Contacts of the helix formed by residues 121 - 135 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115P ILE* 3.7 6.7 - - - +
116P ASN* 3.2 14.1 + - - +
119P PHE* 3.1 3.9 + - - +
120P GLY* 1.3 78.9 - - - +
122P PHE* 1.3 63.3 + - - +
123P GLU* 3.7 10.9 + - - +
124P LYS* 3.4 21.0 + - - +
125P PHE* 3.1 21.0 + - - +
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Residues in contact with PHE 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P GLY 4.1 10.3 - - - -
106P LYS* 3.4 48.7 - - + +
107P PRO* 3.3 32.1 - - + -
115P ILE* 3.9 11.1 - - + +
116P ASN* 3.9 6.2 + - - +
121P SER* 1.3 71.3 - - - +
123P GLU* 1.3 74.3 + - - +
125P PHE* 3.1 22.7 + + - +
126P LYS* 2.8 55.5 + - + +
198P TRP* 4.3 3.6 - + + -
203P TRP* 3.5 29.8 - + - -
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Residues in contact with GLU 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LYS* 3.6 22.0 + - - +
121P SER* 3.3 10.0 + - - +
122P PHE* 1.3 95.2 + - - +
124P LYS* 1.3 62.6 + - - +
126P LYS* 3.3 13.9 + - + +
127P GLU* 3.0 21.7 + - - +
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Residues in contact with LYS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M PHE* 3.4 30.9 + - + -
65M ARG* 3.6 37.9 - - + +
67M GLY* 4.9 6.1 - - - +
119P PHE* 3.2 28.3 - - + +
121P SER* 3.4 12.4 + - - +
122P PHE 3.3 0.6 - - - -
123P GLU* 1.3 75.2 - - - +
125P PHE* 1.3 68.0 + - - +
127P GLU* 2.6 34.4 + - - +
128P GLU* 2.9 21.0 + - - +
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Residues in contact with PHE 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P ILE* 3.4 29.2 - - + -
119P PHE* 3.9 32.9 - + + +
121P SER 3.1 5.2 + - - +
122P PHE* 3.1 25.3 + + - +
124P LYS* 1.3 78.3 - - - +
126P LYS* 1.3 54.8 + - - +
128P GLU* 3.2 1.4 + - - +
129P PHE* 2.8 53.3 + + + +
144P LEU* 3.9 32.8 - - + -
155P ILE* 3.9 18.4 - - + -
173P LEU* 4.3 2.9 - - + -
198P TRP* 3.7 15.5 - + - -
203P TRP* 3.6 28.3 - + - -
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Residues in contact with LYS 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P PHE* 2.8 58.5 + - + +
123P GLU* 3.5 17.6 + - + +
125P PHE* 1.3 73.4 - - - +
127P GLU* 1.3 55.2 + - - +
130P SER* 2.7 39.7 + - - -
198P TRP* 3.7 55.1 - - + +
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Residues in contact with GLU 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M PHE* 3.6 22.7 - - + -
123P GLU 3.0 12.7 + - - +
124P LYS* 2.6 40.1 + - - +
126P LYS* 1.3 76.3 - - - +
128P GLU* 1.3 54.3 + - - +
130P SER* 3.7 3.0 - - - -
131P GLN* 2.7 52.1 + - + +
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Residues in contact with GLU 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M LEU* 3.6 15.1 - - - +
64M PHE* 3.3 29.5 - - + -
65M ARG* 2.8 47.2 + - - +
73M ILE* 3.9 14.6 - - + +
77M LEU* 4.9 1.9 - - - +
119P PHE* 3.5 11.3 - - + -
124P LYS* 2.9 14.3 + - + +
125P PHE* 3.7 4.7 - - - +
127P GLU* 1.3 79.4 - - - +
129P PHE* 1.3 57.8 + - - +
131P GLN* 3.9 3.6 - - - +
132P ALA* 3.0 28.9 + - - +
155P ILE* 3.7 19.8 + - + +
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Residues in contact with PHE 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P PHE* 2.8 39.6 + + + +
128P GLU* 1.3 73.1 - - - +
130P SER* 1.3 57.8 + - - +
132P ALA* 3.4 3.5 + - - +
133P ALA* 3.0 23.7 + - - +
142P ALA* 3.4 25.0 - - + +
143P ILE* 3.8 3.4 - - - -
144P LEU* 3.7 27.4 - - + -
155P ILE* 3.5 24.4 - - + +
173P LEU* 4.1 13.5 - - + -
175P LEU* 3.6 24.9 - - + -
197P TRP* 3.5 29.6 - + - -
198P TRP* 3.8 25.4 - + + -
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Residues in contact with SER 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LYS 2.7 24.5 + - - -
127P GLU* 3.9 3.6 - - - -
129P PHE* 1.3 73.2 - - - +
131P GLN* 1.3 60.7 + - - +
133P ALA* 3.5 1.0 + - - +
134P LYS* 2.9 54.4 + - - +
194P VAL* 3.0 30.7 - - - +
195P ASP* 3.8 4.3 + - - -
198P TRP* 4.1 11.0 + - - -
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Residues in contact with GLN 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M PHE* 5.8 3.6 - - + -
73M ILE* 3.9 15.5 - - + +
127P GLU* 2.7 42.3 + - + +
128P GLU* 4.0 4.9 - - - +
130P SER* 1.3 72.3 + - - +
132P ALA* 1.3 65.5 + - - +
134P LYS* 3.8 26.4 - - - +
135P ASN* 2.9 48.8 + - - +
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Residues in contact with ALA 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M ILE* 3.9 11.4 - - + +
77M LEU* 3.8 27.1 - - + -
128P GLU 3.0 18.4 + - - +
129P PHE 3.6 4.9 - - - +
131P GLN* 1.3 78.9 - - - +
133P ALA* 1.3 61.9 + - - +
136P VAL* 3.3 9.2 + - - +
142P ALA* 4.3 4.9 - - + -
155P ILE* 4.0 12.6 - - + -
156P LEU 5.1 0.7 - - - +
157P GLN* 2.9 29.9 - - + +
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Residues in contact with ALA 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE 3.0 13.1 + - - +
130P SER 3.8 4.7 - - - +
132P ALA* 1.3 77.0 - - - +
134P LYS* 1.3 62.2 + - - +
135P ASN 3.4 0.2 + - - -
136P VAL* 3.5 11.7 + - - +
142P ALA* 3.4 24.2 - - + +
175P LEU* 3.6 25.4 - - + -
177P VAL* 3.5 19.1 - - + +
190P ARG* 3.2 14.6 + - - -
194P VAL* 4.0 5.4 - - + -
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Residues in contact with LYS 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P SER* 2.9 37.2 + - - +
131P GLN* 3.8 22.5 - - - +
133P ALA* 1.3 77.2 - - - +
135P ASN* 1.3 64.2 + - - +
136P VAL 3.4 0.8 - - - +
190P ARG* 3.0 25.6 + - - +
191P GLY* 3.6 28.8 - - - +
194P VAL* 4.0 14.1 - - + -
195P ASP* 2.8 31.1 + - - -
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Residues in contact with ASN 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M ILE* 3.9 20.2 - - + +
74M ARG* 2.7 39.2 + - + +
131P GLN* 2.9 49.2 + - - +
133P ALA 3.2 0.2 - - - -
134P LYS* 1.3 84.6 - - - +
136P VAL* 1.3 57.9 + - - +
137P GLU 3.4 1.0 + - - -
157P GLN* 2.8 16.6 - - - +
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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