Contacts of the strand formed by residues 176 - 183 (chain E) in PDB entry 6DWZ
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 SER 176 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E ALA* 1.3 69.4 - - - +
177E ALA* 1.3 59.3 + - - +
196E LEU* 3.1 11.7 - - - +
197E HIS* 2.4 58.9 + - - -
243E ILE* 4.6 0.7 - - - -
244E LYS 3.5 7.0 - - - -
563E SER* 2.5 38.5 + - - -
564E ILE* 3.5 12.2 - - - +
565E PRO* 3.9 18.8 - - - -
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Residues in contact with ALA 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 SER* 1.3 75.0 - - - +
178E THR* 1.3 59.9 + - - +
194E VAL* 4.7 3.8 - - + -
195E THR 2.9 16.2 - - - +
196E LEU* 4.0 12.6 - - + +
197E HIS* 4.4 1.8 - - - -
232E PHE* 4.1 6.7 - - + -
243E ILE* 4.0 6.5 - - + -
244E LYS 3.1 6.9 + - - -
245E PHE* 3.4 34.2 - - + -
246E VAL* 3.2 25.1 + - - +
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Residues in contact with THR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ALA* 1.3 70.0 - - - +
179E ILE* 1.4 64.9 + - - +
194E VAL* 3.4 2.3 - - - -
195E THR* 2.9 41.4 + - - +
197E HIS* 4.1 3.7 + - - -
246E VAL* 3.3 24.3 - - - +
565E PRO* 3.8 8.8 - - - +
567E SER 3.4 10.0 + - - -
568E SER* 3.4 33.0 - - - +
570E ALA* 4.4 1.5 - - + +
571E SER* 2.9 31.6 + - - +
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Residues in contact with ILE 179 (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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178E THR* 1.4 78.9 - - - +
180E ASP* 1.3 62.8 + - - +
192E LEU* 3.9 18.2 - - + -
193E GLY 3.1 16.4 - - - +
194E VAL* 4.1 15.9 - - + -
224E ILE* 4.6 11.4 - - + -
228E LEU* 4.9 12.3 - - + -
245E PHE* 4.3 24.9 - - + -
246E VAL 3.7 4.4 + - - +
247E THR* 2.9 36.8 + - - +
248E ASP 4.9 0.5 + - - -
253E VAL* 4.4 19.3 - - + -
256E SER* 5.1 1.3 - - - +
257E LEU* 4.6 15.0 - - + -
568E SER* 4.5 4.2 + - - -
571E SER* 3.5 3.6 - - - -
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Residues in contact with ASP 180 (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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179E ILE* 1.3 76.6 - - - +
181E LEU* 1.3 101.8 + - - +
192E LEU* 3.2 7.4 - - - +
193E GLY 3.1 27.4 + - - -
247E THR* 5.1 0.4 - - - -
248E ASP* 3.0 28.2 - - - +
253E VAL* 5.1 3.8 - - - +
268E HIS* 4.2 0.7 - - - -
568E SER* 3.7 7.9 + - - +
571E SER* 3.7 12.9 + - - -
572E GLU* 3.0 24.3 - - - +
575E PHE* 3.8 17.0 - - + -
17G G 5.0 1.0 - - - +
7H C 3.9 9.7 - - - +
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Residues in contact with LEU 181 (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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179E ILE* 5.3 0.4 - - + -
180E ASP* 1.3 105.9 + - - +
182E TRP* 1.3 58.8 + - - +
190E ASN* 6.1 1.1 - - + -
191E PHE 3.3 14.6 - - - +
192E LEU* 4.2 13.5 - - + -
214E LEU* 4.4 17.7 - - + -
219E SER* 4.5 9.6 - - - +
224E ILE* 4.2 28.9 - - + -
252E ASN* 5.3 5.8 - - + +
253E VAL* 3.5 30.1 - - + -
575E PHE* 4.0 2.6 - - - -
17G G 2.7 33.3 - - - +
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Residues in contact with TRP 182 (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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181E LEU* 1.3 75.1 - - - +
183E THR* 1.3 87.9 + - - +
184E ASP* 3.7 28.5 - - + -
185E ASN* 5.3 3.6 - - - -
190E ASN* 3.6 2.4 - - - +
191E PHE* 2.9 61.8 + + + +
211E LEU* 5.1 2.0 - - + -
575E PHE* 3.4 62.6 + + + +
578E ALA* 4.0 24.0 - - + -
579E GLY* 4.2 15.5 - - - -
582E ILE* 4.2 6.7 - - + -
17G G 4.3 10.9 + + - +
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Residues in contact with THR 183 (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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182E TRP* 1.3 99.3 + - - +
184E ASP* 1.3 69.8 + - - +
185E ASN* 3.8 4.0 + - - +
188E LYS* 4.0 9.4 + - - +
189E ARG 2.8 22.5 + - - -
190E ASN* 3.6 13.2 - - + +
17G G 3.1 37.6 - - + +
18G G 5.2 0.2 - - - +
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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