Contacts of the strand formed by residues 164 - 170 (chain E) in PDB entry 4BEI
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 LEU 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E GLU* 3.3 2.1 - - - -
161E LEU* 2.8 56.1 + - + +
162E ASN 3.3 1.4 + - - -
163E GLY* 1.3 73.2 - - - +
165E THR* 1.3 59.1 + - - +
166E ILE* 3.4 13.5 - - + +
190E LEU* 4.4 7.4 - - + -
191E ASN 3.4 14.4 - - - +
192E ASN* 3.5 34.3 - - + +
193E GLY 4.3 1.6 - - - +
194E ARG* 4.1 12.6 - - - +
198E ALA* 4.3 7.4 - - + -
200E VAL* 3.2 37.5 - - + -
224E ILE* 4.4 11.4 - - + -
253E VAL* 4.7 2.0 - - + -
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Residues in contact with THR 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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158E LEU* 3.2 43.3 + - + +
159E PRO 3.7 4.8 + - - -
160E GLU* 4.0 8.3 + - - +
163E GLY 3.4 5.5 + - - +
164E LEU* 1.3 74.7 - - - +
166E ILE* 1.3 61.6 + - - +
167E ASP* 5.8 0.4 - - + -
189E ASP 3.8 1.5 - - - +
190E LEU* 3.4 4.5 - - - -
191E ASN* 2.8 59.3 + - + +
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Residues in contact with ILE 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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158E LEU* 3.6 7.4 - - - +
159E PRO* 2.9 40.8 + - + +
161E LEU* 4.5 4.0 - - + +
164E LEU* 3.4 26.0 - - + +
165E THR* 1.3 79.8 + - - +
167E ASP* 1.3 62.8 + - - +
168E ILE* 3.4 28.3 - - + -
189E ASP 3.7 2.0 - - - -
190E LEU* 4.2 10.1 - - + -
251E ALA 6.1 0.4 - - - +
253E VAL* 3.6 33.2 - - + -
262E VAL* 3.9 24.2 - - + -
263E GLU 5.8 0.4 - - - -
264E GLN* 3.6 14.3 - - + +
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Residues in contact with ASP 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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158E LEU* 3.6 31.9 - - + +
165E THR* 5.8 1.1 - - + -
166E ILE* 1.3 73.7 - - - +
168E ILE* 1.3 63.5 + - - +
169E LYS* 3.2 41.3 + - - +
187E THR* 3.5 5.4 + - - +
189E ASP* 2.7 55.6 + - + +
264E GLN* 4.2 1.2 - - - +
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Residues in contact with ILE 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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166E ILE* 3.4 31.6 - - + -
167E ASP* 1.3 75.5 + - - +
169E LYS* 1.3 71.0 + - - +
186E PHE* 4.7 5.8 - - + -
187E THR 3.3 9.6 - - - +
188E VAL* 4.1 20.0 - - + -
190E LEU* 4.7 1.6 - - + -
202E PHE* 4.5 11.7 - - + -
204E MET* 4.3 15.7 - - + -
251E ALA* 3.5 28.3 - - + -
253E VAL* 5.4 0.9 - - + -
264E GLN* 3.4 29.1 + - + +
266E MET* 3.7 35.0 - - + +
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Residues in contact with LYS 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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167E ASP* 3.2 35.2 + - - +
168E ILE* 1.3 81.0 - - - +
170E ASN* 1.3 63.7 + - - +
171E GLN* 3.1 5.0 + - - -
186E PHE* 3.3 8.6 - - - -
187E THR* 2.9 46.8 + - - +
189E ASP* 5.5 3.0 + - - -
266E MET* 4.2 2.5 - - - -
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Residues in contact with ASN 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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169E LYS* 1.3 70.6 - - - +
171E GLN* 1.3 66.5 + - - +
172E PHE* 3.2 4.9 + - - +
173E GLY* 3.1 29.0 + - - +
174E ILE* 2.8 35.4 + - - +
175E ASN* 4.4 6.9 + - - +
184E VAL* 3.8 15.7 - - - +
185E PRO* 4.2 1.2 + - - +
186E PHE* 3.6 27.5 - - + -
266E MET* 4.0 13.9 - - + +
267E THR 5.1 1.2 - - - +
268E VAL* 4.3 4.9 - - - +
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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
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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