Contacts of the helix formed by residues 105 - 122 (chain F) in PDB entry 4Q9U
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 GLU 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104F ASN* 1.3 72.5 - - - +
106F GLU* 1.3 59.8 + - - +
107F SER 3.2 2.0 - - - -
108F PHE* 3.1 16.2 - - + +
109F ALA* 3.0 24.4 + - - +
142F ALA* 2.8 35.4 - - + +
143F VAL* 3.6 19.1 - - + +
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Residues in contact with GLU 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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104F ASN* 3.3 6.9 - - + -
105F GLU* 1.3 77.5 - - - +
107F SER* 1.3 60.3 + - - +
109F ALA* 3.0 9.1 + - - +
110F ARG* 2.4 62.9 + - + +
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Residues in contact with SER 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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99F VAL 4.7 2.8 - - - +
100F TYR* 3.6 8.6 - - - +
101F ASP* 3.0 34.3 + - - -
104F ASN* 2.9 26.5 + - - +
106F GLU* 1.3 77.2 - - - +
108F PHE* 1.3 68.2 + - - +
110F ARG* 3.5 7.2 + - - +
111F ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 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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100F TYR* 3.2 46.4 - + - -
101F ASP 2.9 26.5 - - - -
104F ASN 3.0 18.4 - - - -
105F GLU* 3.1 15.3 - - + +
107F SER* 1.3 85.5 + - - +
109F ALA* 1.3 57.3 + - - +
111F ALA* 3.1 8.0 + - - +
112F LYS* 2.9 26.0 + - - +
142F ALA* 6.2 0.4 - - + -
143F VAL* 3.5 46.2 - - + -
148F ALA* 4.9 7.9 - - + -
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Residues in contact with ALA 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 GLU 3.0 12.0 + - - +
106F GLU* 3.0 24.0 + - - +
108F PHE* 1.3 76.7 - - - +
110F ARG* 1.3 69.7 + - - +
112F LYS* 2.9 26.2 + - + +
113F ASN* 3.0 11.8 + - - +
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Residues in contact with ARG 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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80F GLU* 5.3 12.8 - - - -
106F GLU* 2.4 68.8 + - + +
107F SER* 3.9 6.7 - - - +
109F ALA* 1.3 81.7 + - - +
111F ALA* 1.3 57.3 + - - +
113F ASN* 3.4 33.6 + - - +
114F TRP* 2.8 55.0 + - + +
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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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98F VAL* 3.6 26.0 - - + -
99F VAL 4.7 3.4 - - - +
100F TYR* 4.4 12.3 - - + -
107F SER 2.9 14.5 + - - +
108F PHE* 3.2 14.8 - - - +
110F ARG* 1.3 77.2 - - - +
112F LYS* 1.3 54.1 + - - +
114F TRP* 3.4 5.2 - - - +
115F VAL* 2.9 37.1 + - + +
130F LEU* 4.5 9.2 - - + -
151F TYR* 6.0 0.2 - - - -
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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 PHE 2.9 10.2 + - - +
109F ALA* 2.9 17.0 + - - +
111F ALA* 1.3 72.1 - - - +
113F ASN* 1.3 66.1 + - - +
114F TRP 3.0 4.4 + - - -
115F VAL* 3.2 4.7 + - - +
116F LYS* 2.9 50.3 + - + +
151F TYR* 3.2 46.1 + - + +
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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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109F ALA 3.0 6.0 + - - +
110F ARG* 3.7 26.8 - - - +
112F LYS* 1.3 83.9 - - - +
114F TRP* 1.3 58.1 + - + +
116F LYS* 3.6 21.9 - - - +
117F GLU* 2.9 34.5 + - - +
120F ARG* 6.1 1.1 - - - +
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Residues in contact with TRP 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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79F GLN 5.9 2.9 - - - -
80F GLU* 5.7 3.6 - - - -
83F HIS* 3.2 45.1 - + + -
86F ALA* 5.8 4.9 - - + -
98F VAL* 4.5 10.8 - - + -
110F ARG* 2.8 48.3 + - + +
111F ALA* 3.4 10.8 - - - +
112F LYS 3.0 0.2 - - - -
113F ASN* 1.3 75.5 - - - +
115F VAL* 1.3 60.3 + - - +
116F LYS 3.1 0.9 - - - -
117F GLU* 3.1 41.4 + - + +
118F LEU* 3.0 33.0 + - + +
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Residues in contact with VAL 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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98F VAL* 3.6 28.5 - - + -
111F ALA 2.9 18.1 + - - +
112F LYS* 3.9 4.0 - - - +
114F TRP* 1.3 75.1 - - - +
116F LYS* 1.3 59.1 + - + +
118F LEU* 4.1 7.9 - - + -
119F GLN* 3.0 52.2 + - + +
128F ILE* 4.9 12.3 - - + -
130F LEU* 5.3 5.2 - - + -
151F TYR* 5.6 9.2 - - + +
155F ASN* 6.1 4.3 - - + -
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Residues in contact with LYS 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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112F LYS* 2.9 35.2 + - + +
113F ASN* 3.6 23.8 - - - +
114F TRP 3.1 0.2 - - - -
115F VAL* 1.3 78.9 - - + +
117F GLU* 1.3 56.9 + - - +
119F GLN* 5.2 2.9 - - - -
120F ARG* 2.8 66.6 + - - +
151F TYR* 4.0 19.2 + - - +
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Residues in contact with GLU 117 (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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83F HIS* 4.4 14.7 - - - +
84F SER* 3.9 18.5 + - - -
113F ASN* 2.9 15.3 + - - +
114F TRP* 3.2 43.8 - - + +
116F LYS* 1.3 78.5 - - - +
118F LEU* 1.3 58.1 + - + +
120F ARG* 3.6 4.3 + - - +
121F GLN* 3.1 45.8 + - + +
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Residues in contact with LEU 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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24F VAL* 5.8 3.8 - - + -
87F PRO* 6.5 1.6 - - + -
96F ALA* 4.7 15.9 - - + -
97F ILE 4.5 5.6 - - - +
98F VAL* 4.0 26.2 - - + -
114F TRP* 3.0 18.0 + - + +
115F VAL* 3.4 8.7 + - + +
117F GLU* 1.3 72.7 - - + +
119F GLN* 1.3 68.1 + - + +
120F ARG 3.1 2.8 + - - -
121F GLN* 4.7 1.1 - - - +
122F ALA* 3.5 39.0 + - + +
126F ILE* 5.0 7.4 - - + -
128F ILE* 4.3 21.8 - - + -
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Residues in contact with GLN 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 VAL* 3.0 40.6 + - + +
116F LYS* 5.2 1.8 - - - -
118F LEU* 1.3 72.7 - - - +
120F ARG* 1.3 67.5 + - + +
122F ALA 4.8 2.1 + - - +
128F ILE* 4.1 21.9 - - + +
155F ASN* 3.8 33.2 + - - +
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Residues in contact with ARG 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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113F ASN* 6.1 1.2 - - - +
116F LYS* 2.8 69.9 + - - +
117F GLU* 3.6 6.4 + - - +
118F LEU 3.1 0.4 - - - -
119F GLN* 1.3 85.1 - - + +
121F GLN* 1.3 71.8 - - + +
122F ALA 3.5 4.3 + - - +
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Residues in contact with GLN 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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87F PRO* 4.8 17.7 - - + +
117F GLU* 3.1 31.5 + - + +
118F LEU* 3.5 1.1 + - - +
120F ARG* 1.3 85.3 - - + +
122F ALA* 1.3 65.2 + - - +
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Residues in contact with ALA 122 (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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87F PRO* 5.7 10.1 - - + -
118F LEU* 3.5 28.5 + - + +
119F GLN 4.8 1.6 + - - +
120F ARG 3.5 5.3 + - - +
121F GLN* 1.3 82.9 - - - +
123F SER* 1.3 74.3 - - - +
124F PRO* 3.7 3.1 - - - +
126F ILE* 4.3 15.0 - - + -
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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