Contacts of the strand formed by residues 183 - 192 (chain A) in PDB entry 3GG0
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 ARG 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A VAL* 3.6 1.7 - - - -
178A GLU* 2.7 70.5 + - - +
181A LYS* 3.1 25.3 - - + +
182A LYS* 1.3 77.5 - - - +
184A VAL* 1.3 69.7 + - - +
185A SER* 3.5 34.6 + - - +
234A HIS* 5.8 1.3 - - + +
377A LEU* 4.6 4.9 - - - +
396A TRP* 3.4 5.6 - - - -
119B GLU* 3.9 33.6 + - - +
121B VAL* 4.3 16.9 - - - +
122B ASN* 4.6 7.7 + - - +
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Residues in contact with VAL 184 (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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175A ALA* 4.2 7.2 - - + -
176A ILE 3.8 6.3 - - - +
177A VAL* 4.5 2.0 - - + +
182A LYS 4.4 0.2 + - - -
183A ARG* 1.3 86.1 + - - +
185A SER* 1.3 60.8 + - - +
186A SER 3.8 17.0 - - - +
187A PHE* 3.7 34.5 - - + -
234A HIS* 3.3 28.8 + - + +
394A ILE* 3.6 30.3 - - + -
396A TRP* 4.8 7.4 - - + -
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Residues in contact with SER 185 (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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176A ILE* 2.8 27.9 + - - -
177A VAL 4.9 2.0 - - - -
178A GLU 5.0 0.2 - - - -
183A ARG* 3.5 32.4 + - - +
184A VAL* 1.3 75.9 - - - +
186A SER* 1.3 62.2 + - - -
233A LYS 5.3 0.2 - - - +
234A HIS* 3.9 6.2 - - - -
235A GLN* 3.5 18.0 + - - +
321A LYS* 4.5 5.2 + - - -
377A LEU* 4.0 21.6 - - - +
122B ASN* 4.1 14.9 + - - -
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Residues in contact with SER 186 (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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175A ALA* 3.5 3.3 - - - -
176A ILE* 2.7 55.2 + - - +
184A VAL* 3.7 4.2 - - - +
185A SER* 1.3 80.9 - - - +
187A PHE* 1.3 63.8 + - - +
234A HIS* 4.6 2.0 - - - -
235A GLN* 3.3 36.3 - - - +
237A ALA* 5.0 5.8 - - - +
321A LYS* 3.7 13.6 + - - -
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Residues in contact with PHE 187 (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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173A LEU* 4.0 31.0 - - + -
174A GLN 3.3 5.4 - - - +
175A ALA* 3.8 29.2 - - + -
176A ILE* 4.3 0.7 - - - -
184A VAL* 3.7 26.5 - - + -
186A SER* 1.3 76.5 - - - +
188A GLU* 1.3 60.3 + - - +
229A LEU* 4.9 4.0 - - + -
231A LEU* 4.1 21.3 - - + -
234A HIS* 4.3 19.3 - + + -
235A GLN 3.1 6.5 + - - +
236A LEU* 3.6 8.8 - - + +
237A ALA* 2.8 26.9 + - - +
391A ILE* 3.7 48.0 - - + -
392A GLY 5.6 0.4 - - - -
394A ILE* 5.3 0.2 - - + -
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Residues in contact with GLU 188 (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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172A ALA 3.5 0.3 - - - +
173A LEU* 3.3 7.6 - - - -
174A GLN* 2.7 33.1 + - + +
176A ILE* 4.0 8.6 - - + +
187A PHE* 1.3 72.8 - - - +
189A ALA* 1.3 63.6 + - - +
190A LEU* 3.4 15.4 + - + +
237A ALA* 3.6 8.5 - - + +
239A ASN* 2.7 20.0 + - - +
272A GLU* 3.3 15.7 - - - +
323A LYS* 2.8 11.1 + - - -
379A GLN* 2.7 39.4 + - - +
501A C2E 2.9 6.8 + - - +
502A MN 2.1 34.5 + - - -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.7 22.5 - - + -
172A ALA 3.4 5.6 - - - +
173A LEU* 3.9 13.4 - - + +
187A PHE 4.0 1.6 + - - -
188A GLU* 1.3 71.6 - - - +
190A LEU* 1.3 59.7 + - - +
219A LYS* 6.1 0.2 - - - -
222A ALA* 4.0 7.6 - - + +
225A LEU* 6.1 0.2 - - + -
236A LEU* 4.3 3.6 - - + -
237A ALA 2.9 16.5 + - - +
238A ILE* 3.8 19.0 - - + +
239A ASN* 3.3 24.3 + - - -
501A C2E 4.2 2.6 + - - +
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Residues in contact with LEU 190 (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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171A PHE* 3.4 2.6 - - - -
172A ALA 2.8 39.2 + - - +
174A GLN* 4.2 17.7 - - + +
188A GLU* 3.4 36.1 - - - +
189A ALA* 1.3 73.2 - - - +
191A ILE* 1.3 65.6 + - - +
192A ARG* 3.4 17.0 + - - +
239A ASN* 3.8 2.2 - - - +
386A PRO* 4.1 13.2 - - + -
501A C2E 3.3 72.5 - - + +
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A CYS* 4.3 3.8 - - + -
170A GLN 3.9 3.4 - - - +
171A PHE* 3.5 20.1 - - + -
190A LEU* 1.3 69.5 - - - +
192A ARG* 1.3 80.6 + - - +
199A PRO* 3.4 30.1 - - + +
202A MET* 3.9 23.8 - - + -
203A PHE* 4.1 15.9 - - + -
214A PHE* 4.0 7.9 - - + -
218A SER* 3.6 32.8 - - - +
501A C2E 3.0 40.7 + - + +
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Residues in contact with ARG 192 (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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169A CYS* 3.8 0.7 - - - +
170A GLN* 2.6 32.4 + - + +
172A ALA* 3.9 15.6 - - - +
190A LEU* 3.4 18.7 + - - +
191A ILE* 1.3 90.7 + - - +
193A SER* 1.3 70.8 + - - +
196A GLY 4.0 12.8 - - - -
197A GLY 3.2 20.4 - - - +
198A SER* 4.7 1.8 - - - +
199A PRO* 3.6 8.0 - - - +
202A MET* 3.7 12.8 - - - +
386A PRO* 3.6 30.1 - - - +
388A LEU* 3.9 28.3 - - + -
501A C2E 3.1 35.3 + - - -
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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