Contacts of the helix formed by residues 124 - 145 (chain A) in PDB entry 2IMT
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 ASN 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 1.3 74.9 - - - +
125A TRP* 1.3 65.2 + - - +
126A GLY* 3.2 7.2 + - - -
127A ARG* 3.0 63.5 + - - +
128A VAL* 3.0 15.7 + - - +
170A TRP* 3.9 12.3 - - + -
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Residues in contact with TRP 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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78A LEU* 5.1 4.5 - - + -
124A ASN* 1.3 75.3 - - - +
126A GLY* 1.3 62.8 + - - +
128A VAL* 3.1 17.4 + - + +
129A VAL* 3.0 27.2 + - + +
170A TRP* 3.7 29.8 - + - -
171A ILE* 3.8 29.8 - - + -
174A ARG* 4.0 30.0 - - + +
176A GLY 4.1 5.8 - - - -
177A TRP* 3.8 29.4 - + - -
179A ALA* 4.1 22.5 + - + +
180A ALA* 3.9 23.3 - - + -
183A LEU* 3.7 38.4 - - + +
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.7 14.7 - - - +
86A ASN* 4.9 0.5 - - - +
89A TYR* 4.3 7.6 - - - -
124A ASN* 3.2 7.8 + - - -
125A TRP* 1.3 77.4 - - - +
127A ARG* 1.3 57.5 + - - +
129A VAL* 3.4 8.5 + - - +
130A ALA* 3.0 25.6 + - - +
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.8 20.1 + - + +
118A LEU* 3.3 27.1 + - + +
119A PHE* 3.4 24.4 - - + -
121A SER* 3.4 30.1 + - - -
122A GLY 2.9 33.5 + - - -
123A ILE 4.9 0.6 - - - -
124A ASN* 3.0 40.6 + - - +
126A GLY* 1.3 73.2 - - - +
128A VAL* 1.3 61.1 + - - +
130A ALA* 3.5 8.7 - - + +
131A LEU* 2.9 24.6 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 5.3 1.3 - - + -
119A PHE* 4.2 7.0 - - + -
123A ILE* 4.3 11.2 - - + -
124A ASN 3.0 14.3 + - - +
125A TRP* 3.4 21.3 - - + +
127A ARG* 1.3 75.6 - - - +
129A VAL* 1.3 60.7 + - - +
131A LEU* 3.2 5.5 + - - +
132A LEU* 3.1 27.1 + - + +
162A MET* 4.5 7.0 - - + -
167A ILE* 3.9 24.5 - - + -
170A TRP* 4.7 2.2 - - + -
171A ILE* 4.4 7.0 - - + -
177A TRP* 3.7 36.6 - - + -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 4.0 8.7 + - + -
78A LEU* 3.9 39.3 - - + +
81A ILE* 4.5 12.3 - - + -
82A GLY* 3.8 27.8 - - - -
85A ILE* 4.1 10.3 - - + -
86A ASN* 3.9 8.3 - - + +
125A TRP* 3.0 19.0 + - + +
126A GLY* 3.7 9.4 - - - +
128A VAL* 1.3 76.0 - - + +
130A ALA* 1.3 56.8 + - - +
132A LEU* 3.3 9.3 + - - +
133A GLY* 2.8 26.5 + - - -
183A LEU* 5.6 0.2 - - + -
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Residues in contact with ALA 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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86A ASN* 3.2 10.5 + - - +
89A TYR* 3.4 39.0 - - + -
93A PHE* 3.3 11.6 - - + -
118A LEU* 3.9 13.2 - - + -
126A GLY 3.0 11.6 + - - +
127A ARG* 3.5 10.8 - - - +
128A VAL 3.2 0.2 - - - -
129A VAL* 1.3 74.5 - - - +
131A LEU* 1.3 61.6 + - - +
133A GLY* 3.3 0.5 + - - -
134A PHE* 2.8 24.8 + - - +
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Residues in contact with LEU 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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111A PHE* 4.0 17.7 - - + -
115A ALA* 3.7 32.8 - - + -
118A LEU* 3.6 9.3 - - + +
119A PHE* 3.9 23.3 - - + -
127A ARG 2.9 12.9 + - - +
128A VAL* 3.2 8.2 + - - +
130A ALA* 1.3 77.2 - - - +
132A LEU* 1.3 63.6 + - - +
134A PHE* 3.1 7.2 + - + +
135A GLY* 3.0 19.9 + - - -
158A VAL* 4.5 14.1 - - + +
161A PHE* 4.1 10.5 - - + -
162A MET* 3.7 35.4 - - + -
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Residues in contact with LEU 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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31A THR* 5.4 0.9 - - + -
34A VAL* 4.4 11.0 - - + -
35A PHE* 3.4 35.6 - - + +
38A TYR* 3.5 37.4 - - + -
78A LEU* 3.9 28.7 - - + -
128A VAL* 3.1 16.9 + - + +
129A VAL* 3.6 9.0 - - - +
131A LEU* 1.3 75.3 - - + +
133A GLY* 1.4 55.4 + - - +
135A GLY 3.2 1.7 + - - -
136A TYR 2.9 24.9 + - - -
158A VAL* 4.1 17.3 - - + -
162A MET* 4.7 4.9 - - - -
177A TRP* 4.6 16.6 - - + -
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Residues in contact with GLY 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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38A TYR* 3.3 20.0 + - - -
42A ARG* 3.4 12.2 + - - -
86A ASN* 4.1 6.1 - - - -
93A PHE* 4.2 6.1 - - - -
129A VAL 2.8 16.5 + - - -
130A ALA 3.6 4.3 - - - -
131A LEU 3.3 0.2 - - - -
132A LEU* 1.4 68.2 - - - +
134A PHE* 1.3 59.6 + - - +
136A TYR* 3.4 3.6 - - - +
137A ARG* 2.9 32.2 + - - +
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Residues in contact with PHE 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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93A PHE* 3.5 39.6 - + + -
96A MET* 5.8 0.4 - - + -
97A LEU* 4.0 20.0 - - + -
110A TYR* 3.7 35.7 - + - -
111A PHE* 3.6 44.6 - + - -
114A ILE* 3.7 26.0 - - + -
115A ALA* 5.0 0.7 - - - -
118A LEU* 4.8 2.0 - - + -
130A ALA 2.8 19.8 + - - +
131A LEU* 3.1 12.3 + - + +
133A GLY* 1.3 71.6 - - - +
135A GLY* 1.4 54.9 + - - +
137A ARG* 3.1 2.5 + - - -
138A LEU* 2.7 39.8 + - + +
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Residues in contact with GLY 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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35A PHE* 3.8 13.2 - - - -
111A PHE* 5.0 2.5 - - - -
131A LEU 3.0 13.1 + - - -
132A LEU 3.5 3.6 - - - -
134A PHE* 1.4 79.1 - - - +
136A TYR* 1.3 55.7 + - - +
138A LEU* 3.4 3.5 + - - +
139A ALA* 2.9 32.4 + - - +
154A VAL* 3.5 18.8 - - - +
158A VAL* 4.5 7.0 - - - -
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Residues in contact with TYR 136 (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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35A PHE* 3.9 6.2 - - - -
38A TYR* 4.0 10.5 - - + -
39A VAL* 3.7 34.8 - - + -
42A ARG* 3.5 32.8 - - + -
43A HIS* 3.0 32.7 + - - -
46A GLU* 2.8 37.2 + - - -
60A MET* 3.4 36.2 - - + +
132A LEU 2.9 13.6 + - - +
133A GLY 3.4 8.3 - - - +
135A GLY* 1.3 75.7 - - - +
137A ARG* 1.3 64.6 + - + +
139A ALA* 3.3 0.4 + - - -
140A LEU* 2.9 41.9 + - + +
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Residues in contact with ARG 137 (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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42A ARG* 3.2 15.7 - - - +
46A GLU* 3.4 30.8 + - - -
50A GLU* 5.2 4.2 + - - -
55A PRO* 4.5 6.3 - - - +
90A ASP* 2.8 42.0 + - - +
93A PHE* 4.1 13.5 - - + -
94A GLN* 3.7 39.0 + - - +
97A LEU* 3.5 20.5 - - + +
133A GLY 2.9 20.4 + - - +
134A PHE 3.6 2.5 - - - +
136A TYR* 1.3 77.0 - - - +
138A LEU* 1.3 61.1 + - - +
140A LEU* 3.4 14.6 + - - +
141A HIS* 2.9 31.2 + - - +
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Residues in contact with LEU 138 (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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97A LEU* 3.7 16.7 - - + +
100A LEU* 3.0 37.2 - - + -
107A ALA* 4.0 15.5 - - + +
110A TYR* 5.3 1.1 - - + -
111A PHE* 4.0 37.7 - - + -
134A PHE* 2.7 25.9 + - + +
135A GLY 3.7 3.4 - - - +
137A ARG* 1.3 72.5 - - - +
139A ALA* 1.3 62.9 + - - +
141A HIS* 3.3 2.1 + - - +
142A VAL* 3.0 30.8 + - + +
154A VAL* 4.2 20.2 - - + -
157A PHE* 4.5 5.4 - - + -
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Residues in contact with ALA 139 (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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57A ASP* 4.1 1.1 - - - +
60A MET* 4.0 5.8 - - + -
135A GLY 2.9 18.6 + - - +
136A TYR* 3.7 4.0 - - - +
138A LEU* 1.3 75.6 - - - +
140A LEU* 1.3 62.2 + - - +
142A VAL* 3.4 6.9 - - - +
143A TYR* 3.0 25.3 + - - +
150A PHE 5.8 0.4 - - - -
151A LEU* 3.6 33.4 - - + -
154A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 140 (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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43A HIS* 4.7 0.9 - - - +
46A GLU* 3.8 13.7 - - - +
55A PRO* 3.6 30.7 - - + +
56A ALA 3.9 6.3 - - - +
57A ASP* 3.7 31.0 - - + -
60A MET* 3.7 8.2 - - + +
136A TYR* 2.9 36.1 + - + +
137A ARG* 3.8 12.3 - - - +
139A ALA* 1.3 77.9 - - - +
141A HIS* 1.3 61.4 + - - +
143A TYR* 3.3 1.9 + - - +
144A GLN* 3.0 52.3 + - + +
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Residues in contact with HIS 141 (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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97A LEU* 3.1 35.8 + - + +
98A GLN* 3.6 17.9 - - - -
100A LEU* 2.9 46.7 + - + +
101A GLN 5.8 0.4 - - - -
137A ARG 2.9 21.5 + - - +
138A LEU* 3.6 4.5 - - - +
140A LEU* 1.3 69.6 - - - +
142A VAL* 1.3 72.8 + - + +
144A GLN* 3.1 11.4 + - - -
145A HIS* 3.0 61.9 + + + +
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Residues in contact with VAL 142 (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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100A LEU* 4.1 5.8 - - + -
102A PRO* 4.4 11.6 - - + +
107A ALA* 4.6 9.6 - - + -
138A LEU* 3.0 36.2 + - + +
139A ALA* 3.4 13.9 - - - +
141A HIS* 1.3 87.2 - - + +
143A TYR* 1.3 66.6 + - + +
145A HIS* 3.2 11.9 + - - +
146A GLY 3.4 0.2 + - - -
147A LEU* 2.9 47.6 + - + +
150A PHE* 3.9 26.9 - - + -
154A VAL* 5.3 0.2 - - + -
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Residues in contact with TYR 143 (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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56A ALA* 3.6 26.2 - - + -
57A ASP* 3.5 18.4 - - + +
58A PRO* 3.3 28.6 - - + +
59A GLU* 3.6 40.6 - - + +
139A ALA 3.0 18.7 + - - +
140A LEU 3.7 2.7 - - - +
142A VAL* 1.3 78.5 - - + +
144A GLN* 1.3 68.8 + - + +
146A GLY* 2.9 16.5 + - - -
147A LEU 3.5 13.9 - - - +
148A THR* 4.3 14.9 - - + +
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Residues in contact with GLN 144 (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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55A PRO* 3.7 23.1 - - - +
56A ALA 4.5 9.2 + - - +
140A LEU* 3.0 45.9 + - + +
141A HIS* 3.1 9.6 + - - +
143A TYR* 1.3 80.7 - - + +
145A HIS* 1.3 67.4 + - + +
146A GLY 3.2 2.7 + - - -
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Residues in contact with HIS 145 (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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98A GLN* 4.3 8.9 - - - -
100A LEU 4.8 3.6 + - - -
102A PRO* 3.5 32.9 - - + +
141A HIS* 3.0 59.1 + + - +
142A VAL* 3.2 6.3 + - - +
143A TYR 3.1 0.8 - - - -
144A GLN* 1.3 87.8 + - + +
146A GLY* 1.3 58.3 + - - +
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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