Contacts of the helix formed by residues 135 - 157 (chain A) in PDB entry 3OMA
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 PHE 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET 4.3 0.4 - - - -
134A ALA* 1.3 87.6 - - + +
136A PRO* 1.4 64.8 - - - +
137A ARG* 3.3 22.7 - - - +
138A MET* 3.1 33.4 + - + -
139A ASN 3.0 6.4 + - - -
206A ILE* 4.1 12.3 - - + -
207A ASN* 2.8 42.1 + - - +
210A THR* 3.6 34.3 - - + -
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Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.5 43.8 - - - +
132A ASP* 4.0 15.7 - - + +
133A MET* 3.4 19.5 - - + +
134A ALA 3.4 5.6 - - - +
135A PHE* 1.4 86.3 - - - +
137A ARG* 1.3 73.4 + - + +
139A ASN* 3.2 9.9 + - + +
140A ASN 3.1 21.5 + - - -
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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
----------------------------------------------------------
24A THR* 4.3 13.6 - - + -
134A ALA 3.4 22.0 + - - -
135A PHE* 3.3 30.5 - - - +
136A PRO* 1.3 81.8 - - + +
138A MET* 1.3 71.4 + - - +
140A ASN* 3.4 5.6 + - - +
141A LEU* 3.1 21.5 + - - +
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 3.1 34.0 + - + +
137A ARG* 1.3 80.4 - - - +
139A ASN* 1.3 60.2 + - - +
141A LEU* 3.2 9.6 + - + +
142A SER* 2.9 28.8 + - - -
203A LEU* 3.8 50.7 - - + +
206A ILE* 3.8 26.0 - - + -
207A ASN* 4.4 3.1 - - - +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR 5.0 0.6 + - - -
26A HIS* 4.1 10.9 - - - +
29A ILE* 3.7 23.4 - - + +
121A ASN* 2.9 41.8 + - - +
133A MET* 3.4 17.8 - - + +
135A PHE 3.0 6.9 + - - +
136A PRO* 3.2 14.1 + - + +
138A MET* 1.3 75.5 - - - +
140A ASN* 1.3 61.2 + - - +
142A SER* 2.7 28.3 + - - -
143A TYR 3.3 3.6 + - - -
203A LEU 6.4 0.4 - - - -
204A GLY* 5.3 4.9 - - - -
207A ASN* 3.5 19.7 + - - +
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE 3.0 23.9 + - - +
22A MET* 3.8 12.1 - - - +
23A SER 2.8 28.6 + - - +
24A THR* 4.3 8.1 - - + -
29A ILE* 3.5 11.3 - - - +
32A LEU* 5.5 2.2 - - - +
136A PRO 3.1 12.2 + - - +
137A ARG* 3.7 8.5 - - - +
138A MET 3.3 0.4 - - - -
139A ASN* 1.3 78.1 - - - +
141A LEU* 1.3 62.1 + - - +
143A TYR* 3.3 14.6 + - - +
144A TRP* 3.3 29.2 + - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG 3.1 14.5 + - - +
138A MET* 3.2 10.7 + - + +
140A ASN* 1.3 75.3 + - - +
142A SER* 1.3 67.3 + - - +
144A TRP* 3.0 12.7 + - + +
145A LEU* 3.0 40.2 + - + +
203A LEU* 3.8 21.8 - - + -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 2.9 17.3 + - - -
121A ASN* 5.1 0.5 + - - -
138A MET 2.9 12.7 + - - -
139A ASN* 2.7 29.5 + - - -
141A LEU* 1.3 76.6 - - - +
143A TYR* 1.3 59.0 + - - +
145A LEU* 3.5 1.1 + - - -
146A TYR 3.2 10.0 + - - -
200A SER* 2.8 45.7 + - - +
203A LEU* 4.0 15.2 - - - +
204A GLY* 4.4 6.0 + - - -
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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
----------------------------------------------------------
21A PHE* 3.8 34.2 - + - -
29A ILE* 4.5 8.3 - - + -
32A LEU* 3.6 45.2 + - + +
33A TYR* 3.4 26.0 - + + -
36A THR* 2.8 21.7 + - - +
139A ASN 3.3 3.7 + - - +
140A ASN* 3.3 11.8 + - - +
141A LEU 3.2 0.6 - - - -
142A SER* 1.3 81.7 + - - +
144A TRP* 1.3 75.9 + + - +
146A TYR* 3.3 19.9 - + - +
147A VAL* 3.1 51.9 + - + +
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Residues in contact with TRP 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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21A PHE* 3.2 66.9 + + + -
22A MET* 4.8 16.5 - - + +
140A ASN* 3.3 34.2 + - - +
141A LEU* 3.0 16.5 + - + +
143A TYR* 1.3 82.9 - + - +
145A LEU* 1.3 60.1 + - - +
147A VAL* 3.4 29.8 + - + +
148A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 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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141A LEU* 3.0 33.4 + - + +
142A SER 3.9 3.4 - - - +
143A TYR 3.3 0.2 - - - -
144A TRP* 1.3 74.2 - - - +
146A TYR* 1.3 56.6 + - - +
148A ALA* 3.2 6.4 + - + +
149A GLY* 2.8 33.1 + - - -
196A LEU* 3.7 42.8 - - + +
199A ALA* 4.0 20.6 - - + -
200A SER* 4.0 6.3 - - - +
203A LEU* 3.9 27.4 - - + -
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.6 32.3 - + + -
36A THR* 3.5 33.6 + - + +
37A GLY* 3.3 22.0 + - - -
40A VAL* 3.8 1.9 - - - +
108A PHE 4.7 1.1 - - - -
109A PHE* 2.7 42.1 + + - -
113A PRO* 3.6 21.7 - - + +
142A SER 3.2 7.6 + - - +
143A TYR* 3.3 18.6 - + - +
145A LEU* 1.3 76.4 - - - +
147A VAL* 1.3 56.1 + - - +
149A GLY* 3.8 1.2 - - - -
150A THR* 2.8 49.0 + - - -
196A LEU 5.2 0.4 - - - -
197A SER* 5.3 3.1 - - - +
200A SER* 3.6 22.4 - - - +
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Residues in contact with VAL 147 (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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36A THR* 4.7 7.2 - - + -
143A TYR* 3.1 52.4 + - + +
144A TRP* 3.7 27.8 - - + +
146A TYR* 1.3 80.5 - - + +
148A ALA* 1.3 54.1 + - - +
150A THR* 3.5 7.4 + - - -
151A SER* 2.7 42.8 + - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP 2.9 18.7 + - - +
145A LEU* 3.2 9.2 + - + +
147A VAL* 1.3 73.9 - - - +
149A GLY* 1.3 63.5 + - - +
151A SER* 3.3 6.6 + - - -
152A LEU* 3.1 28.5 + - + +
196A LEU* 3.7 18.4 - - + -
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Residues in contact with GLY 149 (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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109A PHE* 3.3 13.3 - - - -
145A LEU 2.8 19.6 + - - -
148A ALA* 1.3 73.1 - - - +
150A THR* 1.3 61.6 + - - +
152A LEU 3.3 0.9 + - - -
153A ALA 3.0 19.9 + - - -
193A ALA* 3.2 20.3 - - - +
196A LEU* 3.6 21.7 - - - +
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Residues in contact with THR 150 (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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36A THR* 5.6 1.5 - - + +
40A VAL* 3.7 35.4 - - + -
43A ILE* 6.6 0.2 - - + -
105A LEU* 4.7 1.8 - - + -
109A PHE* 3.2 22.7 - - + -
146A TYR* 2.8 35.8 + - - -
147A VAL* 3.7 8.0 - - - -
149A GLY* 1.3 74.4 - - - +
151A SER* 1.3 58.1 + - - +
153A ALA* 3.3 3.8 + - - +
154A VAL* 3.0 38.6 + - + +
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 2.7 29.6 + - - +
148A ALA* 3.6 8.4 - - - -
149A GLY 3.2 0.2 - - - -
150A THR* 1.3 76.8 - - - +
152A LEU* 1.3 61.1 + - - +
154A VAL* 3.5 6.9 + - - +
155A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 152 (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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148A ALA* 3.1 16.6 + - + +
149A GLY 3.3 6.7 + - - +
151A SER* 1.3 78.4 - - - +
153A ALA* 1.3 58.5 + - - +
155A ALA* 3.2 9.1 + - + +
156A SER* 2.9 31.5 + - - -
189A LEU* 3.8 32.8 - - + +
192A PHE* 3.7 29.4 - - + -
193A ALA* 3.9 4.5 - - + +
196A LEU* 3.8 18.8 - - + -
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Residues in contact with ALA 153 (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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104A ILE* 4.4 8.7 - - + -
105A LEU* 4.2 13.2 - - + -
109A PHE* 3.7 24.2 - - + -
149A GLY 3.0 13.4 + - - +
150A THR 3.3 9.2 + - - +
152A LEU* 1.3 74.8 - - - +
154A VAL* 1.3 59.7 + - - +
156A SER* 2.6 26.5 + - - -
157A LEU* 3.8 8.1 + - - +
190A ALA* 5.2 2.2 - - - +
193A ALA* 3.4 10.4 - - + +
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Residues in contact with VAL 154 (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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40A VAL* 6.2 0.7 - - + -
43A ILE* 5.6 14.4 - - + -
105A LEU* 4.6 15.0 - - + -
150A THR* 3.0 33.0 + - + +
151A SER* 3.8 6.1 - - - +
153A ALA* 1.3 74.7 - - - +
155A ALA* 1.3 64.5 + - - +
157A LEU* 3.1 34.1 + - + +
158A PHE* 3.2 23.4 - - + -
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Residues in contact with ALA 155 (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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151A SER 2.9 18.8 + - - +
152A LEU* 3.2 13.7 + - + +
154A VAL* 1.3 76.8 - - - +
156A SER* 1.3 57.5 + - - +
158A PHE* 2.9 25.9 + - - +
159A ALA* 3.2 12.0 + - - +
189A LEU* 4.3 11.4 - - + +
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Residues in contact with SER 156 (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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152A LEU 2.9 13.1 + - - -
153A ALA* 2.6 22.6 + - - -
155A ALA* 1.3 75.6 - - - +
157A LEU* 1.3 63.9 + - - +
159A ALA* 3.4 14.0 + - - -
167A GLY* 3.2 6.5 - - - -
168A SER* 5.2 3.0 + - - -
186A SER* 2.7 46.5 + - - -
189A LEU* 3.9 9.8 - - - +
190A ALA* 4.0 12.8 - - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 6.2 0.2 - - + -
47A PHE* 3.7 30.3 - - + -
97A VAL* 3.8 35.7 - - + +
98A MET* 5.8 1.3 - - - -
101A GLY* 4.4 15.0 - - - +
105A LEU* 5.6 3.1 - - + -
153A ALA 3.9 8.7 - - - +
154A VAL* 3.1 30.6 + - + +
155A ALA 3.1 0.6 - - - -
156A SER* 1.3 83.3 + - - +
158A PHE* 1.3 77.8 + - + +
159A ALA 3.5 0.2 - - - -
166A LEU* 3.5 17.8 - - - +
167A GLY* 3.7 9.9 + - - -
168A SER 6.0 0.9 - - - +
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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