Contacts of the helix formed by residues 137 - 154 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP 4.0 3.1 + - - +
136B ILE* 1.3 101.7 + - + +
138B GLY* 1.3 61.2 + - - +
140B LEU* 3.8 9.0 + - - +
141B GLY* 3.0 33.3 + - - +
216B ARG 5.2 1.4 - - - +
217B TYR* 3.9 37.4 + - + +
219B PRO* 5.6 0.3 - - - +
17D T 4.2 2.1 + - - -
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 5.1 11.3 - - - +
134B PHE 3.2 11.4 + - - +
135B SER 4.3 4.1 + - - -
136B ILE 3.5 3.2 + - - -
137B ASN* 1.3 78.9 - - - +
139B LYS* 1.3 51.8 + - - -
141B GLY 3.2 1.2 + - - -
142B SER* 2.7 38.9 + - - -
17D T 4.1 5.6 - - - -
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE 5.0 0.4 + - - -
135A SER* 2.5 36.6 + - - +
138A GLY* 5.6 7.1 - - - +
138B GLY* 1.3 68.9 - - - -
140B LEU* 1.3 56.9 - - - +
142B SER* 3.3 13.7 + - - +
143B ILE* 2.6 39.8 + - - +
179B GLY* 3.3 23.5 - - - +
180B ILE* 4.1 17.3 - - + -
189B ILE* 4.0 17.9 - - + -
17D T 3.3 34.6 + - - +
18D G 3.6 17.9 - - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN 3.9 5.6 - - - +
138B GLY 3.3 0.2 - - - -
139B LYS* 1.3 77.0 - - - +
141B GLY* 1.3 57.3 + - - +
143B ILE* 3.7 1.3 - - + +
144B CYS* 3.0 49.4 + - - -
189B ILE* 4.2 22.2 - - + +
192B LYS* 6.0 2.9 - - + -
193B LEU* 4.8 14.6 - - + -
213B TYR* 5.5 4.9 - - - +
217B TYR* 3.7 34.1 - - + +
16D T 6.2 4.3 - - - -
17D T 3.2 23.9 + - - +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASP 4.1 13.1 - - - +
134B PHE* 4.7 0.7 - - - -
137B ASN* 3.0 31.5 + - - +
138B GLY 3.5 3.8 - - - -
140B LEU* 1.3 74.4 - - - +
142B SER* 1.3 55.3 + - - +
144B CYS* 4.0 1.9 - - - +
145B GLY* 2.8 33.3 + - - -
217B TYR* 4.4 15.3 - - - +
218B ALA* 5.0 0.2 - - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.2 54.9 + - - +
138B GLY 2.7 27.5 + - - -
139B LYS* 3.1 20.9 + - - +
141B GLY* 1.3 73.8 - - - +
143B ILE* 1.3 55.9 + - - +
146B GLN* 3.1 25.1 + - - +
178B SER* 3.8 15.3 + - - -
179B GLY 5.0 0.4 - - - -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS 2.6 21.7 + - - +
140B LEU 3.7 4.0 - - - +
142B SER* 1.3 70.3 - - - +
144B CYS* 1.3 61.9 + - - +
146B GLN* 3.1 5.5 + - - +
147B LEU* 2.9 48.0 + - + +
174B LEU* 4.1 24.6 - - + +
178B SER* 3.3 19.3 - - - +
180B ILE* 4.1 18.8 - - + -
186B VAL* 4.5 11.2 - - + -
189B ILE* 3.8 36.3 - - + +
190B ILE* 4.3 4.3 - - + -
193B LEU* 4.9 5.4 - - + -
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.0 41.5 + - - +
141B GLY 4.0 0.9 - - - +
143B ILE* 1.3 79.7 - - - +
145B GLY* 1.3 63.2 + - - +
147B LEU* 3.6 4.5 - - - +
148B LEU* 3.0 25.1 + - - +
193B LEU* 4.2 19.7 - - - -
213B TYR* 4.6 9.4 - - - -
214B LEU* 3.9 24.6 - - + +
217B TYR* 4.0 28.3 - - + -
218B ALA* 4.7 1.8 - - - -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASP* 5.5 0.2 - - - -
134B PHE* 4.4 3.4 - - - -
141B GLY 2.8 22.6 + - - -
142B SER 3.9 1.1 - - - -
144B CYS* 1.3 75.0 - - - +
146B GLN* 1.3 60.7 + - - +
148B LEU* 3.3 5.2 + - - +
149B ILE* 3.2 24.9 + - - +
218B ALA* 3.7 21.9 - - - +
221B LEU* 3.6 15.5 - - - +
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.2 7.7 - - - -
130B LYS* 3.5 26.4 + - - +
134B PHE* 4.2 5.8 - - + -
142B SER 3.1 14.7 + - - +
143B ILE 3.5 7.6 - - - +
145B GLY* 1.3 74.5 - - - +
147B LEU* 1.3 63.5 + - - +
149B ILE* 3.2 14.6 + - - +
150B LEU* 3.2 58.9 + - + +
174B LEU* 3.8 20.0 - - + -
177B SER* 3.4 37.1 + - - +
178B SER* 4.5 5.4 - - - +
301B GSH 4.3 6.9 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 2.9 37.8 + - + +
144B CYS* 3.6 8.1 - - - +
146B GLN* 1.3 76.3 - - - +
148B LEU* 1.3 53.1 + - - +
150B LEU* 3.2 9.8 + - + +
151B THR* 2.7 37.4 + - - +
164B ILE* 4.8 17.6 - - + +
169B LEU* 6.5 0.2 - - + -
174B LEU* 4.3 25.1 - - + -
190B ILE* 4.9 6.7 - - + -
193B LEU* 4.2 18.8 - - + -
199B ILE* 5.1 14.8 - - + -
206B PHE* 5.1 13.7 - - + -
208B VAL* 5.8 5.6 - - + -
214B LEU* 4.4 11.2 - - + -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B CYS 3.0 17.1 + - - +
145B GLY* 3.3 6.7 + - - +
147B LEU* 1.3 75.2 - - - +
149B ILE* 1.3 65.4 + - - +
151B THR* 3.3 17.4 + - - -
152B TYR* 3.3 37.7 + - + -
211B LEU* 4.2 12.1 - - + -
214B LEU* 3.6 15.7 - - + +
215B LYS* 3.5 42.6 - - + +
218B ALA* 4.2 9.0 - - + +
221B LEU* 4.4 10.8 - - + -
222B ASP* 4.2 20.6 - - + +
225B PHE* 4.7 2.7 - - + -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 3.2 22.9 - - + +
130B LYS* 4.0 15.7 - - - -
134B PHE* 5.1 0.2 - - + -
145B GLY 3.2 16.4 - - - +
146B GLN* 3.3 21.1 - - - +
147B LEU 3.2 0.2 - - - -
148B LEU* 1.3 77.1 - - + +
150B LEU* 1.3 61.8 + - - +
152B TYR* 3.2 3.3 + - - +
153B VAL* 3.1 25.1 + - + +
221B LEU* 3.9 25.1 - - + -
225B PHE* 4.3 20.0 - - + -
301B GSH 3.5 40.4 - - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B TYR* 3.9 13.5 - - + -
146B GLN* 3.2 46.1 + - + +
147B LEU* 3.7 9.0 - - + +
149B ILE* 1.3 75.2 - - - +
151B THR* 1.3 58.3 + - - +
154B TYR* 3.0 63.3 + - + +
155B GLY* 3.8 0.2 - - - -
164B ILE* 3.9 31.3 - - + +
166B LEU* 5.2 2.0 - - + -
169B LEU* 3.9 28.7 - - + -
174B LEU* 4.8 4.9 - - + -
301B GSH 4.0 2.9 - - - +
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU 2.7 21.1 + - - -
148B LEU* 3.4 14.2 - - - -
149B ILE 3.2 0.2 - - - -
150B LEU* 1.3 77.9 - - - +
152B TYR* 1.3 58.8 + - + +
155B GLY* 3.1 23.1 - - - -
162B ILE* 3.7 26.6 - - + +
164B ILE* 4.9 5.9 - - - +
208B VAL* 3.5 25.1 - - + +
211B LEU* 4.1 29.8 - - + -
214B LEU* 5.5 1.6 - - - +
236B LEU* 4.0 7.4 - - + +
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU* 3.3 23.9 + - + -
149B ILE 3.2 7.2 + - - +
151B THR* 1.3 84.5 - - + +
153B VAL* 1.3 68.0 + - - +
154B TYR 3.4 0.2 + - - -
155B GLY 3.5 6.4 + - - +
211B LEU* 4.2 15.2 - - + +
215B LYS* 2.8 20.4 + - - -
222B ASP* 2.4 30.3 + - - -
225B PHE* 3.4 41.3 - + + -
232B THR* 3.8 21.7 - - + +
233B TRP* 3.3 24.5 + + - -
235B LYS* 5.0 2.6 + - - -
236B LEU* 3.9 39.3 - - + +
237B ASN* 4.1 3.2 + - - -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS* 3.7 40.0 + - + -
149B ILE 3.1 12.0 + - - +
152B TYR* 1.3 75.9 - - - +
154B TYR* 1.3 93.9 + - + +
155B GLY 3.9 0.3 + - - -
156B LYS* 4.6 5.0 + - - -
165B THR* 5.1 0.2 - - - +
225B PHE* 3.6 27.6 - - + -
232B THR* 4.7 7.3 - - + +
301B GSH 3.8 31.6 - - + +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.3 44.3 - - + +
62B TYR* 3.2 31.6 - + + +
64B LYS* 3.7 20.1 + - + +
150B LEU* 3.0 42.2 + - + +
153B VAL* 1.3 96.0 - - + +
155B GLY* 1.3 54.3 + - - +
156B LYS* 4.5 0.4 - - - -
164B ILE* 3.0 15.4 - - + -
165B THR* 2.4 54.5 + - + +
166B LEU* 4.9 10.8 - - + -
301B GSH 3.6 19.8 + - - -
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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