Contacts of the strand formed by residues 191 - 197 (chain A) in PDB entry 4GB1
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 TRP 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER* 3.3 45.8 - - - -
124A CYS 3.9 5.2 - - - -
125A SER* 3.7 24.7 + - - -
128A GLU* 5.0 1.6 + - - -
130A ARG* 4.0 27.4 - - + +
132A PHE* 3.4 26.2 - + - -
174A ARG* 4.1 17.7 - - - +
176A GLU* 5.2 6.1 - - - +
185A CYS* 3.5 24.7 - - - -
186A HIS* 3.2 31.7 + + + -
190A LYS* 1.3 74.8 - - - +
192A MET* 1.3 62.0 - - - +
193A THR* 4.2 8.1 + - + +
208A HIS 3.9 0.7 - - - +
209A TYR* 3.4 4.3 - - - -
210A GLY* 2.9 30.0 + - - +
211A GLY 4.7 0.7 + - - -
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Residues in contact with MET 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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184A ALA* 3.4 1.9 - - - +
185A CYS* 2.9 43.5 + - - +
187A ASP* 6.5 0.2 - - + -
190A LYS 3.8 1.2 + - - +
191A TRP* 1.3 73.2 - - - +
193A THR* 1.3 63.9 + - - +
194A VAL* 3.9 20.4 - - + -
207A ILE* 3.9 16.4 - - + -
208A HIS 3.2 15.0 - - - +
209A TYR* 3.9 16.8 - - + -
232A CYS* 3.6 29.8 - - - -
239A CYS* 4.0 15.3 - - + -
241A TRP* 4.0 16.2 - - + -
259A ALA* 3.9 28.3 - - - -
262A GLY* 4.7 3.4 - - - +
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Residues in contact with THR 193 (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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132A PHE* 4.5 2.2 - - + -
158A LEU* 4.1 11.7 - - + -
176A GLU* 3.4 35.6 + - + +
177A ALA* 4.1 1.6 - - - +
183A THR 3.4 8.3 - - - -
184A ALA* 4.0 13.0 - - + -
191A TRP* 4.9 7.0 - - + +
192A MET* 1.3 81.1 - - - +
194A VAL* 1.3 65.4 + - - +
206A VAL 3.7 0.2 - - - +
207A ILE* 3.4 4.3 - - - +
208A HIS* 2.7 59.8 + - + +
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Residues in contact with VAL 194 (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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158A LEU* 4.9 1.1 - - - +
181A SER 3.7 1.2 - - - +
182A ALA* 3.3 7.7 - - - -
183A THR* 2.8 49.9 + - + +
192A MET* 3.9 21.3 - - + -
193A THR* 1.3 82.0 - - - +
195A GLY* 1.3 59.4 + - - +
196A VAL* 4.0 1.5 + - + -
205A ALA* 4.0 24.2 - - + -
206A VAL 3.5 5.8 - - - +
207A ILE* 3.9 20.2 - - + -
217A VAL* 5.9 0.4 - - + -
227A THR* 4.6 2.6 - - + +
241A TRP* 4.1 21.8 - - + +
243A MET* 4.6 6.3 - - + -
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Residues in contact with GLY 195 (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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158A LEU* 5.3 0.2 - - - -
177A ALA* 4.2 12.9 - - - +
178A VAL 3.5 9.1 - - - +
179A ALA* 3.0 24.0 - - - -
182A ALA* 4.8 0.7 - - - -
193A THR 4.2 0.8 - - - -
194A VAL* 1.3 72.3 - - - +
196A VAL* 1.3 63.5 + - - -
197A THR* 3.7 0.7 + - - +
204A VAL 3.6 1.7 - - - +
205A ALA* 3.5 0.8 - - - -
206A VAL* 3.1 36.0 + - - +
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Residues in contact with VAL 196 (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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179A ALA* 3.2 0.5 - - - -
180A TRP* 2.9 43.4 + - + -
181A SER* 3.0 22.4 + - - +
194A VAL* 4.9 1.8 - - + +
195A GLY* 1.3 72.7 - - - -
197A THR* 1.3 62.2 + - - +
203A ALA* 3.8 12.1 - - + -
204A VAL 3.1 11.0 - - - +
205A ALA* 4.0 4.5 - - + +
225A LEU* 3.1 37.0 - - + +
226A ARG* 4.5 0.9 - - - -
227A THR* 4.4 9.0 - - + -
243A MET* 4.0 25.1 - - + -
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Residues in contact with THR 197 (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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153A SER 4.6 5.4 + - - -
154A PRO* 4.9 4.7 - - - +
156A ARG 5.3 0.5 + - - -
178A VAL* 3.6 42.3 - - + +
179A ALA* 4.3 0.7 - - - -
180A TRP* 3.4 21.6 + - - +
195A GLY 4.8 1.3 - - - +
196A VAL* 1.3 75.6 - - - +
198A GLY* 1.3 69.8 + - - +
203A ALA* 3.7 1.6 - - - -
204A VAL* 2.8 49.0 + - + +
206A VAL* 5.8 3.8 - - + -
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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