Contacts of the helix formed by residues 137 - 154 (chain A) in PDB entry 5X6E
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP 4.9 0.9 - - - +
136A ILE* 1.3 88.4 - - - +
138A GLY* 1.3 57.1 + - - +
139A LYS 3.7 0.2 + - - -
140A LEU* 3.8 4.6 + - - +
141A GLY* 2.9 28.4 + - - -
216A ARG 4.9 3.6 + - - -
217A TYR* 3.6 49.2 + - + +
17C T 5.0 0.2 - - - -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE 3.4 11.3 - - - +
135A SER 4.5 4.4 + - - -
136A ILE 3.3 2.9 - - - +
137A ASN* 1.3 83.7 - - - +
139A LYS* 1.3 60.9 + - - -
142A SER* 3.2 16.6 + - - -
139B LYS* 5.6 6.7 - - - +
17C T 3.4 11.4 - - - -
18D G 6.0 1.7 + - - -
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY* 1.3 71.3 - - - -
140A LEU* 1.3 60.6 + - - +
141A GLY 3.1 2.5 - - - -
142A SER* 2.9 12.1 + - - +
143A ILE* 2.8 33.1 + - - +
179A GLY* 3.4 45.3 + - - +
180A ILE* 4.1 18.2 - - + +
189A ILE* 5.4 1.6 - - + -
135B SER* 3.7 20.1 + - - +
136B ILE 5.7 0.6 + - - -
138B GLY* 5.1 11.5 - - - +
17C T 2.8 19.2 + - - +
18C G 2.5 42.1 + - - +
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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
----------------------------------------------------------
137A ASN 4.3 4.0 - - - +
138A GLY 3.4 0.2 - - - -
139A LYS* 1.3 78.8 - - - +
141A GLY* 1.3 56.7 + - - +
143A ILE* 3.6 1.7 + - - +
144A CYS* 3.2 44.6 + - - -
189A ILE* 3.9 30.5 - - + +
192A LYS* 4.0 24.2 - - + +
193A LEU* 4.8 11.4 - - + -
213A TYR* 5.3 7.4 - - - +
217A TYR* 4.5 26.0 - - + +
16C A 5.7 5.4 - - - +
17C T 3.5 19.9 + - - +
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 4.5 10.1 - - - +
134A PHE* 5.0 0.3 - - - -
137A ASN* 2.9 30.2 + - - +
138A GLY 4.3 0.2 - - - -
140A LEU* 1.3 76.0 - - - +
142A SER* 1.3 52.9 + - - +
144A CYS* 3.2 8.8 + - - +
145A GLY* 2.6 33.1 + - - -
217A TYR* 4.3 17.8 - - - +
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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
----------------------------------------------------------
133A ASP 4.7 0.8 + - - -
134A PHE* 3.4 52.0 + - - -
138A GLY 3.2 16.2 + - - -
139A LYS* 2.9 19.0 + - - +
141A GLY* 1.3 74.1 - - - +
143A ILE* 1.3 59.7 + - - +
145A GLY* 3.1 1.4 + - - -
146A GLN* 3.0 27.7 + - - +
178A SER* 4.1 14.1 - - - -
179A GLY 4.6 3.5 + - - -
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Residues in contact with ILE 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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139A LYS 2.8 19.0 + - - +
140A LEU 3.8 5.4 - - - +
142A SER* 1.3 74.7 - - - +
144A CYS* 1.3 58.5 + - - +
145A GLY 3.2 0.3 + - - -
146A GLN* 3.3 6.3 + - + +
147A LEU* 2.9 51.7 + - + +
174A LEU* 4.4 14.3 - - + +
178A SER* 3.5 27.6 - - - +
180A ILE* 3.7 18.8 - - + -
186A VAL* 4.7 14.4 - - + -
189A ILE* 3.8 29.2 - - + -
190A ILE* 4.1 13.5 - - + -
193A LEU* 4.4 2.9 - - + -
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Residues in contact with CYS 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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140A LEU* 3.2 31.5 + - - +
141A GLY 3.2 7.4 + - - +
143A ILE* 1.3 75.3 - - - +
145A GLY* 1.3 65.1 + - - +
147A LEU* 4.2 3.8 - - - -
148A LEU* 3.2 22.9 + - - +
193A LEU* 4.6 9.0 - - - -
213A TYR* 4.2 21.5 - - - -
214A LEU* 3.8 32.6 - - + +
217A TYR* 3.9 23.6 - - + -
218A ALA* 4.4 3.4 - - - +
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Residues in contact with GLY 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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133A ASP* 6.1 0.7 - - - -
134A PHE* 3.9 12.8 - - - -
141A GLY 2.6 19.2 + - - -
142A SER 3.1 5.1 + - - -
144A CYS* 1.3 72.8 - - - +
146A GLN* 1.3 62.0 + - - +
148A LEU* 3.1 6.8 + - - +
149A ILE* 3.1 29.5 + - - +
218A ALA* 4.1 16.2 - - - -
221A LEU* 4.4 3.7 - - - +
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Residues in contact with GLN 146 (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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59A ASN 5.6 0.2 - - - +
60A LEU 5.3 0.7 - - - +
61A GLN* 5.7 1.6 - - - -
62A TYR* 5.6 2.9 - - - -
130A LYS* 3.2 24.8 + - - -
134A PHE* 4.2 5.2 - - + -
142A SER 3.0 14.4 + - - +
143A ILE* 3.8 7.2 - - - +
145A GLY* 1.3 70.6 - - - +
147A LEU* 1.3 58.2 + - - +
149A ILE* 2.9 10.4 + - - +
150A LEU* 2.7 66.3 + - + +
174A LEU* 4.7 11.2 - - + +
177A SER* 2.7 46.2 + - - +
178A SER* 4.5 3.4 - - - +
301A GSH 4.2 10.8 + - - +
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Residues in contact with LEU 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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143A ILE* 2.9 32.3 + - + +
144A CYS* 4.0 9.6 - - - +
146A GLN* 1.3 75.9 - - - +
148A LEU* 1.3 51.9 - - - +
150A LEU* 4.0 8.9 - - + +
151A THR* 2.3 39.3 + - - +
164A ILE* 5.3 0.3 - - - +
174A LEU* 4.7 23.1 - - + -
190A ILE* 4.8 0.4 - - + -
193A LEU* 3.7 30.7 - - + -
198A VAL 6.1 0.7 - - - +
199A ILE* 4.1 21.3 - - + -
206A PHE* 4.8 12.8 - - + -
214A LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A CYS 3.2 12.5 + - - +
145A GLY 3.1 8.8 + - - +
146A GLN 3.1 0.6 - - - -
147A LEU* 1.3 74.4 - - - +
149A ILE* 1.3 67.0 + - - +
151A THR* 3.2 6.7 + - - -
152A TYR* 3.0 54.1 + - + -
211A LEU* 4.1 9.2 - - + -
214A LEU* 3.7 41.7 - - + +
215A LYS* 3.7 20.0 - - - +
218A ALA* 4.2 9.0 - - + +
221A LEU* 4.2 10.5 - - + -
222A ASP* 4.2 14.1 - - + +
225A PHE* 4.1 13.9 - - + -
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Residues in contact with ILE 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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126A TYR* 3.5 12.3 - - + +
130A LYS* 3.3 30.5 - - - +
134A PHE* 4.9 1.6 - - + -
145A GLY 3.1 17.2 + - - +
146A GLN* 2.9 19.5 + - - +
148A LEU* 1.3 75.6 - - + +
150A LEU* 1.3 63.0 + - - +
152A TYR* 3.2 8.5 + - - +
153A VAL* 3.1 23.8 + - + +
221A LEU* 3.5 28.9 - - + -
225A PHE* 4.0 18.8 - - + -
301A GSH 3.4 35.7 - - - +
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Residues in contact with LEU 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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62A TYR* 4.2 8.3 - - + -
146A GLN* 2.7 44.8 + - - +
147A LEU* 4.1 8.3 - - + +
149A ILE* 1.3 71.8 - - - +
151A THR* 1.3 60.5 + - - +
152A TYR 3.4 0.3 + - - -
154A TYR* 3.3 46.7 - - + +
163A LYS* 3.9 0.3 + - - -
164A ILE* 3.6 22.4 - - + +
166A LEU* 4.1 13.7 - - + -
169A LEU* 3.7 33.7 - - + -
174A LEU* 4.3 16.4 - - + -
301A GSH 4.1 8.1 - - - +
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Residues in contact with THR 151 (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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147A LEU* 2.3 27.5 + - - +
148A LEU* 3.4 10.0 - - - -
149A ILE 3.2 0.2 - - - -
150A LEU* 1.3 77.4 - - - +
152A TYR* 1.3 61.9 + - + +
162A ILE* 3.5 36.2 - - + +
163A LYS* 3.1 20.2 + - - +
164A ILE* 4.0 11.9 - - - +
208A VAL* 5.9 0.9 - - - +
211A LEU* 4.5 22.4 - - + -
214A LEU* 4.2 7.3 - - + +
236A LEU* 3.7 18.9 - - + +
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Residues in contact with TYR 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 LEU* 3.0 50.0 + - + +
149A ILE 3.2 0.6 + - - -
151A THR* 1.3 76.3 - - - +
153A VAL* 1.3 60.5 + - - +
154A TYR 3.1 2.0 - - - -
155A GLY* 2.6 29.3 + - - -
211A LEU* 4.5 11.9 - - + +
215A LYS* 2.4 40.2 + - - -
222A ASP* 4.3 2.0 - - - -
225A PHE* 3.5 32.5 - + + -
232A THR* 3.2 15.0 - - + +
233A TRP* 3.1 51.4 + + - -
236A LEU* 4.2 18.9 - - + +
237A ASN* 3.3 6.1 + - - -
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Residues in contact with VAL 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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64A LYS* 3.8 33.4 + - + +
149A ILE* 3.1 18.6 - - + +
152A TYR* 1.3 76.9 - - - +
154A TYR* 1.3 82.3 + - + +
155A GLY* 4.6 0.2 - - - -
225A PHE* 4.1 10.7 - - + -
229A CYS* 6.4 0.9 - - - -
232A THR* 3.7 17.7 + - + +
301A GSH 4.1 49.4 - - + +
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Residues in contact with TYR 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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45A ILE* 3.5 33.0 - - + +
62A TYR* 3.3 32.8 - + - +
63A TYR 4.3 3.6 + - - -
64A LYS* 3.4 31.2 - - + +
150A LEU* 3.3 47.5 + - + +
152A TYR 3.1 1.0 - - - -
153A VAL* 1.3 94.4 - - + +
155A GLY* 1.3 68.1 + - - +
156A LYS* 4.7 0.2 - - - +
163A LYS* 3.1 18.9 - - - +
164A ILE* 5.7 0.2 - - + -
165A THR* 4.1 12.5 + - - +
166A LEU* 3.5 24.9 - - + -
301A GSH 4.0 3.9 + - - -
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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