Contacts of the helix formed by residues 102 - 113 (chain F) in PDB entry 6Q2J
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 ASP 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F VAL* 5.3 3.4 - - - -
43F ASP* 4.1 8.5 - - - +
100F SER* 3.9 3.7 + - - +
101F LEU* 1.3 75.4 - - - +
103F HIS* 1.3 67.5 + - - +
104F SER* 2.6 23.4 + - - +
105F SER* 2.4 36.8 + - - -
106F TRP* 3.5 15.5 - - - -
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Residues in contact with HIS 103 (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 VAL* 3.9 28.6 - - + +
43F ASP* 4.7 6.0 + - - -
102F ASP* 1.3 77.4 - - - +
104F SER* 1.3 55.9 + - - +
106F TRP* 3.4 6.0 + - - +
107F GLU* 3.0 37.3 + - + +
151F ASN* 3.9 27.2 + - - -
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Residues in contact with SER 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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102F ASP* 2.6 28.5 + - - +
103F HIS* 1.3 79.9 - - - +
105F SER* 1.3 56.9 + - - +
107F GLU* 3.8 7.3 - - - +
108F LYS* 2.9 39.6 + - - +
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Residues in contact with SER 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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85F TRP* 3.2 38.1 + - - -
99F ARG* 5.8 1.0 + - - -
101F LEU* 4.9 1.1 - - - -
102F ASP* 2.4 32.0 + - - -
103F HIS 3.2 0.8 - - - -
104F SER* 1.3 80.2 + - - +
106F TRP* 1.3 66.2 + - - +
108F LYS* 3.2 11.3 + - - +
109F LEU* 2.9 32.7 + - - +
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Residues in contact with TRP 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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40F LEU* 4.6 8.1 - - + -
42F VAL* 5.6 0.7 - - + -
72F LEU* 6.5 0.9 - - + -
101F LEU* 3.4 37.7 - - + +
102F ASP 3.5 16.4 - - - -
103F HIS* 3.4 7.2 + - - +
105F SER* 1.3 76.2 - - - +
107F GLU* 1.3 60.5 + - - +
109F LEU* 3.8 22.3 - - + +
110F SER* 2.9 31.4 + - - -
118F LEU* 3.6 35.6 - - + +
121F VAL* 4.0 24.2 - - + -
149F PHE* 3.3 75.1 - + + -
151F ASN* 5.8 2.0 - - - +
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Residues in contact with GLU 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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103F HIS* 3.0 25.3 + - + +
104F SER* 3.9 7.6 - - - +
106F TRP* 1.3 78.9 - - - +
108F LYS* 1.3 61.8 + - - +
110F SER* 4.2 6.9 - - - +
111F VAL* 3.3 30.5 + - - +
151F ASN* 5.6 4.0 + - - -
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Residues in contact with LYS 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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81F HIS* 4.8 25.6 - - + +
85F TRP* 6.1 3.4 - - + -
104F SER* 2.9 31.5 + - - +
105F SER* 3.2 10.4 + - - +
107F GLU* 1.3 78.5 - - - +
109F LEU* 1.3 62.9 + - + +
111F VAL* 3.9 12.5 + - - +
112F ARG* 4.2 6.1 + - - +
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Residues in contact with LEU 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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72F LEU* 4.7 19.5 - - + -
80F LEU* 3.9 25.0 - - + +
81F HIS* 3.7 32.3 - - + +
85F TRP* 5.0 9.9 - - + -
101F LEU* 6.4 0.4 - - + -
105F SER 2.9 19.9 + - - +
106F TRP* 3.9 37.2 - - + +
108F LYS* 1.3 79.7 - - + +
110F SER* 1.3 63.7 + - - +
112F ARG* 3.3 17.5 + - + +
113F ASN* 3.5 9.0 + - - +
118F LEU* 3.7 17.0 - - + +
121F VAL* 5.0 4.3 - - + -
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Residues in contact with SER 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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106F TRP 2.9 20.2 + - - -
107F GLU* 3.6 9.8 + - - -
108F LYS 3.4 0.2 - - - -
109F LEU* 1.3 74.8 - - - +
111F VAL* 1.3 64.0 + - - +
112F ARG 3.4 0.2 - - - -
113F ASN* 3.3 20.4 + - - +
115F GLY* 4.7 5.2 + - - -
116F PHE 3.9 14.0 + - - +
117F PRO* 4.8 2.1 - - - +
118F LEU* 4.7 15.6 + - - -
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Residues in contact with VAL 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 GLU* 3.3 19.7 + - - +
108F LYS* 4.1 7.6 - - - +
109F LEU 3.2 0.6 - - - -
110F SER* 1.3 78.8 - - - +
112F ARG* 1.3 62.2 + - - +
113F ASN 3.1 2.3 + - - -
114F HIS* 3.7 8.0 + - - -
115F GLY 4.5 3.3 + - - -
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Residues in contact with ARG 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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78F THR* 4.3 11.8 - - + +
79F ARG* 3.4 19.2 + - - +
80F LEU* 3.7 40.8 + - + +
108F LYS 4.2 6.1 + - - +
109F LEU* 3.3 12.6 + - - +
111F VAL* 1.3 74.8 - - - +
113F ASN* 1.3 54.9 + - - +
114F HIS* 3.0 37.6 + - - -
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Residues in contact with ASN 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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74F GLY* 5.7 0.3 - - - -
75F THR* 4.7 17.5 + - - -
78F THR* 5.9 0.2 - - - -
80F LEU* 4.5 9.6 - - + +
109F LEU 3.5 6.3 + - - +
110F SER* 3.3 19.5 - - - +
111F VAL 3.1 1.6 - - - -
112F ARG* 1.3 73.5 - - - +
114F HIS* 1.3 71.3 + - - +
115F GLY 3.3 1.1 - - - -
116F PHE* 2.5 45.5 + - - +
117F PRO 3.4 3.2 + - - -
118F LEU* 3.4 40.6 - - + +
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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