + - - -
108F PHE* 1.3 75.4 - - - +
110F GLN* 1.3 65.6 + - - +
111F ALA* 3.7 10.4 + - - +
112F GLN* 2.9 46.5 + - - +
113F VAL* 3.2 8.7 + - - +
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Residues in contact with GLN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.6 27.0 - - + +
108F PHE 3.7 1.9 + - - -
109F SER* 1.3 73.8 - - - +
111F ALA* 1.3 62.4 + - - +
113F VAL* 4.6 7.9 - - + -
114F TYR* 3.0 26.1 + - + +
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.6 22.5 - - + +
109F SER* 3.0 10.2 + - - +
110F GLN* 1.3 80.1 - - - +
112F GLN* 1.3 64.7 + - + +
114F TYR* 3.6 2.4 - - - +
115F GLU* 3.4 25.3 + - - +
138F LEU* 4.8 0.8 - - - +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PHE* 3.4 16.7 - - + +
109F SER* 2.9 34.5 + - - +
111F ALA* 1.3 74.7 - - + +
113F VAL* 1.3 67.5 + - - +
114F TYR 2.9 1.2 + - - -
115F GLU* 3.0 14.2 + - - +
116F LEU* 3.0 17.8 + - + +
138F LEU* 2.7 46.1 + - + +
139F LYS* 3.7 7.3 + - - +
140F LEU* 3.4 31.5 - - + +
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Residues in contact with VAL 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PHE* 3.5 37.5 - - + +
109F SER 3.2 9.1 + - - +
110F GLN* 4.2 8.5 - - + +
112F GLN* 1.3 76.3 - - - +
114F TYR* 1.3 61.2 + - - +
116F LEU* 3.8 9.6 - - - +
117F GLU* 3.1 34.4 + - + +
148F TRP* 4.8 11.2 - - + +
14G A 4.9 7.2 - - - +
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PRO 5.5 2.1 + - - -
131A MET* 5.0 2.3 - - - -
132A PRO* 3.5 33.1 - - + +
164A HIS* 3.5 37.7 + + + +
165A LEU* 4.0 21.3 - - + -
110F GLN* 3.0 22.2 + - + +
111F ALA 3.6 5.4 - - - +
112F GLN 2.9 1.0 + - - -
113F VAL* 1.3 77.3 - - - +
115F GLU* 1.3 80.4 + - - +
117F GLU* 3.2 10.1 + - + +
118F ARG* 2.9 34.8 + - + +
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Residues in contact with GLU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 5.2 5.4 - - - -
165A LEU* 5.3 3.1 - - - +
111F ALA 3.4 13.9 - - - +
112F GLN 3.0 1.9 + - - +
114F TYR* 1.3 92.9 - - - +
116F LEU* 1.3 66.6 + - - +
118F ARG* 2.9 40.5 + - - +
119F ARG* 3.0 17.5 + - - +
134F LEU* 5.4 4.9 - - + -
138F LEU* 3.6 30.5 - - + -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PHE* 3.9 19.7 - - + -
112F GLN 3.0 21.1 + - - +
113F VAL* 3.8 5.4 - - - +
115F GLU* 1.3 75.2 - - - +
117F GLU* 1.3 56.9 + - - +
119F ARG* 3.8 5.2 + - - +
120F PHE* 3.2 19.8 + - - +
134F LEU* 4.1 15.0 - - + -
138F LEU* 3.7 22.4 - - + -
140F LEU* 4.0 12.6 - - + -
145F VAL* 4.2 18.2 - - + -
148F TRP* 3.2 58.1 - - + +
149F PHE* 4.2 8.9 - - + -
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Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F VAL* 3.1 28.2 + - + +
114F TYR* 3.3 9.2 - - + +
115F GLU 3.0 0.2 - - - -
116F LEU* 1.3 76.6 - - - +
118F ARG* 1.3 65.0 + - - +
120F PHE* 3.3 3.7 + - - +
121F LYS* 3.1 46.6 + - - +
148F TRP* 3.9 15.8 - - + -
152F ARG* 3.3 39.6 + - - -
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Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 5.5 1.8 - - - +
128A GLU* 3.4 28.8 + - - +
129A PRO* 4.4 17.9 - - + +
164A HIS* 5.6 7.9 + - - -
174A ASN* 5.7 0.6 - - - +
114F TYR* 2.9 22.2 + - + +
115F GLU* 2.9 30.5 + - - +
117F GLU* 1.3 78.2 - - - +
119F ARG* 1.3 66.5 + - + +
121F LYS* 3.4 14.9 + - - +
122F GLN* 3.4 37.9 + - - +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F GLU 3.0 14.1 + - - +
116F LEU 3.9 4.9 - - - +
118F ARG* 1.3 79.7 - - + +
120F PHE* 1.3 60.8 - - - +
122F GLN* 2.8 33.2 + - - +
123F GLN* 2.5 58.1 + - - +
126F LEU* 3.2 19.6 - - - +
130F GLU* 3.2 27.3 + - - +
133F GLN* 4.9 9.3 + - - -
134F LEU* 4.1 29.9 - - + +
149F PHE* 4.0 11.7 - - + -
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Residues in contact with PHE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU 3.2 16.3 + - - +
117F GLU* 3.7 7.2 - - - +
118F ARG 3.3 0.4 - - - -
119F ARG* 1.3 79.8 - - - +
121F LYS* 1.3 64.3 + - + +
122F GLN 3.1 0.7 + - - -
123F GLN 3.6 12.0 + - - -
124F ARG* 3.5 34.6 + - + +
148F TRP* 3.9 7.0 - - + -
149F PHE* 3.7 26.7 - + + -
152F ARG* 3.6 47.8 - - + -
153F ARG* 3.8 24.2 - - + -
156F SER* 3.3 26.7 - - - -
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Residues in contact with LYS 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PRO* 5.5 10.7 - - + +
139E PRO 5.5 4.6 + - - -
140E ASP* 5.6 6.3 + - - +
117F GLU* 3.1 42.8 + - - +
118F ARG* 3.7 8.5 - - - +
119F ARG 3.2 0.4 - - - -
120F PHE* 1.3 81.5 - - + +
122F GLN* 1.3 60.3 + - + +
152F ARG* 5.1 6.7 - - - +
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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