Contacts of the strand formed by residues 168 - 175 (chain E) in PDB entry 3QS7
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 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167E THR* 1.4 75.5 - - - +
169E ARG* 1.3 63.3 + - - +
170E ARG 3.5 2.6 + - - -
187E GLU 3.7 1.1 - - - +
188E SER* 3.8 12.1 - - - -
192E PRO* 4.7 0.4 - - + -
233E ALA* 4.3 23.8 - - + +
235E ASN* 3.4 26.2 - - + +
237E LEU* 3.9 16.6 - - + +
238E GLY* 3.5 36.8 - - - +
239E ARG 3.9 3.4 - - - +
240E GLU* 4.0 21.2 - - + +
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Residues in contact with ARG 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 THR* 5.0 3.9 - - - -
168E LEU* 1.3 72.6 - - - +
170E ARG* 1.4 68.5 + - - +
186E SER* 4.0 2.8 - - - -
187E GLU* 2.8 50.8 + - + +
233E ALA* 5.3 2.1 - - - +
240E GLU* 5.1 0.4 - - - -
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Residues in contact with ARG 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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168E LEU 3.5 4.9 + - - -
169E ARG* 1.4 76.3 - - - +
171E PRO* 1.4 78.3 - - + +
172E TYR* 3.7 2.6 + - - +
185E ILE 4.3 2.8 - - - +
186E SER* 4.4 0.2 - - - -
187E GLU 4.7 0.3 + - - -
233E ALA* 5.7 0.2 - - - -
240E GLU* 4.1 17.0 - - + +
241E CYS 5.1 6.3 - - - +
242E THR* 5.1 3.1 - - - -
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Residues in contact with PRO 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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170E ARG* 1.4 90.2 - - + +
172E TYR* 1.3 56.6 - - - +
173E PHE* 4.8 1.7 - - + -
184E CYS* 3.3 26.9 - - - -
185E ILE 3.8 6.5 - - - +
186E SER* 3.8 16.4 - - - -
231E CYS* 3.8 17.5 - - + +
233E ALA* 4.1 8.7 - - + +
240E GLU 3.4 22.2 - - - +
242E THR* 3.2 34.7 - - - +
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Residues in contact with TYR 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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170E ARG 4.9 2.0 - - - +
171E PRO* 1.3 71.6 - - - +
173E PHE* 1.3 74.6 + - - +
184E CYS* 3.6 0.7 - - - -
185E ILE* 2.8 49.9 + - + +
267E PRO* 4.4 20.9 - - + -
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Residues in contact with PHE 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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171E PRO* 4.8 3.6 - - + -
172E TYR* 1.3 88.2 - - - +
174E ARG* 1.4 62.7 + - - +
182E LEU* 4.1 7.9 - - + -
183E VAL 3.5 3.6 - - - +
184E CYS* 4.3 2.2 - - - -
185E ILE* 5.3 0.9 - - - -
196E TRP* 3.4 39.3 - + - -
231E CYS* 3.8 15.0 - - + -
242E THR* 3.7 28.0 - - - -
243E ARG 4.5 2.7 - - - -
244E LEU* 3.9 35.2 - - + -
267E PRO* 4.2 13.0 - - - +
269E TRP* 3.0 58.5 + + + +
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Residues in contact with ARG 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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173E PHE* 1.4 74.9 - - - +
175E LYS* 1.3 64.0 + - - +
176E MET* 3.4 0.3 + - - -
182E LEU* 4.1 2.0 - - - -
183E VAL* 3.0 38.7 + - + +
185E ILE* 3.6 28.3 - - + -
269E TRP* 4.1 2.9 - - - -
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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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174E ARG* 1.3 71.8 - - - +
176E MET* 1.3 66.7 + - - +
177E GLU* 3.2 4.9 + - - +
181E ALA 3.7 10.1 - - - +
182E LEU* 3.9 7.9 - - + -
269E TRP* 3.8 26.8 - - + -
298E PHE* 6.4 0.7 - - + -
314E PHE* 4.7 13.2 - - + -
316E PHE* 6.0 4.7 - - + -
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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