Contacts of the strand formed by residues 205 - 212 (chain A) 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 ASN 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A SER 4.8 1.2 + - - -
175A ASP* 3.0 35.6 + - + +
176A SER 3.6 16.9 + - - +
177A LYS* 3.8 19.2 - - - +
178A VAL* 3.0 22.7 + - - +
203A GLU 3.2 5.8 + - - +
204A LEU* 1.3 66.0 - - - +
206A ILE* 1.3 60.9 + - - +
207A VAL* 3.3 13.1 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 4.6 12.3 - - + -
163A ILE* 6.0 0.2 - - + -
178A VAL* 3.3 18.2 - - + +
180A LEU* 3.7 32.3 - - + -
193A ALA 5.2 2.0 - - - +
194A THR* 5.2 1.1 - - - -
197A ALA* 3.6 30.3 - - + -
204A LEU* 2.9 24.3 + - + +
205A ASN* 1.3 70.7 - - - +
207A VAL* 1.3 61.0 + - - +
208A GLY 3.7 7.9 - - - +
324A PHE* 3.5 55.6 - - + +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LYS* 3.6 26.5 - - + -
178A VAL 2.9 15.7 + - - +
179A ALA* 4.8 1.1 - - + -
205A ASN* 3.5 23.3 - - - +
206A ILE* 1.3 72.0 - - - +
208A GLY* 1.3 59.0 + - - +
324A PHE* 4.3 7.0 - - - -
325A PRO* 3.4 21.5 - - - +
384A ALA* 3.4 40.2 - - + +
385A PHE* 3.8 23.3 - - + +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A VAL 3.7 0.6 + - - -
179A ALA* 3.2 12.6 - - - +
180A LEU 3.2 19.6 + - - -
206A ILE* 3.5 9.0 - - - +
207A VAL* 1.3 84.3 - - - +
209A ALA* 1.3 63.4 + - - +
324A PHE* 4.0 4.9 - - - -
325A PRO 3.3 11.9 - - - -
380A PHE* 4.6 0.7 - - - -
381A ILE* 4.5 1.1 - - - -
384A ALA* 3.9 13.9 - - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.3 16.8 - - + +
190A THR* 4.7 3.6 - - + -
194A THR* 3.6 31.0 - - + -
208A GLY* 1.3 76.4 - - - +
210A SER* 1.3 62.5 + - - +
211A HIS* 4.9 4.7 - - + -
324A PHE* 3.8 9.6 - - + -
325A PRO 3.3 6.3 + - - -
326A ARG* 3.3 11.4 - - + +
327A PHE 3.0 23.7 + - - +
380A PHE* 3.6 4.9 - - - -
381A ILE* 4.3 1.5 - - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 2.9 6.9 + - - -
181A GLU* 3.1 27.5 - - - +
182A GLY 3.1 4.0 + - - -
190A THR* 4.4 0.5 - - - +
209A ALA* 1.3 75.4 - - - +
211A HIS* 1.3 62.6 + - - +
327A PHE* 3.2 30.5 - - - +
329A TRP* 4.1 2.2 - - - -
377A SER* 3.2 29.7 + - - -
380A PHE* 4.0 1.3 - - - -
381A ILE* 3.6 20.4 - - - -
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY 3.1 14.8 - - - +
187A ALA* 3.6 14.6 - - + -
190A THR* 3.7 26.2 - - + -
191A VAL* 3.7 33.3 - - + +
194A THR* 5.0 4.0 + - + +
209A ALA* 4.9 6.5 - - + -
210A SER* 1.3 78.9 - - - +
212A GLY* 1.3 59.7 + - - +
214A THR* 2.9 29.5 + - + +
326A ARG* 5.2 6.6 + - + +
327A PHE 3.1 4.6 + - - -
328A ILE* 3.1 42.0 - - + +
329A TRP* 3.0 27.9 + - - -
345A TYR* 5.1 1.8 - + - -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY 3.2 5.7 + - - -
183A TYR* 3.3 11.7 - - - -
184A SER 2.9 20.8 + - - -
187A ALA* 3.0 4.2 - - - +
211A HIS* 1.3 77.2 - - - +
213A GLY* 1.3 67.4 + - - -
214A THR* 3.1 4.0 - - - -
329A TRP* 3.0 30.2 - - - -
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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