Contacts of the helix formed by residues 115 - 136 (chain N) in PDB entry 2D2C
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 GLU 115 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLN* 4.8 9.7 - - - +
110N PHE* 3.3 28.5 - - + +
111N LYS 3.4 11.2 - - - +
112N LYS* 2.5 40.9 - - - +
114N ARG* 1.3 78.7 + - - +
116N LEU* 1.3 61.8 + - - +
117N THR 3.4 0.9 - - - -
118N TRP* 3.0 7.6 - - - +
119N ILE* 3.0 29.2 + - + +
112O PRO* 3.8 24.0 - - + +
116O ASN* 5.1 4.5 - - - +
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Residues in contact with LEU 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.6 22.0 - - + -
18A ALA* 5.5 10.8 - - + +
114N ARG* 3.3 27.4 - - + -
115N GLU* 1.3 76.3 - - - +
117N THR* 1.3 78.4 + - + +
118N TRP 2.5 15.9 + - - -
119N ILE* 2.6 12.5 + - + +
120N SER* 2.6 30.4 + - - +
205N MET* 3.5 21.5 - - + -
208N LYS* 5.6 0.9 - - - -
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Residues in contact with THR 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N PHE* 5.5 0.2 - - - -
114N ARG* 3.2 44.5 + - + +
116N LEU* 1.3 78.5 - - + +
118N TRP* 1.3 54.4 + - - +
120N SER* 3.3 2.2 + - - -
202N HIS* 2.7 37.9 + - - -
205N MET* 3.1 48.0 - - + -
206N ILE* 3.9 20.4 - - - +
302N HEM 4.1 12.2 - - - +
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Residues in contact with TRP 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N VAL* 5.6 0.6 - - - +
104N VAL* 3.7 6.2 - - + +
105N TYR* 5.5 1.8 - - - +
110N PHE* 3.4 39.2 - + + -
115N GLU 3.0 14.4 - - - +
116N LEU 2.5 3.8 + - - -
117N THR* 1.3 75.7 + - - +
119N ILE* 1.3 81.6 + - + +
121N GLY* 2.8 6.1 + - - -
122N VAL* 2.7 36.7 + - + +
302N HEM 3.3 50.8 - - + +
108O LEU* 2.9 50.0 - - + -
109O ILE* 3.2 29.6 - - - -
111O VAL* 4.1 8.7 - - + -
112O PRO* 3.3 24.0 - - + -
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Residues in contact with ILE 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N GLU* 3.0 11.1 + - + +
116N LEU* 2.6 17.3 + - + +
118N TRP* 1.3 93.7 - - + +
120N SER* 1.3 69.1 + - - +
122N VAL* 2.6 16.9 + - - +
123N ILE* 2.7 20.4 - - + +
109O ILE* 3.2 44.9 - - + +
112O PRO* 4.7 4.3 - - + -
113O PHE* 4.8 16.8 - - + -
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Residues in contact with SER 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116N LEU* 2.6 20.1 + - - +
117N THR 3.3 8.1 + - - -
119N ILE* 1.3 73.1 - - - +
121N GLY* 1.3 74.2 + - - -
123N ILE* 2.7 27.7 + - - +
124N LEU* 2.9 12.0 + - - +
198N PHE* 4.2 19.7 - - - -
201N LEU* 4.8 6.7 - - - -
202N HIS* 3.4 7.4 + - - -
205N MET* 3.3 24.3 - - - +
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Residues in contact with GLY 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N THR 3.5 0.2 + - - -
118N TRP 2.8 11.1 + - - -
120N SER* 1.3 82.9 + - - +
122N VAL* 1.3 65.4 + - - +
124N LEU* 2.6 26.2 + - - +
202N HIS* 3.4 26.7 - - - -
302N HEM 2.9 17.8 - - - +
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Residues in contact with VAL 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N TRP* 2.7 43.5 + - + +
119N ILE* 2.6 21.2 + - - +
121N GLY* 1.3 66.7 - - - -
123N ILE* 1.3 60.4 + - + +
125N ALA* 2.5 36.9 + - + +
126N VAL* 3.3 10.6 + - + +
302N HEM 3.7 10.6 - - + +
105O PRO* 4.4 22.4 - - + +
108O LEU* 3.6 17.9 - - + -
109O ILE* 4.1 12.3 - - + -
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Residues in contact with ILE 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N ILE* 2.7 45.1 - - + +
120N SER* 2.7 16.6 + - - +
122N VAL* 1.3 76.7 - - + +
124N LEU* 1.3 63.2 + - - +
126N VAL* 2.7 25.9 + - + +
127N ILE* 3.1 24.4 + - + +
198N PHE* 3.3 40.2 - - + -
109O ILE* 4.6 4.5 - - + -
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Residues in contact with LEU 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N SER 2.9 6.0 + - - +
121N GLY* 2.6 22.8 + - - +
123N ILE* 1.3 73.0 - - - +
125N ALA* 1.3 49.3 + - - +
127N ILE* 3.8 5.5 + - - +
128N THR* 2.6 36.8 + - - -
195N ILE* 3.6 9.8 - - + +
198N PHE* 3.5 28.7 - - + +
199N MET* 3.5 27.1 - - + +
202N HIS* 3.2 44.4 - - + +
302N HEM 3.6 36.3 - - + +
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Residues in contact with ALA 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N MET* 4.0 16.6 - - + -
121N GLY 3.0 2.2 + - - -
122N VAL* 2.5 22.6 + - + +
124N LEU* 1.3 71.8 - - - +
126N VAL* 1.3 58.8 + - + +
128N THR* 3.6 1.1 - - - -
129N VAL* 2.9 37.0 + - + +
302N HEM 3.4 21.3 - - + +
1201O CLA 3.9 21.3 - - + +
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Residues in contact with VAL 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N VAL* 4.1 11.9 - - + +
123N ILE* 2.7 23.4 + - + +
125N ALA* 1.3 70.9 - - + +
127N ILE* 1.3 55.9 + - + +
129N VAL* 3.3 6.0 + - + +
130N SER* 2.3 49.0 + - - +
105O PRO* 4.7 19.1 - - + -
1201O CLA 4.8 33.2 - - + -
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Residues in contact with ILE 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N ILE* 3.1 27.5 + - + +
124N LEU* 3.8 9.2 - - - +
126N VAL* 1.3 80.1 - - + +
128N THR* 1.3 66.5 + - - +
130N SER* 2.7 20.8 + - - -
131N PHE* 2.8 35.4 + - + -
191N LEU* 3.9 14.5 - - + +
194N LEU* 3.2 26.0 - - + +
195N ILE* 3.2 39.3 - - + +
198N PHE* 4.5 5.6 - - + -
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Residues in contact with THR 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N MET* 3.8 25.2 - - + +
94N VAL* 4.5 20.2 - - + +
97N MET* 3.8 22.0 - - + -
124N LEU 2.6 21.5 + - - -
125N ALA 3.6 4.9 - - - -
127N ILE* 1.3 76.7 - - - +
129N VAL* 1.3 67.2 + - - +
131N PHE* 2.8 30.2 + - - +
132N GLY 3.7 1.6 + - - -
195N ILE* 4.5 3.0 - - - +
301N HEM 4.8 4.8 - - + +
302N HEM 3.5 17.7 - - - +
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Residues in contact with VAL 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N VAL* 5.3 10.5 - - + -
97N MET* 4.7 12.3 - - + -
125N ALA* 2.9 34.8 + - + +
126N VAL* 3.6 6.3 - - + +
128N THR* 1.3 73.0 - - - +
130N SER* 1.3 63.7 + - - +
132N GLY* 3.1 13.3 + - - -
133N VAL* 3.7 18.9 + - + +
80O TYR* 5.1 12.3 - - + +
81O LEU* 5.0 11.4 - - + -
1201O CLA 4.3 37.2 - - + +
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Residues in contact with SER 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N VAL* 2.3 41.3 + - - +
127N ILE* 2.7 14.4 + - - -
129N VAL* 1.3 70.3 - - - +
131N PHE* 1.3 52.6 + - - -
132N GLY 3.3 0.3 + - - -
133N VAL* 3.7 12.1 + - - +
134N THR* 2.5 33.3 + - - +
191N LEU* 3.4 17.6 - - - +
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Residues in contact with PHE 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N PHE* 4.7 4.5 - + - -
127N ILE* 2.8 42.2 + - + -
128N THR* 2.8 21.5 + - - +
130N SER* 1.3 70.6 - - - +
132N GLY* 1.3 65.3 + - - +
134N THR* 2.8 6.8 + - - -
187N HIS* 2.7 56.3 + + - -
191N LEU* 3.7 8.0 - - + +
192N PRO* 3.4 33.7 - - + -
195N ILE* 3.8 19.5 - - + -
301N HEM 3.4 55.0 - + + -
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Residues in contact with GLY 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N THR 3.7 2.0 + - - -
129N VAL 3.1 8.5 + - - -
131N PHE* 1.3 76.1 - - - +
133N VAL* 1.3 50.6 + - - +
134N THR 2.4 20.1 + - - -
136N TYR* 2.5 38.3 + - - -
301N HEM 4.3 17.5 - - - +
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Residues in contact with VAL 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N VAL* 3.7 17.2 + - + +
130N SER* 3.8 13.0 - - - +
132N GLY* 1.3 69.6 - - - +
134N THR* 1.3 61.9 + - + +
136N TYR* 3.8 9.1 - - - +
137N SER* 3.9 2.8 + - - -
148N VAL* 3.1 30.3 - - + +
151N VAL* 4.0 28.5 - - + -
183N TYR* 4.0 11.3 - - + +
81O LEU* 3.8 28.5 - - + -
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Residues in contact with THR 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N SER 2.5 25.6 + - - +
131N PHE* 2.8 10.6 + - - -
132N GLY 2.4 9.6 + - - -
133N VAL* 1.3 70.0 - - + +
135N GLY* 1.3 67.4 - - - +
137N SER* 2.7 22.7 + - - -
138N LEU* 3.4 8.7 + - - +
183N TYR* 3.4 52.5 - - + +
186N ALA* 4.1 10.8 - - + -
187N HIS* 3.7 13.5 + - - +
191N LEU* 4.5 3.9 - - + +
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Residues in contact with GLY 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N GLY 2.9 4.0 + - - -
134N THR* 1.3 76.7 - - - +
136N TYR* 1.3 53.2 + - - +
137N SER 2.8 1.7 + - - -
138N LEU* 2.8 48.6 + - - +
187N HIS* 2.9 24.9 + - - -
301N HEM 3.0 21.7 - - - +
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Residues in contact with TYR 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N GLY* 2.5 33.7 + - - +
133N VAL* 3.8 4.9 - - - +
135N GLY* 1.3 68.4 - - - +
137N SER* 1.3 57.0 + - - +
139N PRO* 4.3 3.5 - - - +
141N ASP* 4.0 5.9 - - - +
143N VAL* 3.3 20.0 - - + +
144N GLY* 3.5 17.7 - - - -
147N ALA* 4.2 13.7 - - + -
148N VAL* 4.5 13.9 - - + -
301N HEM 3.6 23.8 - - + +
76O LEU 3.2 24.6 + - - -
77O PRO* 3.7 18.7 + - + +
78O GLU* 3.7 37.6 + - + -
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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
------------------------------------------------------------
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