Contacts of the strand formed by residues 164 - 178 (chain E) in PDB entry 5IXM
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 ARG 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E LYS 3.4 13.5 - - - +
150E GLN* 3.2 50.3 + - - +
151E PHE 4.5 13.5 + - - +
159E ASN* 5.1 6.9 + - - +
162E ALA* 4.4 7.8 + - + +
163E TYR* 1.3 78.6 - - - +
165E ALA* 1.3 60.0 + - - +
166E GLN* 3.7 19.7 + - + +
191E LYS 3.2 14.2 - - - +
192E PHE* 3.2 17.3 - - - -
193E THR* 2.9 22.5 + - - +
194E SER* 5.9 1.8 - - - +
195E VAL* 4.6 20.7 - - - +
114F LEU* 4.0 6.1 - - - -
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Residues in contact with ALA 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E SER* 3.6 6.9 + - - -
149E LYS* 2.9 49.3 + - + +
164E ARG* 1.3 70.1 - - - +
166E GLN* 1.3 59.9 + - - +
167E PRO* 3.8 5.2 - - - +
168E GLN* 3.8 34.1 - - + +
190E ALA* 5.3 0.2 - - + -
191E LYS 3.7 2.9 - - - +
192E PHE* 4.3 13.5 - - + -
114F LEU* 4.0 11.6 - - + +
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Residues in contact with GLN 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E SER* 3.4 26.2 + - - -
150E GLN* 3.8 18.8 + - - +
164E ARG* 4.5 22.2 + - + +
165E ALA* 1.3 75.1 - - - +
167E PRO* 1.3 64.9 - - - +
191E LYS* 2.9 33.7 + - - +
193E THR* 4.7 10.3 - - + +
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Residues in contact with PRO 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E LEU* 4.3 21.8 - - + -
147E SER 3.4 15.0 - - - +
148E SER* 4.9 4.3 - - - -
166E GLN* 1.3 88.5 + - - +
168E GLN* 1.3 61.7 + - - +
189E ALA 3.9 1.3 - - - +
190E ALA* 3.5 2.3 - - - -
191E LYS* 3.1 30.8 + - + +
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Residues in contact with GLN 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E THR 3.6 2.8 - - - +
146E LEU* 3.7 3.9 - - - +
147E SER* 2.9 41.2 + - - +
149E LYS* 3.0 43.1 + - - +
165E ALA* 3.8 18.3 - - + +
166E GLN 4.3 0.2 - - - +
167E PRO* 1.3 74.7 - - - +
169E LEU* 1.3 62.0 + - - +
170E ASP* 3.4 22.7 - - - +
188E GLN* 3.0 33.8 + - + -
189E ALA 3.5 3.8 - - - -
190E ALA* 4.2 8.3 - - + -
192E PHE* 5.9 1.5 - - - -
204E ARG* 5.2 1.7 + - - -
304E ASP* 5.4 1.7 - - - +
114F LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ALA* 4.8 4.5 - - + -
145E THR 3.3 28.5 - - - +
146E LEU* 4.1 18.8 - - + +
168E GLN* 1.3 73.0 - - - +
170E ASP* 1.3 62.6 + - - +
171E MET* 4.3 25.2 - - + +
188E GLN* 3.1 8.7 - - - +
189E ALA* 2.9 52.5 + - + +
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Residues in contact with ASP 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ASN* 4.1 1.0 - - - +
144E ALA* 3.3 3.6 - - - -
145E THR* 2.8 50.8 + - - +
147E SER* 5.4 2.8 + - - -
149E LYS* 5.0 3.8 + - - -
168E GLN* 3.4 20.1 - - - +
169E LEU* 1.3 72.7 - - - +
171E MET* 1.3 64.2 + - - +
172E ASN* 4.9 4.5 - - - +
186E TYR* 2.7 33.3 + - + +
187E GLY 3.6 1.6 - - - -
188E GLN* 2.9 19.3 + - - +
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Residues in contact with MET 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E TRP* 4.0 27.4 - - + -
143E ASN 3.5 4.5 - - - +
144E ALA* 4.1 9.9 - - + -
169E LEU* 4.3 24.7 - - + -
170E ASP* 1.3 79.3 - - - +
172E ASN* 1.3 63.8 + - - +
185E VAL 4.6 0.4 - - - -
186E TYR* 3.2 9.0 - - - -
187E GLY* 2.9 41.9 + - - +
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Residues in contact with ASN 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E TRP* 3.1 8.5 - - - +
143E ASN* 2.9 55.9 + - - +
170E ASP* 4.9 4.0 - - - +
171E MET* 1.3 80.5 + - - +
173E TYR* 1.3 60.3 + - - +
174E TYR* 3.7 27.3 + - + -
184E HIS* 3.0 23.1 + - - +
185E VAL 3.5 3.6 - - - -
186E TYR* 3.2 25.3 - - - -
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Residues in contact with TYR 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASN* 3.9 12.6 - - + -
142E TRP* 3.9 18.6 - + + -
172E ASN* 1.3 75.1 - - - +
174E TYR* 1.3 78.5 + - - +
175E LYS* 3.3 34.3 + - + +
183E MET* 6.3 2.2 - - + -
184E HIS* 3.3 5.4 - - - -
185E VAL* 2.9 53.4 + - + +
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Residues in contact with TYR 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E GLU 5.2 0.4 - - - +
141E ASN* 2.8 33.2 + - - +
143E ASN* 3.7 11.6 + - - -
172E ASN* 3.7 30.3 + - + -
173E TYR* 1.3 87.0 - - - +
175E LYS* 1.3 66.3 + - - +
176E ASN* 5.6 4.3 - - - +
183E MET 3.7 3.6 - - - +
184E HIS* 3.3 38.3 + + + -
30F ARG* 3.3 56.8 - - - +
34F GLN* 4.6 11.0 - - - -
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Residues in contact with LYS 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASN* 6.1 0.7 - - - +
173E TYR* 3.3 29.8 + - + +
174E TYR* 1.3 77.9 - - - +
176E ASN* 1.3 70.0 + - - +
178E VAL* 3.7 24.9 - - + +
183E MET* 2.9 40.1 + - + +
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Residues in contact with ASN 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TYR* 5.6 3.5 - - - +
175E LYS* 1.3 85.9 + - - +
177E ASP* 1.3 78.6 + - - +
178E VAL* 3.2 4.3 + - - +
182E ASP* 3.4 27.7 - - - +
183E MET 5.0 1.2 + - - +
34F GLN* 6.2 2.0 - - - +
37F ARG* 3.8 28.8 - - - +
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Residues in contact with ASP 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASN* 1.3 79.4 - - - +
178E VAL* 1.3 60.6 + - - +
179E GLY 2.9 19.5 + - - +
180E PRO 5.6 0.4 - - - -
181E PHE 3.3 4.0 + - - -
182E ASP* 3.1 10.3 + - - -
37F ARG* 2.7 30.5 + - - +
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Residues in contact with VAL 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LYS* 3.7 45.3 - - + +
176E ASN 4.1 0.4 - - - +
177E ASP* 1.3 71.9 - - - +
179E GLY* 1.3 60.7 + - - +
180E PRO* 3.5 3.3 - - - +
181E PHE* 2.9 26.7 + - - +
183E MET* 3.7 37.7 - - + -
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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