Contacts of the helix formed by residues 103 - 113 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PRO 4.0 17.0 - - - -
42B GLU* 5.1 1.8 - - - -
43B LEU* 5.4 5.2 - - + -
99B LYS* 3.0 39.7 + - + +
100B ILE 3.7 2.0 - - - -
102B LYS* 1.3 113.4 - - + +
104B PHE* 1.3 53.0 + - - +
105B PRO* 3.2 7.4 - - - -
106B HIS* 2.7 42.4 + - + -
107B VAL* 3.0 15.9 + - + -
163B PRO* 3.1 26.7 - - + -
164B LYS 3.7 3.4 - - - -
165B PRO* 3.6 42.4 - - + -
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 2.8 21.6 + - + +
101B GLU 3.1 19.7 - - - +
102B LYS 4.6 1.1 - - - -
103B PHE* 1.3 74.7 - - - +
105B PRO* 1.3 96.1 - - + +
107B VAL* 3.7 5.5 - - - +
108B LEU* 3.2 28.4 + - - +
130B ALA* 4.8 8.7 - - + +
133B PHE* 3.6 25.1 - + + -
134B MET* 3.9 43.3 - - + -
137B THR* 4.5 18.4 - - + -
158B LEU* 4.4 12.3 - - + -
162B VAL* 4.1 13.0 - - + -
81C TYR* 3.7 24.0 - + - -
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Residues in contact with PRO 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE 3.2 7.0 - - - +
104B PHE* 1.3 121.8 - - + +
106B HIS* 1.3 57.7 + - + +
108B LEU* 3.5 2.3 + - - +
109B GLU* 3.0 29.6 + - - +
134B MET* 4.0 16.3 - - + +
158B LEU* 3.8 26.0 - - + +
159B PHE* 4.0 12.3 - - + +
162B VAL* 3.7 24.5 - - + -
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 2.7 26.3 + - + +
105B PRO* 1.3 73.9 - - + +
107B VAL* 1.3 64.6 + - - +
109B GLU* 3.9 0.6 - - - +
110B LYS* 3.1 26.7 + - - +
159B PHE* 2.8 66.9 - + + -
162B VAL* 2.7 25.6 + - + +
163B PRO 3.4 17.9 - - - -
164B LYS* 3.4 32.1 - - + +
165B PRO* 5.0 6.3 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.1 19.5 - - + -
99B LYS 4.5 1.1 - - - +
100B ILE* 4.1 19.7 - - + +
103B PHE* 3.0 27.7 + - + +
104B PHE* 3.7 9.4 - - - +
106B HIS* 1.3 78.8 - - - +
108B LEU* 1.3 59.4 + - - +
110B LYS* 4.0 4.3 - - - +
111B GLU* 3.2 22.9 + - - +
121B SER* 6.1 0.2 - - - -
122B LEU* 3.3 38.8 - - + +
130B ALA* 4.4 12.6 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE 3.2 14.4 + - - +
105B PRO 3.9 3.4 - - - +
107B VAL* 1.3 77.2 - - + +
109B GLU* 1.3 58.6 + - - +
111B GLU* 3.5 4.0 + - - +
112B LYS* 3.0 28.8 + - - +
122B LEU* 5.2 0.2 - - + -
127B LEU* 4.0 15.0 - - + -
130B ALA* 3.8 30.7 - - + +
131B ARG* 4.0 24.5 - - + +
134B MET* 3.4 49.1 - - + -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PRO 3.0 10.3 + - - +
106B HIS 4.3 0.4 - - - +
107B VAL 3.5 0.2 - - - -
108B LEU* 1.3 76.9 - - - +
110B LYS* 1.3 62.1 + - - +
112B LYS* 3.4 21.4 + - - +
113B THR* 3.2 41.3 + - + +
159B PHE* 3.4 42.6 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 4.4 15.4 + - - -
43B LEU 4.8 6.3 + - - -
106B HIS 3.1 21.5 + - - +
107B VAL* 4.0 4.7 - - - +
109B GLU* 1.3 74.0 - - - +
111B GLU* 1.3 67.0 + - - +
113B THR* 3.5 7.3 + - - -
114B ARG* 3.1 26.3 + - + +
118B GLU* 4.6 15.0 - - - -
121B SER* 3.9 24.1 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL 3.2 15.8 + - - +
108B LEU* 3.8 6.5 - - - +
110B LYS* 1.3 78.2 - - - +
112B LYS* 1.3 64.1 + - - +
114B ARG* 3.1 53.1 + - - +
120B SER* 2.8 26.5 + - - -
121B SER 4.5 2.1 + - - -
122B LEU* 4.3 13.3 - - + +
127B LEU* 4.1 30.9 - - + +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU 3.0 18.6 + - - +
109B GLU* 3.5 27.2 + - - +
110B LYS 3.2 0.2 - - - -
111B GLU* 1.3 78.9 - - - +
113B THR* 1.3 62.5 + - + +
114B ARG 3.7 1.7 + - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 3.2 36.9 + - + +
110B LYS* 3.7 7.2 + - - -
112B LYS* 1.3 83.2 - - + +
114B ARG* 1.3 62.9 + - - +
115B PRO* 3.3 8.8 - - - +
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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