Contacts of the helix formed by residues 121 - 135 (chain F) in PDB entry 1P7G
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 121 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F ILE* 3.7 9.4 - - - +
116F ASN* 4.6 7.0 - - - +
119F PHE 2.6 11.7 + - - +
120F GLY* 1.3 74.6 - - - +
122F PHE* 1.3 64.3 + - - +
123F GLU* 3.6 13.4 + - - +
124F LYS* 3.0 25.3 + - - +
125F PHE* 3.3 20.6 + - - +
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Residues in contact with PHE 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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105F GLY 4.3 6.7 - - - -
106F LYS* 4.0 22.9 - - + -
107F PRO* 3.2 46.9 - - + -
115F ILE* 4.0 9.4 - - + +
116F ASN* 4.6 5.1 + - - +
121F SER* 1.3 73.2 - - - +
123F GLU* 1.3 74.9 + - - +
125F PHE* 3.8 19.1 - + - -
126F LYS* 2.7 54.9 + - + +
198F TRP* 4.5 13.5 - + + -
203F TRP* 3.7 26.9 - + - -
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Residues in contact with GLU 123 (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 LYS* 4.8 11.6 + - - +
121F SER* 3.3 10.3 - - - +
122F PHE* 1.3 99.9 + - - +
124F LYS* 1.3 60.3 + - - +
126F LYS* 3.7 27.3 + - - +
127F GLU* 3.0 26.9 + - - +
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Residues in contact with LYS 124 (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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119F PHE* 3.0 28.9 - - + +
121F SER* 3.0 15.2 + - - +
123F GLU* 1.3 76.9 - - - +
125F PHE* 1.3 61.9 + - - +
127F GLU* 2.8 27.9 + - - +
128F GLU* 3.1 19.2 + - - +
64G PHE* 3.0 36.2 + - + +
65G ARG* 3.5 35.7 - - + +
67G GLY* 4.4 9.3 - - - +
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Residues in contact with PHE 125 (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 ILE* 3.8 22.0 - - + -
119F PHE* 3.6 32.9 - + + +
121F SER 3.3 15.6 + - - +
122F PHE* 3.7 21.8 - + - +
124F LYS* 1.3 75.7 - - - +
126F LYS* 1.3 61.9 + - - +
127F GLU 3.0 2.0 - - - -
128F GLU* 3.0 2.6 + - - +
129F PHE* 2.8 46.4 + + - +
144F LEU* 3.8 33.7 - - + -
155F ILE* 3.6 30.5 - - + -
173F LEU* 4.4 4.7 - - + -
198F TRP* 3.7 25.6 - + - -
203F TRP* 4.2 3.1 - + - -
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Residues in contact with LYS 126 (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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122F PHE* 2.7 43.0 + - + +
123F GLU* 3.7 31.6 + - - +
124F LYS 3.3 0.2 - - - -
125F PHE* 1.3 79.5 - - - +
127F GLU* 1.3 52.1 + - - +
129F PHE 4.0 0.2 - - - -
130F SER* 2.6 36.4 + - - +
198F TRP* 3.6 42.4 - - + +
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Residues in contact with GLU 127 (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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123F GLU 3.0 13.1 + - - +
124F LYS* 2.8 39.0 + - - +
125F PHE 3.0 0.2 - - - -
126F LYS* 1.3 74.9 - - - +
128F GLU* 1.3 56.8 + - - +
130F SER* 3.4 3.3 + - - -
131F GLN* 2.6 61.7 + - + +
64G PHE* 3.0 20.8 - - + -
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Residues in contact with GLU 128 (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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119F PHE* 4.0 2.0 - - + -
124F LYS 3.1 6.0 + - - +
125F PHE* 3.0 5.3 + - - +
127F GLU* 1.3 81.2 - - - +
129F PHE* 1.3 57.9 + - - +
131F GLN* 4.3 2.7 - - - -
132F ALA* 2.9 34.3 + - - +
155F ILE* 3.4 34.9 + - + +
61G LEU* 3.8 17.7 - - - +
64G PHE* 3.3 31.6 - - + -
65G ARG* 3.1 42.7 + - - +
73G ILE* 3.8 17.6 - - + +
77G LEU* 4.8 0.2 - - - +
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Residues in contact with PHE 129 (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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125F PHE* 2.8 38.2 + + + +
128F GLU* 1.3 73.8 - - - +
130F SER* 1.3 55.9 + - - +
132F ALA* 3.9 0.7 - - - +
133F ALA* 3.0 27.5 + - - +
142F ALA* 3.2 25.1 - - + +
143F ILE* 3.5 29.6 - - - -
144F LEU* 3.6 7.6 - - + -
155F ILE* 3.4 16.2 - - + +
173F LEU* 3.9 14.1 - - + -
175F LEU* 3.5 19.5 - - + -
197F TRP* 3.3 32.1 - + - -
198F TRP* 3.3 33.0 - + + -
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Residues in contact with SER 130 (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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126F LYS* 2.6 23.4 + - - +
127F GLU* 3.4 4.7 + - - -
129F PHE* 1.3 76.5 - - - +
131F GLN* 1.3 62.3 + - - +
132F ALA 3.1 2.0 - - - -
134F LYS* 2.9 48.6 + - - +
194F VAL* 3.6 27.6 - - - -
195F ASP* 5.2 1.3 - - - -
198F TRP* 4.0 12.5 + - - -
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Residues in contact with GLN 131 (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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127F GLU* 2.6 56.1 + - + +
128F GLU* 3.9 3.1 - - - +
130F SER* 1.3 74.0 + - - +
132F ALA* 1.3 57.8 + - - +
134F LYS* 5.0 3.6 - - - -
135F ASN* 2.6 47.1 + - - +
64G PHE* 3.9 11.7 - - - -
70G GLN* 5.2 6.2 + - - -
71G ILE* 3.8 20.6 - - - +
73G ILE* 3.2 15.3 - - + +
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Residues in contact with ALA 132 (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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128F GLU 2.9 18.1 + - - +
129F PHE 3.9 2.7 - - - +
131F GLN* 1.3 78.1 - - - +
133F ALA* 1.3 64.8 + - - +
134F LYS 3.3 0.4 - - - -
135F ASN 3.4 5.2 + - - -
136F VAL* 2.9 19.5 - - - +
142F ALA* 4.4 4.3 - - + -
155F ILE* 4.2 8.7 - - + -
156F LEU 5.4 0.2 - - - +
157F GLN* 3.3 12.0 - - + +
73G ILE* 3.2 27.6 - - + +
77G LEU* 3.7 16.4 - - + -
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Residues in contact with ALA 133 (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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129F PHE 3.0 20.5 + - - +
130F SER 3.7 4.5 - - - +
132F ALA* 1.3 76.9 - - - +
134F LYS* 1.3 58.4 + - - +
136F VAL* 3.2 6.9 - - - +
142F ALA* 3.3 23.3 - - + +
175F LEU* 3.8 23.3 - - + -
177F VAL* 3.0 26.4 - - + +
190F ARG* 3.1 11.4 + - - -
194F VAL* 3.9 8.5 - - + -
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Residues in contact with LYS 134 (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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130F SER* 2.9 27.9 + - - +
131F GLN* 4.6 4.0 - - - +
133F ALA* 1.3 73.0 - - - +
135F ASN* 1.3 62.2 + - - +
136F VAL 3.1 9.9 + - - -
190F ARG* 3.1 25.7 + - + +
191F GLY* 3.3 32.5 + - - +
194F VAL* 3.6 24.9 - - + -
195F ASP* 2.6 32.4 + - - -
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Residues in contact with ASN 135 (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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131F GLN* 2.6 37.6 + - - +
132F ALA 3.4 6.0 + - - +
134F LYS* 1.3 78.6 - - - +
136F VAL* 1.3 55.6 + - - +
137F GLU 3.2 0.7 + - - -
157F GLN* 3.4 2.8 - - - +
73G ILE* 3.5 23.4 - - + +
74G ARG* 2.7 45.3 + - + +
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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