Contacts of the helix formed by residues 121 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.8 3.3 - - - +
116A ASN* 3.6 14.4 - - - +
119A PHE* 3.2 5.2 - - - +
120A GLY* 1.3 81.5 - - - +
122A PHE* 1.3 63.7 + - - +
123A GLU* 3.5 16.4 + - - +
124A LYS* 3.0 24.8 + - - +
125A PHE* 3.0 21.3 + - - +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY 3.9 11.9 - - - -
106A LYS* 4.0 29.8 - - + -
107A PRO* 3.3 38.6 - - + -
115A ILE* 3.8 10.5 - - + -
116A ASN* 3.7 8.0 + - - +
121A SER* 1.3 73.6 - - - +
123A GLU* 1.3 71.5 + - + +
125A PHE* 3.0 14.8 + + - +
126A LYS* 2.8 68.6 + - + +
198A TRP* 4.8 2.9 - + + -
203A TRP* 3.7 23.3 - + - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS* 3.3 26.0 + - - -
121A SER* 3.5 13.9 - - - +
122A PHE* 1.3 93.5 + - - +
124A LYS* 1.3 56.5 + - - +
126A LYS* 3.2 12.1 + - + +
127A GLU* 2.9 26.9 + - - +
208E ARG* 4.1 27.4 - - - +
222E LEU* 6.0 2.2 - - + -
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.0 30.5 - - + +
121A SER* 3.0 19.2 + - - +
123A GLU* 1.3 73.8 - - - +
125A PHE* 1.3 64.1 + - - +
127A GLU* 3.2 27.7 + - - +
128A GLU* 3.1 21.3 + - - +
64D PHE* 2.9 41.3 + - + -
65D ARG* 3.3 31.9 - - + +
66D LYS 5.4 0.2 - - - -
67D GLY* 4.6 6.2 - - - +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.6 29.8 - - + -
119A PHE* 3.7 28.7 - + + +
121A SER 3.0 12.8 + - - +
122A PHE* 3.0 18.7 + + - +
124A LYS* 1.3 76.5 - - - +
126A LYS* 1.3 60.8 + - - +
128A GLU* 3.4 1.7 + - - +
129A PHE* 2.9 46.7 + + + +
144A LEU* 4.0 29.6 - - + -
155A ILE* 3.8 24.9 - - + -
173A LEU* 4.4 8.1 - - + -
198A TRP* 3.9 13.9 - + - -
203A TRP* 3.8 24.2 - + - -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 2.8 56.0 + - + +
123A GLU* 3.5 12.8 - - + +
125A PHE* 1.3 74.2 - - + +
127A GLU* 1.3 60.7 + - - +
130A SER* 2.8 37.9 + - - +
198A TRP* 3.6 57.4 - - + +
222E LEU* 4.1 28.5 - - + +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 2.9 13.7 + - - +
124A LYS* 3.2 29.5 + - - +
125A PHE 3.2 0.2 - - - -
126A LYS* 1.3 76.4 - - - +
128A GLU* 1.3 58.2 + - - +
130A SER* 4.8 2.2 - - - -
131A GLN* 2.9 51.2 + - + +
64D PHE* 3.1 34.6 - - + -
70D GLN* 4.9 3.3 - - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.3 15.0 - - + -
124A LYS 3.1 12.3 + - - +
125A PHE 3.9 1.1 - - - +
127A GLU* 1.3 79.8 - - - +
129A PHE* 1.3 57.3 + - - +
131A GLN* 3.9 3.2 - - - +
132A ALA* 2.9 30.5 + - - +
155A ILE* 3.7 25.5 + - + +
61D LEU* 3.5 16.9 - - - +
64D PHE* 3.9 19.5 - - + -
65D ARG* 2.6 55.7 + - - +
73D ILE* 4.3 16.7 - - + +
77D LEU* 5.0 0.5 - - - +
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 2.9 36.7 + + + +
128A GLU* 1.3 76.1 - - - +
130A SER* 1.3 66.0 + - - +
132A ALA* 3.2 4.3 + - - +
133A ALA* 3.0 18.9 + - - +
142A ALA* 3.3 25.9 - - + +
143A ILE* 3.6 27.6 - - - -
144A LEU* 3.7 7.4 - - + -
155A ILE* 3.3 21.9 - - + +
173A LEU* 3.9 12.1 - - + -
175A LEU* 3.5 28.3 - - + -
197A TRP* 3.6 23.1 - + - -
198A TRP* 3.8 22.0 - + + -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS* 2.8 26.0 + - - +
127A GLU* 4.1 2.0 - - - -
129A PHE* 1.3 74.4 - - - +
131A GLN* 1.3 65.6 + - - +
133A ALA* 3.3 1.9 + - - +
134A LYS* 2.9 40.0 + - - +
194A VAL* 3.8 18.6 - - - +
195A ASP* 4.6 4.6 + - - -
198A TRP* 2.8 33.1 + - - -
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 2.9 42.2 + - + +
128A GLU* 3.9 4.3 - - - +
130A SER* 1.3 78.2 - - - +
132A ALA* 1.3 67.7 + - - +
134A LYS* 3.4 25.6 + - - +
135A ASN* 3.0 43.1 + - - +
64D PHE* 5.6 3.4 - - + -
71D ILE* 6.6 0.2 - - + -
73D ILE* 4.0 14.4 - - + -
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU 2.9 18.5 + - - +
129A PHE 3.5 4.7 - - - +
131A GLN* 1.3 76.1 - - - +
133A ALA* 1.3 61.8 + - - +
135A ASN 3.3 4.9 + - - -
136A VAL* 3.4 8.5 + - - +
142A ALA* 4.4 5.8 - - + -
155A ILE* 4.1 11.9 - - + -
156A LEU 5.0 0.2 - - - +
157A GLN* 2.8 31.0 - - + +
73D ILE* 4.0 8.2 - - + +
77D LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE 3.0 9.4 + - - +
130A SER 3.6 7.2 - - - +
131A GLN 3.2 0.2 - - - -
132A ALA* 1.3 77.7 - - - +
134A LYS* 1.3 61.5 + - - +
135A ASN 3.3 0.5 + - - -
136A VAL* 3.6 11.6 + - - +
142A ALA* 3.4 25.9 - - + +
175A LEU* 3.8 23.8 - - + -
177A VAL* 3.7 17.5 - - + +
190A ARG* 3.6 13.0 - - - -
194A VAL* 3.9 9.4 - - + -
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A SER* 2.9 19.2 + - - +
131A GLN* 3.4 26.3 + - - +
133A ALA* 1.3 76.3 - - - +
135A ASN* 1.3 68.8 + - - +
136A VAL 3.5 1.0 + - - +
190A ARG* 3.9 20.9 + - - +
191A GLY* 3.5 27.9 + - - -
194A VAL* 3.9 20.4 - - + -
195A ASP* 3.0 38.3 + - - -
215E ASN* 4.3 15.4 - - - +
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Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN* 3.0 41.7 + - - +
133A ALA 3.1 0.4 - - - -
134A LYS* 1.3 86.1 - - - +
136A VAL* 1.3 59.6 + - - +
157A GLN* 3.0 16.9 - - - +
73D ILE* 4.0 14.3 - - + +
74D ARG* 3.0 36.5 + - + +
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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