Contacts of the strand formed by residues 177 - 183 (chain B) in PDB entry 3GUU
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 LYS 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 5.4 13.2 - - + +
85B PRO 3.4 11.3 + - - +
86B LYS* 3.5 13.4 - - + +
87B ILE* 2.8 32.6 + - - +
175B ASP 3.2 1.5 + - - +
176B SER* 1.3 73.2 - - - +
178B VAL* 1.3 55.3 + - - +
205B ASN* 3.5 21.5 - - - +
207B VAL* 3.8 19.1 - - + -
384B ALA 5.2 0.6 + - - -
385B PHE* 3.1 47.1 + - + +
386B ASP 4.8 6.7 + - - -
387B GLY* 4.9 3.2 - - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.4 17.7 - - + +
89B SER* 5.3 0.2 - - - -
163B ILE* 3.8 49.8 - - + -
167B LYS* 5.2 1.6 - - + -
176B SER 3.7 11.0 - - - +
177B LYS* 1.3 79.8 - - - +
179B ALA* 1.3 64.9 + - - +
180B LEU* 4.1 7.9 - - + -
204B LEU* 4.7 7.0 - - + -
205B ASN 2.9 20.0 + - - +
206B ILE* 3.2 21.7 - - + +
207B VAL* 2.7 31.0 + - - +
385B PHE* 4.0 2.0 - - - -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE 3.0 7.9 + - - +
88B PHE* 3.5 3.4 - - + -
89B SER* 2.9 25.5 + - - -
178B VAL* 1.3 74.8 - - - +
180B LEU* 1.3 65.4 + - - +
207B VAL* 4.8 2.2 - - + -
208B GLY* 3.2 18.4 - - - +
381B ILE* 4.0 22.0 - - + +
384B ALA* 5.3 0.2 - - + -
385B PHE* 3.5 29.1 - - + -
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Residues in contact with LEU 180 (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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88B PHE* 5.0 0.9 - - - -
89B SER* 3.3 11.4 - - - -
91B GLN* 3.8 8.7 - - - +
159B ILE* 3.9 16.6 - - + -
160B LEU* 5.3 2.0 - - + -
163B ILE* 4.1 10.8 - - + -
178B VAL* 4.1 8.7 - - + -
179B ALA* 1.3 81.1 - - - +
181B GLU* 1.3 56.1 + - - +
190B THR* 3.8 15.7 - - + -
193B ALA* 3.8 29.6 - - + -
194B THR* 4.4 12.1 - - + -
206B ILE* 3.7 35.0 - - + -
208B GLY 3.2 6.2 + - - +
209B ALA* 3.1 4.7 - - + -
210B SER 2.8 29.8 + - - -
381B ILE* 3.5 5.9 - - - +
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Residues in contact with GLU 181 (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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88B PHE* 3.7 25.3 - - + -
89B SER 3.0 6.1 + - - -
90B TYR* 3.1 34.3 - - - -
91B GLN* 2.8 28.8 + - - -
126B ILE* 3.9 13.9 - - - +
180B LEU* 1.3 75.4 - - - +
182B GLY* 1.3 72.1 + - - +
183B TYR* 5.7 0.9 - - - +
190B THR* 3.6 7.4 - - - -
210B SER* 3.1 18.2 - - - +
329B TRP* 3.5 14.2 - - - -
374B LEU* 5.6 1.2 - - - -
377B SER* 3.0 28.0 + - - +
378B LEU* 4.3 13.1 - - + +
381B ILE* 4.5 2.0 - - + -
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Residues in contact with GLY 182 (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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90B TYR* 4.5 2.0 - - - -
91B GLN 3.6 13.5 - - - -
181B GLU* 1.3 89.7 + - - +
183B TYR* 1.3 61.2 + - - +
186B GLY 3.9 1.3 - - - -
187B ALA* 3.8 5.8 - - - -
190B THR* 3.7 9.2 + - - -
210B SER 3.2 4.8 + - - -
211B HIS* 3.1 26.9 - - - +
212B GLY 3.3 2.3 + - - -
329B TRP* 4.3 2.4 - - - -
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Residues in contact with TYR 183 (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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90B TYR* 5.4 3.1 + - - +
91B GLN 4.3 1.6 + - - -
93B TYR* 3.6 16.4 - + + -
122B ASP* 5.1 3.1 - - - +
181B GLU* 5.7 0.7 - - - +
182B GLY* 1.3 73.6 - - - -
184B SER* 1.3 79.0 + - - +
185B GLY 3.3 0.2 + - - -
186B GLY* 2.8 18.7 + - - -
187B ALA 3.4 3.5 - - - +
212B GLY* 3.2 37.0 - - - -
213B GLY* 3.3 10.6 - - - -
329B TRP* 3.5 33.2 - + + -
331B ALA 5.3 0.9 + - - -
334B ASP* 4.5 1.2 + - - -
366B HIS* 2.6 48.4 + + - -
369B ALA* 3.9 7.0 - - + +
370B GLU* 3.4 51.6 + - + +
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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