Contacts of the strand formed by residues 188 - 194 (chain B) in PDB entry 4H3E
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 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B TYR* 3.5 63.0 - - + +
22B THR* 4.7 0.7 - - - -
162B CYS* 4.0 1.6 - - - -
163B VAL* 2.8 41.3 + - + +
165B PRO* 3.6 35.7 - - + +
169B ASN* 5.6 0.6 + - - -
186B GLY 4.5 2.4 + - - +
187B LEU* 1.3 74.9 - - - +
189B PRO* 1.3 70.5 - - - +
190B VAL* 3.6 2.4 + - - +
230B GLN 4.8 0.8 + - - -
231B ALA* 2.8 50.7 + - + -
233B LYS* 4.8 7.3 + - - -
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Residues in contact with PRO 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.6 25.4 + - + +
108B PHE* 4.2 20.9 - - + -
112B PHE* 3.5 16.6 - - + -
160B TRP* 3.6 34.3 - - + -
161B LEU 3.8 6.5 - - - +
162B CYS* 3.8 7.1 - - - -
182B PRO* 4.6 8.7 - - + -
183B LEU* 5.1 5.8 - - + +
187B LEU 3.7 9.4 - - - +
188B ARG* 1.3 85.0 - - - +
190B VAL* 1.3 62.0 + - - +
227B MET* 4.0 6.9 - - - +
231B ALA* 5.5 0.5 - - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.6 14.6 - - - -
116B CYS* 4.2 1.2 - - - -
128B PHE* 4.4 3.1 - - + -
161B LEU* 2.9 44.3 + - + +
163B VAL* 4.0 15.7 - - + +
171B LEU* 4.4 7.0 - - + -
188B ARG 3.9 8.5 - - - +
189B PRO* 1.3 78.5 - - - +
191B LEU* 1.3 58.7 + - - +
224B VAL* 3.3 46.1 - - + +
227B MET* 3.9 6.5 - - - +
228B HIS* 3.6 29.6 - - + +
231B ALA* 4.7 0.7 - - + -
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Residues in contact with LEU 191 (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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112B PHE* 3.7 6.2 - - - -
116B CYS* 3.9 22.2 - - + -
142B PHE* 4.3 7.4 - - + -
146B PHE* 3.9 27.6 - - + -
160B TRP* 3.2 9.8 - - - +
161B LEU* 3.0 36.6 + - + +
190B VAL* 1.3 80.2 - - - +
192B ALA* 1.3 73.5 + - - +
193B VAL* 4.4 1.6 - - + -
216B TRP* 4.2 11.7 - - + -
219B ILE* 3.9 19.3 - - + -
221B TRP* 4.1 25.1 - - + -
224B VAL* 4.1 15.7 - - + -
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Residues in contact with ALA 192 (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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109B ASN 4.9 0.4 - - - +
112B PHE* 3.8 11.0 - - + -
113B TYR* 3.3 23.7 - - + +
116B CYS* 3.6 11.9 - - - +
158B TRP* 4.4 12.6 - - + -
159B THR 3.6 4.7 - - - -
160B TRP* 3.4 33.2 - - + -
191B LEU* 1.3 81.2 - - - +
193B VAL* 1.3 69.4 + - - +
219B ILE* 5.5 0.3 - - - +
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Residues in contact with VAL 193 (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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113B TYR* 3.9 2.2 - - - -
146B PHE* 3.6 30.3 - - + -
158B TRP* 3.5 3.9 - - - -
159B THR* 2.8 38.6 + - - +
191B LEU* 4.4 11.2 - - + -
192B ALA* 1.3 79.4 - - - +
194B ASP* 1.3 67.4 + - - +
195B VAL* 3.5 3.5 + - + +
211B TYR* 3.6 19.3 - - + +
212B LEU* 3.7 27.8 - - + -
215B ILE* 4.2 24.2 - - + -
216B TRP* 5.7 1.1 - - + -
219B ILE* 4.7 4.7 - - + -
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Residues in contact with ASP 194 (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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59B HIS* 2.8 11.4 + - - -
110B HIS* 3.5 1.0 + - - -
113B TYR* 3.5 21.0 - - + -
157B GLY 3.5 0.9 - - - +
158B TRP* 3.4 26.9 - - + -
193B VAL* 1.3 70.0 - - - +
195B VAL* 1.3 58.7 + - - +
196B TRP* 3.1 37.3 + - - +
198B HIS* 3.6 0.2 + - - -
199B ALA* 3.7 17.4 - - + +
211B TYR* 2.7 31.9 + - - -
301B FE2 1.9 31.8 - - - -
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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