Contacts of the helix formed by residues 153 - 169 (chain B) in PDB entry 6FEQ
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 THR 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B THR 4.7 2.4 + - - -
152B MET* 1.3 76.8 - - - +
154B ASN* 1.3 58.6 + - + +
155B HIS* 3.7 26.9 - - + +
156B GLU* 3.0 31.3 + - - +
157B LYS* 2.7 35.8 + - - +
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Residues in contact with ASN 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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141B GLN* 5.5 0.9 + - - -
152B MET 4.1 0.4 + - - -
153B THR* 1.3 75.9 - - + +
155B HIS* 1.3 61.0 + - + +
157B LYS* 4.3 9.0 - - - +
158B ASN* 2.4 71.6 + - - +
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Residues in contact with HIS 155 (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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153B THR* 3.2 20.4 - - + -
154B ASN* 1.3 79.1 - - + +
156B GLU* 1.3 62.9 + - + +
158B ASN* 4.3 4.6 + - - +
159B GLU* 3.3 33.2 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR 4.9 0.4 - - - +
152B MET* 3.3 31.1 - - + +
153B THR* 3.0 38.0 + - - +
155B HIS* 1.3 79.0 - - + +
157B LYS* 1.3 61.6 + - - +
159B GLU* 3.5 10.7 + - - +
160B ARG* 3.3 24.6 + - - +
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Residues in contact with LYS 157 (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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144B ALA* 4.0 30.7 + - + +
145B ALA* 4.4 10.8 + - - +
148B LEU* 4.0 19.2 + - + +
149B ALA 3.1 26.9 + - - -
150B THR* 4.6 5.9 - - - +
152B MET* 3.8 31.1 + - + +
153B THR 2.7 22.3 + - - +
154B ASN* 4.1 9.2 - - - +
156B GLU* 1.3 73.9 - - - +
158B ASN* 1.3 62.7 + - - +
160B ARG* 3.3 10.1 + - - +
161B ILE* 3.2 27.6 + - + +
375B HIS* 5.6 4.2 + - - -
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Residues in contact with ASN 158 (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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137B ARG* 4.8 2.9 + - - +
141B GLN* 3.3 28.9 + - - +
154B ASN* 2.4 51.4 + - - +
155B HIS* 4.4 4.5 + - - +
157B LYS* 1.3 75.0 - - - +
159B GLU* 1.3 60.7 + - + +
161B ILE* 3.3 14.6 + - - +
162B ASN* 2.8 40.5 + - - +
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Residues in contact with GLU 159 (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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155B HIS* 3.3 22.9 + - - +
156B GLU* 3.9 9.2 - - - +
157B LYS 3.3 0.4 - - - -
158B ASN* 1.3 75.6 - - + +
160B ARG* 1.3 59.3 + - + +
162B ASN* 3.2 13.0 + - + +
163B ARG* 2.8 40.7 + - - +
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Residues in contact with ARG 160 (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* 4.7 16.5 - - + +
152B MET* 4.1 25.1 - - + +
156B GLU 3.3 15.9 - - - +
157B LYS* 3.3 8.9 + - - +
158B ASN 3.3 0.6 - - - -
159B GLU* 1.3 77.7 - - + +
161B ILE* 1.3 63.9 + - + +
163B ARG* 3.3 39.3 + - - +
164B VAL* 3.2 25.8 + - - +
201B ILE* 3.4 21.9 + - + +
202B THR* 4.1 5.7 + - - +
203B ASP* 2.5 40.0 + - - +
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Residues in contact with ILE 161 (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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137B ARG* 3.5 25.8 - - - +
140B LEU* 3.8 46.7 - - + +
141B GLN* 3.7 30.5 - - + -
144B ALA* 4.3 10.8 - - + -
157B LYS* 3.2 18.3 + - + +
158B ASN* 3.6 15.9 - - - +
159B GLU 3.3 0.2 - - - -
160B ARG* 1.3 76.4 - - + +
162B ASN* 1.3 58.4 + - - +
164B VAL* 2.9 8.2 + - - +
165B ILE* 2.8 30.4 + - + +
201B ILE* 5.0 6.5 - - + -
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Residues in contact with ASN 162 (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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137B ARG* 3.2 28.2 + - - +
158B ASN* 2.8 31.3 + - - +
159B GLU* 3.2 16.2 + - + +
161B ILE* 1.3 73.1 - - - +
163B ARG* 1.3 62.4 + - - +
165B ILE* 3.9 6.9 - - - +
166B GLN* 3.3 30.5 + - - +
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Residues in contact with ARG 163 (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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159B GLU* 2.8 26.9 + - - +
160B ARG* 3.3 43.9 - - - +
161B ILE 3.2 0.2 - - - -
162B ASN* 1.3 75.4 - - - +
164B VAL* 1.3 63.0 + - + +
166B GLN* 4.4 2.8 - - - +
167B GLU* 3.3 26.2 + - - +
203B ASP* 4.8 5.2 + - - -
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Residues in contact with VAL 164 (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* 4.6 10.8 - - + -
160B ARG 3.2 15.2 + - - +
161B ILE* 2.9 10.5 + - - +
163B ARG* 1.3 79.3 - - + +
165B ILE* 1.3 60.5 + - - +
167B GLU* 2.9 12.4 + - - +
168B LEU* 2.8 49.4 + - + +
197B GLY* 4.1 18.2 - - - +
200B LEU* 4.1 28.5 - - + +
201B ILE* 4.5 11.7 - - + -
203B ASP* 4.9 4.9 - - - +
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Residues in contact with ILE 165 (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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136B VAL* 4.2 20.6 - - + -
137B ARG* 4.1 26.7 - - - +
140B LEU* 4.8 11.9 - - + -
161B ILE 2.8 22.4 + - - +
162B ASN* 3.9 12.6 - - - +
164B VAL* 1.3 75.0 - - - +
166B GLN* 1.3 60.5 + - + +
168B LEU* 4.4 6.1 - - - +
169B GLY 3.2 4.0 + - - -
170B LEU* 3.1 62.3 + - + +
171B ASP* 3.6 10.7 - - - +
174B ALA* 3.8 24.5 - - + +
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Residues in contact with GLN 166 (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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162B ASN* 3.3 19.5 + - - +
163B ARG* 4.4 2.7 - - - +
164B VAL 3.2 0.4 - - - -
165B ILE* 1.3 80.7 - - + +
167B GLU* 1.3 63.6 + - - +
169B GLY* 3.3 10.6 + - - -
171B ASP* 3.9 21.3 - - - +
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Residues in contact with GLU 167 (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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163B ARG 3.3 21.2 + - - +
164B VAL* 2.9 11.1 + - - +
166B GLN* 1.3 80.2 - - - +
168B LEU* 1.3 64.3 + - + +
169B GLY 3.4 0.5 + - - -
200B LEU* 5.4 9.9 - - - +
227B LEU* 3.8 18.2 - - + +
230B ARG 5.6 0.2 - - - +
231B MET* 4.6 5.8 - - + +
234B GLN* 4.6 4.9 - - - +
236B ARG* 2.7 37.1 + - - -
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Residues in contact with LEU 168 (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* 5.6 3.8 - - + -
164B VAL* 2.8 31.8 + - + +
165B ILE* 4.2 4.3 - - - +
167B GLU* 1.3 77.4 - - + +
169B GLY* 1.3 62.7 + - - +
170B LEU* 4.0 23.6 - - + +
193B ARG* 3.3 43.0 + - + +
194B THR* 5.1 0.7 - - - +
196B ILE* 5.4 1.6 - - + -
197B GLY* 3.8 23.6 - - - +
200B LEU* 4.4 7.0 - - + -
227B LEU* 3.8 20.4 - - + +
231B MET* 3.7 30.5 - - + -
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Residues in contact with GLY 169 (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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165B ILE 3.2 5.9 + - - -
166B GLN* 3.3 8.6 + - - -
167B GLU 3.2 4.8 + - - -
168B LEU* 1.3 79.3 - - - +
170B LEU* 1.3 61.0 + - - +
171B ASP* 3.4 11.5 + - - -
172B LYS* 5.1 1.6 + - - +
190B GLU* 5.4 1.0 - - - +
193B ARG* 4.4 7.7 + - - -
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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
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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