Contacts of the helix formed by residues 121 - 135 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115J ILE* 3.8 3.9 - - - +
116J ASN* 3.4 12.5 - - - +
119J PHE* 2.9 7.9 + - - +
120J GLY* 1.3 76.6 - - - +
122J PHE* 1.3 64.7 + - - +
123J GLU* 3.6 16.9 + - - +
124J LYS* 3.2 21.7 + - - +
125J PHE* 3.1 20.4 + - - +
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Residues in contact with PHE 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J GLY 4.5 7.6 - - - -
106J LYS* 3.9 32.5 - - + -
107J PRO* 3.3 27.4 - - + -
115J ILE* 3.8 10.5 - - + -
116J ASN* 3.7 7.8 + - - +
121J SER* 1.3 75.0 - - - +
123J GLU* 1.3 73.8 + - - +
125J PHE* 3.2 18.9 + + - +
126J LYS* 2.8 47.5 + - + +
198J TRP* 4.1 18.6 - + + -
203J TRP* 3.4 35.0 - + - -
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Residues in contact with GLU 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J LYS* 3.7 21.0 + - - +
121J SER* 3.2 19.9 - - - +
122J PHE* 1.3 101.3 + - + +
124J LYS* 1.3 56.7 + - - +
126J LYS* 3.5 10.7 + - + +
127J GLU* 3.1 25.5 + - - +
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Residues in contact with LYS 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J PHE* 2.8 29.8 - - + +
120J GLY* 5.2 0.2 - - - -
121J SER* 3.2 15.3 + - - +
123J GLU* 1.3 74.7 - - - +
125J PHE* 1.3 64.2 + - - +
127J GLU* 2.7 34.4 + - - +
128J GLU* 3.1 20.8 + - - +
64K PHE* 3.3 30.6 + - + -
65K ARG* 3.4 39.5 - - + +
67K GLY* 4.5 7.7 - - - +
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Residues in contact with PHE 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J ILE* 3.5 27.6 - - + -
119J PHE* 3.7 36.5 - + + +
121J SER 3.1 6.1 + - - +
122J PHE* 3.4 22.7 - + - +
124J LYS* 1.3 76.6 - - - +
126J LYS* 1.3 63.4 + - - +
128J GLU* 3.2 1.2 + - - +
129J PHE* 2.8 49.3 + + - +
144J LEU* 3.5 41.1 - - + -
155J ILE* 3.8 9.9 - - + -
173J LEU* 4.7 3.1 - - + -
198J TRP* 3.8 21.3 - + - -
203J TRP* 4.0 17.7 - + - -
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Residues in contact with LYS 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PHE* 2.8 37.1 + - + +
123J GLU* 3.8 10.5 - - + +
125J PHE* 1.3 76.8 - - - +
127J GLU* 1.3 55.8 + - - +
130J SER* 2.6 39.6 + - - +
195J ASP* 5.4 3.5 + - - +
198J TRP* 3.4 61.0 - - + +
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Residues in contact with GLU 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J GLU 3.1 14.1 + - - +
124J LYS* 2.7 39.8 + - - +
126J LYS* 1.3 76.3 - - - +
128J GLU* 1.3 65.9 + - - +
130J SER* 3.8 2.8 - - - -
131J GLN* 3.0 39.1 + - + +
64K PHE* 3.2 25.3 - - + -
70K GLN* 5.6 1.7 + - - -
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Residues in contact with GLU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J PHE* 3.6 11.4 - - + -
124J LYS 3.1 12.0 + - - +
125J PHE 3.8 1.1 - - - +
127J GLU* 1.3 80.1 - - - +
129J PHE* 1.3 62.8 + - - +
131J GLN* 3.8 3.6 - - - +
132J ALA* 3.0 25.1 + - - +
155J ILE* 3.6 23.8 + - + +
61K LEU* 3.5 19.1 - - - +
64K PHE* 3.7 18.3 - - + -
65K ARG* 2.7 54.8 + - - +
73K ILE* 3.9 20.3 - - + +
77K LEU* 4.8 1.9 - - - +
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Residues in contact with PHE 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J PHE* 2.8 38.3 + + + +
128J GLU* 1.3 74.2 - - - +
130J SER* 1.3 61.6 + - - +
132J ALA* 3.3 3.3 + - - +
133J ALA* 3.1 18.9 + - - +
142J ALA* 3.3 28.4 - - + +
143J ILE* 3.7 25.6 - - - -
144J LEU* 3.7 8.5 - - + -
155J ILE* 3.4 24.1 - - + +
173J LEU* 4.2 11.2 - - + -
175J LEU* 3.8 17.5 - - + -
197J TRP* 3.7 29.2 - + - -
198J TRP* 3.8 27.1 - + + -
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J LYS* 2.6 28.2 + - - +
127J GLU* 3.8 4.5 - - - -
129J PHE* 1.3 77.0 - - - +
131J GLN* 1.3 63.6 + - - +
133J ALA* 3.2 2.9 + - - +
134J LYS* 2.8 47.1 + - - +
194J VAL* 4.0 16.7 - - - +
195J ASP* 4.8 2.6 + - - -
198J TRP* 3.2 23.6 + - - -
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Residues in contact with GLN 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLU* 3.0 31.1 + - + +
128J GLU* 3.9 4.3 - - - +
130J SER* 1.3 77.2 - - - +
132J ALA* 1.3 60.7 + - - +
134J LYS* 3.4 33.2 - - - +
135J ASN* 2.9 57.0 + - - +
64K PHE* 6.0 3.1 - - + -
71K ILE* 6.4 0.7 - - + -
73K ILE* 3.3 13.6 - - + +
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Residues in contact with ALA 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLU 3.0 17.9 + - - +
129J PHE 3.6 4.7 - - - +
130J SER 3.2 0.2 - - - -
131J GLN* 1.3 75.5 - - - +
133J ALA* 1.3 63.1 + - - +
136J VAL* 3.3 5.0 + - - +
142J ALA* 4.2 4.7 - - + -
155J ILE* 3.9 13.5 - - + -
156J LEU 5.1 0.4 - - - +
157J GLN* 2.9 34.8 - - + +
73K ILE* 3.9 11.6 - - + +
77K LEU* 3.7 27.6 - - + -
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Residues in contact with ALA 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J PHE 3.1 9.0 + - - +
130J SER* 3.6 7.4 - - - +
132J ALA* 1.3 76.0 - - - +
134J LYS* 1.3 64.6 + - - +
135J ASN 3.2 0.7 + - - -
136J VAL* 3.3 11.3 + - - +
142J ALA* 3.4 25.0 - - + +
175J LEU* 3.8 25.1 - - + -
177J VAL* 3.8 13.4 - - + +
190J ARG* 3.1 20.7 + - - -
194J VAL* 4.1 5.6 - - + -
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Residues in contact with LYS 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J SER* 2.8 24.9 + - - +
131J GLN* 3.4 32.5 - - - +
133J ALA* 1.3 72.0 - - - +
135J ASN* 1.3 64.9 + - - +
136J VAL 4.6 0.5 - - - +
190J ARG* 3.5 21.5 + - - +
191J GLY* 3.6 25.3 - - - +
194J VAL* 3.6 27.4 - - + -
195J ASP* 2.8 34.5 + - - -
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Residues in contact with ASN 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J GLN* 2.9 49.2 + - - +
133J ALA 3.1 0.4 - - - -
134J LYS* 1.3 83.5 - - - +
136J VAL* 1.3 59.9 + - - +
137J GLU 3.3 0.9 + - - -
157J GLN* 2.8 12.4 - - - +
73K ILE* 3.9 18.7 - - + +
74K ARG* 2.8 37.0 + - + +
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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