Contacts of the helix formed by residues 117 - 137 (chain P) in PDB entry 2IMW
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 ASP 117 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P ILE* 4.1 10.1 - - - -
115P VAL* 3.9 5.4 - - - +
116P ARG* 1.3 82.8 - - - +
118P TYR* 1.3 59.2 + - - +
119P ARG* 3.2 20.9 + - - +
120P GLU* 3.1 34.8 + - - +
121P ALA* 3.0 23.7 + - - +
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Residues in contact with TYR 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P MET 4.5 1.7 + - - -
2P ILE* 4.0 18.8 - - + +
117P ASP* 1.3 75.3 - - - +
119P ARG* 1.3 56.3 + - - +
121P ALA* 3.4 6.3 - - + +
122P TYR* 2.8 32.1 + - - +
144P ILE* 3.6 31.0 - - + -
145P SER* 3.2 15.1 - - - -
146P LYS* 3.0 35.3 + - - +
165P VAL* 3.6 25.4 - - + +
166P ILE 4.1 3.4 + - - -
167P ASP* 3.8 27.1 - - + -
168P ASP* 3.9 13.6 + - - -
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Residues in contact with ARG 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P ARG* 6.0 1.2 - - - +
117P ASP* 3.2 15.9 + - - +
118P TYR* 1.3 77.3 - - - +
120P GLU* 1.3 87.7 + - - +
122P TYR* 3.5 6.0 + - - +
123P ASN* 3.1 53.1 + - - +
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Residues in contact with GLU 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P LYS 4.8 2.3 - - - +
115P VAL* 3.7 22.3 - - + +
116P ARG* 3.3 53.9 + - - +
117P ASP* 3.1 14.4 + - - +
119P ARG* 1.3 102.2 + - - +
121P ALA* 1.3 61.2 + - - +
123P ASN* 3.4 10.3 + - - +
124P LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P ILE* 4.1 12.6 - - + -
4P LEU* 4.0 1.2 - - - +
111P ILE* 4.2 5.8 - - + -
115P VAL* 4.1 9.3 - - + +
117P ASP 3.0 16.3 + - - +
118P TYR* 3.4 18.2 - - + +
119P ARG 3.3 0.2 - - - -
120P GLU* 1.3 73.8 - - - +
122P TYR* 1.3 60.4 + - - +
124P LEU* 3.2 4.6 + - - +
125P GLY 2.9 25.1 + - - -
144P ILE* 3.4 32.5 - - + +
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Residues in contact with TYR 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P TYR 2.8 20.5 + - - +
119P ARG* 3.6 7.0 - - - +
121P ALA* 1.3 70.4 - - - +
123P ASN* 1.3 63.7 + - - +
125P GLY 3.1 1.7 + - - -
126P LEU* 2.9 54.5 + - + +
144P ILE* 3.8 8.9 - - - +
163P ILE* 3.4 57.7 + - + +
164P LYS* 4.9 1.6 - - - -
165P VAL* 4.0 18.4 - - + -
505P EDO 3.6 43.4 + - - +
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Residues in contact with ASN 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P ARG* 3.1 42.2 + - - +
120P GLU* 3.6 12.4 - - - +
122P TYR* 1.3 83.6 - - - +
124P LEU* 1.3 56.4 + - - +
126P LEU* 3.1 17.2 + - - +
127P GLU* 3.0 27.1 + - - +
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Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P LEU* 4.3 4.3 - - + -
95P TYR* 3.7 33.2 - - + +
111P ILE* 3.8 32.8 - - + -
114P LYS* 4.6 8.3 - - + -
115P VAL* 4.1 19.5 - - + -
120P GLU 2.9 20.9 + - - +
121P ALA 3.6 4.9 - - - +
123P ASN* 1.3 73.4 - - - +
125P GLY* 1.3 57.4 + - - +
127P GLU* 3.4 15.2 + - - +
128P ILE* 3.0 38.2 + - + +
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Residues in contact with GLY 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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4P LEU* 3.8 14.7 - - - +
121P ALA 2.9 14.2 + - - -
122P TYR 3.1 5.6 + - - -
124P LEU* 1.3 74.9 - - - +
126P LEU* 1.3 62.4 + - - +
128P ILE* 3.9 2.1 - - - +
129P LYS* 3.1 29.1 + - - +
142P VAL* 3.9 11.2 - - - +
163P ILE* 3.6 16.4 - - - -
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Residues in contact with LEU 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 TYR* 2.9 47.1 + - + +
123P ASN* 3.1 17.0 + - - +
125P GLY* 1.3 75.0 - - - +
127P GLU* 1.3 64.2 + - - +
129P LYS* 3.4 9.8 + - + +
130P ASN* 3.0 36.8 + - - +
163P ILE* 3.8 18.6 - - + +
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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
----------------------------------------------------------
95P TYR* 3.4 29.4 + - + +
123P ASN 3.0 13.0 + - - +
124P LEU* 3.4 21.7 + - + +
126P LEU* 1.3 75.4 - - - +
128P ILE* 1.3 55.8 + - - +
130P ASN* 3.3 9.7 + - - +
131P LYS* 2.9 31.9 + - + +
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Residues in contact with ILE 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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4P LEU* 3.8 30.1 - - + -
6P VAL* 4.2 11.2 - - + -
92P LEU* 3.6 25.4 - - + -
95P TYR* 3.8 43.5 - - + -
109P LEU* 4.4 8.1 - - + -
124P LEU* 3.0 29.5 + - + +
125P GLY* 3.9 5.4 - - - +
126P LEU 3.3 0.2 - - - -
127P GLU* 1.3 75.3 - - - +
129P LYS* 1.3 62.5 + - - +
131P LYS* 3.2 7.1 + - - +
132P ILE* 3.0 38.5 + - + +
142P VAL* 5.0 3.1 - - + -
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Residues in contact with LYS 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 GLY 3.1 22.5 + - - +
126P LEU* 3.4 12.1 + - + +
128P ILE* 1.3 74.9 - - - +
130P ASN* 1.3 60.2 + - - +
132P ILE* 3.4 2.1 + - - +
133P LEU* 3.0 30.4 + - - +
138P ILE 4.7 1.2 - - - +
139P THR* 5.4 1.3 - - - +
140P VAL* 3.1 32.4 + - + +
142P VAL* 3.7 17.7 - - + -
161P ASN* 2.8 30.4 + - - -
162P GLY 2.9 34.5 - - - +
163P ILE* 4.2 15.5 - - + -
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Residues in contact with ASN 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 3.0 30.4 + - - +
127P GLU* 3.5 8.2 - - + +
129P LYS* 1.3 77.4 - - - +
131P LYS* 1.3 58.3 + - - +
133P LEU* 3.4 9.0 + - - +
134P GLU* 3.0 43.5 + - - +
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Residues in contact with LYS 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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91P LEU* 4.6 17.7 - - + -
95P TYR* 3.2 32.1 - - + +
127P GLU* 2.9 19.7 + - + +
128P ILE* 3.6 4.7 - - - +
130P ASN* 1.3 77.2 - - - +
132P ILE* 1.3 58.8 + - + +
134P GLU* 3.5 4.5 + - + +
135P LYS* 3.0 60.2 + - + +
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Residues in contact with ILE 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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6P VAL* 4.2 4.0 - - + -
88P ILE* 3.9 37.7 - - + -
91P LEU* 4.6 14.1 - - + -
92P LEU* 4.0 11.7 - - + -
128P ILE* 3.0 36.3 + - + +
129P LYS* 4.0 3.6 - - - +
131P LYS* 1.3 78.0 - - + +
133P LEU* 1.3 57.4 + - - +
136P GLU* 2.9 26.0 + - + +
137P LYS 3.3 4.3 + - - -
138P ILE* 3.5 28.0 + - + +
140P VAL* 4.1 26.7 - - + -
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Residues in contact with LEU 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 LYS 3.0 18.1 + - - +
130P ASN* 3.8 8.5 - - - +
131P LYS 3.3 0.2 - - - -
132P ILE* 1.3 76.8 - - - +
134P GLU* 1.3 59.8 + - + +
137P LYS* 2.9 53.4 + - + +
138P ILE 3.5 9.0 + - - +
139P THR* 3.7 31.4 - - + -
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Residues in contact with GLU 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 ASN* 3.0 31.1 + - - +
131P LYS* 4.1 4.4 - - + +
132P ILE 3.3 0.2 - - - -
133P LEU* 1.3 81.3 - - + +
135P LYS* 1.3 60.4 + - + +
137P LYS* 2.6 31.9 + - - +
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Residues in contact with LYS 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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91P LEU* 3.8 30.7 - - + -
131P LYS* 3.0 51.4 + - + +
134P GLU* 1.3 78.3 - - + +
136P GLU* 1.3 69.9 + - + +
137P LYS* 4.7 2.8 + - - -
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Residues in contact with GLU 136 (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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18P VAL* 3.9 14.4 - - - +
84P VAL* 4.0 9.1 - - - +
87P ARG* 2.8 56.4 + - + +
88P ILE* 3.9 22.9 - - + -
91P LEU* 4.5 8.5 - - + +
132P ILE 2.9 11.2 + - - +
135P LYS* 1.3 90.4 - - + +
137P LYS* 1.3 75.0 + - - +
138P ILE* 3.4 20.5 + - + +
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Residues in contact with LYS 137 (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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14P GLN* 3.8 7.1 + - - -
18P VAL* 3.4 26.8 - - + +
132P ILE 3.3 0.4 + - - -
133P LEU* 2.9 47.4 + - + +
134P GLU* 2.6 30.2 + - - +
135P LYS 4.7 3.2 + - - -
136P GLU* 1.3 80.5 - - - +
138P ILE* 1.3 58.2 + - - +
139P THR* 5.4 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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