Contacts of the helix formed by residues 103 - 113 (chain F) in PDB entry 2Q9Q
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 PHE 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F PRO 4.1 15.9 - - - -
42F GLU* 5.4 1.6 - - - -
43F LEU* 5.7 1.6 - - + -
99F LYS* 3.0 39.9 + - + +
100F ILE 3.5 2.5 - - - -
102F LYS* 1.3 105.0 - - + +
104F PHE* 1.3 63.6 + - - +
105F PRO* 3.3 5.2 - - - -
106F HIS* 2.9 27.2 + - + -
107F VAL* 2.9 19.0 + - + -
163F PRO* 3.3 21.8 - - + -
164F LYS 3.7 5.8 - - - -
165F PRO* 3.6 42.2 - - + -
166F ASP 5.4 0.2 - - - -
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Residues in contact with PHE 104 (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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100F ILE* 2.7 25.2 + - + +
101F GLU 3.0 20.9 - - - +
102F LYS 4.6 0.7 - - - -
103F PHE* 1.3 70.5 - - - +
105F PRO* 1.3 93.6 - - + +
107F VAL* 3.8 4.3 - - - +
108F LEU* 3.0 30.5 + - + +
130F ALA* 4.5 12.3 - - + +
133F PHE* 3.6 24.2 - + + -
134F MET* 3.7 32.5 - - + -
137F THR* 4.4 8.1 - - + -
158F LEU* 3.6 28.9 - - + -
162F VAL* 4.1 10.1 - - + -
81G TYR* 3.3 32.3 - + - -
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Residues in contact with PRO 105 (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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103F PHE* 3.3 7.9 - - - +
104F PHE* 1.3 121.7 - - + +
106F HIS* 1.3 59.9 + - + +
108F LEU* 3.9 2.0 - - + +
109F GLU* 3.0 28.9 + - - +
134F MET* 4.3 14.9 - - - +
158F LEU* 3.5 28.9 - - + +
159F PHE* 3.9 19.7 - - + +
162F VAL* 3.8 13.5 - - + -
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Residues in contact with HIS 106 (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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103F PHE* 2.9 17.9 + - + +
105F PRO* 1.3 76.4 - - + +
107F VAL* 1.3 66.7 + - + +
109F GLU* 3.9 0.5 - - - +
110F LYS* 2.9 26.2 + - - +
159F PHE* 3.0 57.5 - + + -
162F VAL* 2.6 27.9 + - - +
163F PRO 3.2 19.7 + - - -
164F LYS* 3.3 29.4 - - + +
165F PRO* 4.3 13.5 - - + -
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Residues in contact with VAL 107 (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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43F LEU* 4.1 24.0 - - + -
99F LYS 4.5 1.6 - - - +
100F ILE* 4.3 20.0 - - + +
103F PHE* 2.9 31.7 + - + +
104F PHE* 3.8 6.3 - - - +
106F HIS* 1.3 78.4 - - + +
108F LEU* 1.3 62.5 + - - +
110F LYS* 3.8 5.8 - - - +
111F GLU* 3.3 22.0 + - - +
121F SER* 6.1 0.2 - - - -
122F LEU* 3.3 39.3 - - + +
130F ALA* 5.0 3.4 - - + -
165F PRO* 6.2 1.1 - - + -
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Residues in contact with LEU 108 (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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104F PHE 3.0 21.0 + - - +
105F PRO 3.9 3.1 - - - +
107F VAL* 1.3 75.6 - - - +
109F GLU* 1.3 58.9 + - - +
111F GLU* 3.3 5.5 + - - +
112F LYS* 3.0 29.4 + - - +
122F LEU* 5.0 1.1 - - + -
127F LEU* 3.7 20.4 - - + +
130F ALA* 3.8 35.9 - - + +
131F ARG* 3.7 29.2 - - + +
134F MET* 3.2 39.9 - - + -
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Residues in contact with GLU 109 (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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105F PRO 3.0 19.9 + - - +
106F HIS 3.4 2.7 + - - +
108F LEU* 1.3 76.9 - - - +
110F LYS* 1.3 63.3 + - - +
112F LYS* 3.3 32.9 + - - +
113F THR* 3.1 37.2 + - + +
159F PHE* 3.8 31.7 - - + +
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Residues in contact with LYS 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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42F GLU* 4.0 21.6 + - - +
43F LEU 5.0 3.6 + - - -
106F HIS 2.9 18.6 + - - +
107F VAL* 3.8 6.3 - - - +
109F GLU* 1.3 77.6 - - - +
111F GLU* 1.3 62.8 + - - +
113F THR* 3.2 10.1 + - - +
114F ARG* 3.1 22.3 + - + +
121F SER* 4.1 23.8 + - - +
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Residues in contact with GLU 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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107F VAL 3.3 14.0 + - - +
108F LEU* 3.8 4.5 - - - +
110F LYS* 1.3 79.5 - - - +
112F LYS* 1.3 63.8 + - - +
114F ARG* 2.9 53.1 + - - +
120F SER* 2.9 25.5 + - - -
121F SER 4.6 1.6 + - - -
122F LEU* 3.8 18.8 - - + +
127F LEU* 4.2 31.8 - - + +
131F ARG* 6.0 0.9 - - - +
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Residues in contact with LYS 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 LEU 3.0 17.5 + - - +
109F GLU* 3.6 31.1 + - - +
110F LYS 3.2 0.2 - - - -
111F GLU* 1.3 78.1 - - - +
113F THR* 1.3 64.2 + - + +
114F ARG 3.3 2.5 + - - +
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Residues in contact with THR 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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109F GLU* 3.1 32.1 + - + +
110F LYS* 3.2 9.5 + - - +
111F GLU 3.2 0.4 - - - -
112F LYS* 1.3 83.0 - - + +
114F ARG* 1.3 65.4 + - - +
115F PRO* 3.3 8.3 - - - +
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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