Contacts of the helix formed by residues 121 - 135 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115Q ILE* 4.1 4.0 - - - -
116Q ASN* 3.2 16.4 - - - +
119Q PHE* 3.2 9.0 - - - +
120Q GLY* 1.3 82.7 - - - +
122Q PHE* 1.3 60.7 + - - +
123Q GLU* 3.0 26.7 + - - +
124Q LYS* 3.2 18.7 + - - +
125Q PHE* 3.1 17.0 + - - +
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Residues in contact with PHE 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Q GLY 4.4 9.9 - - - -
106Q LYS* 3.6 37.2 - - + +
107Q PRO* 3.4 36.3 - - + -
115Q ILE* 3.7 11.7 - - + -
116Q ASN* 3.4 10.0 + - - +
121Q SER* 1.3 72.2 - - - +
123Q GLU* 1.3 65.9 + - + +
125Q PHE* 2.9 29.6 + + - +
126Q LYS* 2.8 55.0 + - + +
198Q TRP* 4.3 18.8 - + + -
203Q TRP* 3.7 13.5 - + - -
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Residues in contact with GLU 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q LYS* 3.4 24.5 + - - +
121Q SER* 3.0 29.4 + - - +
122Q PHE* 1.3 87.9 + - + +
124Q LYS* 1.3 56.2 + - - +
126Q LYS* 3.4 8.6 + - - +
127Q GLU* 3.1 25.6 + - - +
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Residues in contact with LYS 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q PHE* 3.3 28.7 - - + +
121Q SER* 3.2 14.7 + - - +
123Q GLU* 1.3 76.0 - - - +
125Q PHE* 1.3 66.3 + - - +
127Q GLU* 2.6 33.1 + - - +
128Q GLU* 3.0 21.0 + - - +
64T PHE* 2.8 37.7 + - + -
65T ARG* 3.4 37.0 - - + +
67T GLY* 4.7 6.2 - - - +
69T ALA 5.4 0.2 + - - -
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Residues in contact with PHE 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q ILE* 3.6 27.6 - - + -
119Q PHE* 3.8 26.2 - + + +
121Q SER 3.1 4.9 + - - +
122Q PHE* 2.9 25.9 + + - +
124Q LYS* 1.3 78.6 - - - +
126Q LYS* 1.3 55.0 + - - +
128Q GLU* 3.2 1.9 + - - +
129Q PHE* 2.8 51.9 + + - +
144Q LEU* 3.9 33.2 - - + -
155Q ILE* 3.6 26.2 - - + -
173Q LEU* 4.5 3.4 - - + -
198Q TRP* 3.7 24.2 - + - -
203Q TRP* 3.7 18.6 - + - -
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Residues in contact with LYS 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q PHE* 2.8 36.5 + - + +
123Q GLU* 3.6 9.2 - - - +
125Q PHE* 1.3 78.4 - - - +
127Q GLU* 1.3 56.2 + - - +
130Q SER* 2.8 39.0 + - - +
195Q ASP* 5.1 6.0 + - - +
198Q TRP* 3.5 60.6 - - + +
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Residues in contact with GLU 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Q GLU 3.1 16.1 + - - +
124Q LYS* 2.6 41.5 + - - +
125Q PHE 3.2 0.2 - - - -
126Q LYS* 1.3 77.9 - - - +
128Q GLU* 1.3 56.5 + - - +
130Q SER* 4.1 2.7 - - - -
131Q GLN* 3.0 43.3 + - + +
64T PHE* 3.7 22.2 - - + -
70T GLN* 4.7 5.7 - - - +
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Residues in contact with GLU 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q PHE* 3.5 15.0 - - + -
124Q LYS 3.0 16.5 + - - +
125Q PHE 3.6 3.4 - - - +
127Q GLU* 1.3 76.0 - - - +
129Q PHE* 1.3 65.9 + - - +
131Q GLN* 3.8 2.7 - - - +
132Q ALA* 3.1 23.2 + - - +
155Q ILE* 3.7 22.9 + - + +
61T LEU* 4.0 15.2 - - - +
64T PHE* 4.2 19.8 - - + -
65T ARG* 3.0 52.6 + - - +
73T ILE* 4.2 19.1 - - + +
77T LEU* 5.2 0.2 - - - +
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Residues in contact with PHE 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Q PHE* 2.8 31.4 + + + +
128Q GLU* 1.3 73.2 - - - +
130Q SER* 1.3 61.9 + - - +
132Q ALA* 3.4 3.1 + - - +
133Q ALA* 3.1 19.4 + - - +
142Q ALA* 3.5 23.9 - - + +
143Q ILE 3.8 23.6 - - - -
144Q LEU* 3.8 7.9 - - + -
155Q ILE* 3.5 29.8 - - + +
173Q LEU* 4.0 11.2 - - + -
175Q LEU* 3.7 20.9 - - + -
197Q TRP* 3.3 33.9 - + - -
198Q TRP* 3.6 29.8 - + + -
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Residues in contact with SER 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Q LYS* 2.8 25.3 + - - +
127Q GLU* 4.1 2.9 - - - -
129Q PHE* 1.3 75.6 - - - +
131Q GLN* 1.3 62.2 + - - +
133Q ALA* 3.2 1.4 + - - +
134Q LYS* 2.9 48.9 + - - +
194Q VAL* 3.9 17.7 - - - +
195Q ASP* 4.5 2.4 + - - -
198Q TRP* 3.1 27.9 + - - -
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Residues in contact with GLN 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q GLU* 3.0 34.9 + - + +
128Q GLU* 3.8 4.5 - - - +
130Q SER* 1.3 78.8 - - - +
132Q ALA* 1.3 62.0 + - - +
134Q LYS* 4.7 14.3 - - - +
135Q ASN* 2.7 50.2 + - - +
64T PHE* 5.4 6.1 - - + -
71T ILE* 5.7 3.6 - - + +
73T ILE* 3.5 16.1 - - + +
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Residues in contact with ALA 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Q GLU 3.1 16.8 + - - +
129Q PHE 3.6 5.2 - - - +
131Q GLN* 1.3 77.6 - - - +
133Q ALA* 1.3 62.4 + - - +
135Q ASN 3.3 0.3 + - - -
136Q VAL* 3.1 16.2 + - - +
142Q ALA* 4.4 5.8 - - + -
155Q ILE* 4.1 9.9 - - + -
156Q LEU 5.0 0.7 - - - +
157Q GLN* 3.0 29.5 - - + +
73T ILE* 3.9 18.6 - - + +
77T LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q PHE 3.1 10.1 + - - +
130Q SER 3.8 3.6 - - - +
132Q ALA* 1.3 77.0 - - - +
134Q LYS* 1.3 63.8 + - - +
135Q ASN 3.4 0.2 + - - -
136Q VAL* 3.7 6.6 + - - +
142Q ALA* 3.4 24.8 - - + +
175Q LEU* 3.5 28.0 - - + -
177Q VAL* 2.9 30.9 - - + +
190Q ARG* 3.3 3.7 + - - -
194Q VAL* 4.0 8.1 - - + -
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Residues in contact with LYS 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q SER* 2.9 26.4 + - - +
131Q GLN* 4.3 14.6 - - - +
133Q ALA* 1.3 76.4 - - - +
135Q ASN* 1.3 67.7 + - - +
136Q VAL 3.5 0.4 - - - -
190Q ARG* 3.1 24.0 + - - +
191Q GLY* 3.3 31.5 + - - +
194Q VAL* 3.5 26.0 - - + -
195Q ASP* 2.7 36.9 + - - -
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Residues in contact with ASN 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q GLN* 2.7 53.1 + - - +
132Q ALA 3.3 0.2 + - - -
133Q ALA 3.2 0.2 - - - -
134Q LYS* 1.3 84.1 - - - +
136Q VAL* 1.3 60.4 + - - +
137Q GLU 3.2 1.0 + - - -
157Q GLN* 3.2 10.9 - - - +
73T ILE* 4.1 15.7 - - + +
74T ARG* 2.7 37.2 + - + +
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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