Contacts of the strand formed by residues 191 - 201 (chain A) in PDB entry 4MDH
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 TYR 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ILE 3.1 10.2 - - - +
182A ILE* 3.6 2.6 - - - -
183A TRP* 3.0 44.5 + + + +
190A GLN* 1.3 74.8 - - - +
192A PRO* 1.4 68.8 - - - +
193A ASP* 2.9 46.4 + - - -
194A VAL 5.2 0.5 + - - -
195A ASN* 3.9 4.9 + - - -
209A TYR* 4.9 3.6 + - - -
223A ILE* 3.4 23.6 - - + -
307A PHE* 3.4 25.7 - + - -
308A SER* 3.6 25.6 + - - -
311A LYS* 3.5 43.5 - - + +
312A MET* 4.1 8.3 - - + -
315A THR* 5.4 0.4 - - + -
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Residues in contact with PRO 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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162A ALA* 4.1 14.1 - - + -
180A VAL* 5.4 0.9 - - - -
181A ILE 3.8 4.5 - - - +
182A ILE* 4.1 7.9 - - + -
190A GLN* 3.6 15.0 - - + +
191A TYR* 1.4 93.4 - - + +
193A ASP* 1.3 58.8 + - - +
194A VAL* 3.8 2.5 + - - +
218A LEU 5.3 0.7 - - - +
222A PHE* 3.6 32.8 - - + -
223A ILE* 4.1 27.9 - - + +
226A VAL* 3.8 29.6 - - + -
227A GLN* 5.5 0.7 - - + -
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Residues in contact with ASP 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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179A ASN 4.7 1.2 - - - +
180A VAL* 4.1 5.5 - - - +
181A ILE* 2.9 36.1 + - + +
183A TRP* 2.7 39.7 + - + +
191A TYR* 2.9 28.9 + - + -
192A PRO* 1.3 70.3 - - - +
194A VAL* 1.3 64.3 + - - +
195A ASN* 3.0 33.1 + - - +
196A HIS* 4.9 10.3 + - - -
304A ILE* 5.8 1.2 - - - +
308A SER* 4.2 6.6 - - - -
312A MET* 5.0 0.3 - - - +
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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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166A ILE* 4.1 14.8 - - + -
180A VAL* 4.9 5.6 - - + -
191A TYR* 5.2 0.6 + - - -
192A PRO 3.8 1.7 + - - +
193A ASP* 1.3 80.0 + - - +
195A ASN* 1.3 60.3 + - - +
196A HIS 3.1 6.8 + - - -
197A ALA* 3.4 19.5 + - + +
208A VAL* 3.7 27.6 + - + +
209A TYR* 3.0 36.6 + - + +
218A LEU* 4.2 10.5 - - + -
222A PHE* 3.7 33.7 - - + -
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Residues in contact with ASN 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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191A TYR* 3.9 5.4 + - - -
193A ASP* 3.0 22.9 + - - +
194A VAL* 1.3 76.3 + - - +
196A HIS* 1.3 77.8 + - + +
197A ALA 3.6 1.3 - - - +
209A TYR* 3.9 29.1 + - - -
305A ASN* 3.8 27.1 + - - +
307A PHE* 5.8 0.5 - - - -
308A SER* 3.8 14.6 + - - -
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Residues in contact with HIS 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 ASN* 3.8 17.4 + - - +
181A ILE* 3.8 31.9 - - + -
183A TRP* 5.4 2.8 - + - -
193A ASP* 4.6 9.2 + - - -
194A VAL* 3.1 0.6 - - - +
195A ASN* 1.3 95.1 + - + +
197A ALA* 1.3 63.4 + - - +
198A LYS* 4.3 8.9 - - - +
265A PHE* 4.4 10.0 - - + -
302A LEU* 3.7 34.4 - - + +
303A PRO* 3.2 41.2 + - + +
304A ILE* 5.4 2.8 - - - +
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Residues in contact with ALA 197 (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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177A VAL* 5.0 0.7 - - + -
178A LYS 3.1 18.8 - - - +
179A ASN 3.5 9.9 + - - +
180A VAL* 4.3 9.0 - - + -
194A VAL* 3.4 19.3 + - + +
195A ASN 5.2 1.0 - - - +
196A HIS* 1.3 80.5 - - - +
198A LYS* 1.3 70.9 + - - +
207A GLY* 3.7 16.6 - - - -
208A VAL* 3.3 27.0 + - + -
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Residues in contact with LYS 198 (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 ASP 3.7 2.4 - - - +
177A VAL* 4.0 0.3 - - - -
178A LYS* 3.1 43.1 + - + +
179A ASN* 5.4 2.7 - - - +
196A HIS* 4.3 9.4 - - - +
197A ALA* 1.3 88.1 - - - +
199A VAL* 1.3 60.8 + - - +
205A GLU* 3.5 37.3 + - + +
206A VAL* 3.1 12.8 - - - +
207A GLY* 4.1 17.7 - - - +
208A VAL* 4.5 3.6 - - - -
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Residues in contact with VAL 199 (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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170A LEU* 3.6 18.4 - - + -
172A VAL* 3.8 25.8 - - + -
176A ASP 3.4 12.3 - - - +
177A VAL* 4.4 6.5 - - + -
198A LYS* 1.3 75.2 - - - +
200A LYS* 1.3 70.5 + - - +
201A LEU* 3.8 12.1 - - + -
204A LYS 3.8 0.7 - - - +
205A GLU* 2.8 8.3 - - - -
206A VAL* 2.6 47.6 + - + +
207A GLY 4.2 2.0 - - - +
208A VAL* 4.4 10.5 - - + +
211A ALA* 3.3 33.7 - - + -
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Residues in contact with LYS 200 (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 VAL* 3.6 19.8 - - - +
176A ASP* 3.2 36.1 + - - +
199A VAL* 1.3 74.8 - - - +
201A LEU* 1.3 69.1 + - - +
202A GLN* 5.6 2.1 + - - -
204A LYS 5.4 0.2 - - - -
205A GLU* 4.1 22.9 - - + +
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Residues in contact with LEU 201 (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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170A LEU* 5.1 7.0 - - + +
172A VAL* 4.0 18.4 - - + -
199A VAL* 4.1 14.4 - - + -
200A LYS* 1.3 87.7 - - - +
202A GLN* 1.3 70.1 + - - +
203A ALA* 3.0 7.1 + - + +
204A LYS* 3.0 27.8 + - - +
206A VAL* 4.2 13.0 - - + -
211A ALA* 3.9 25.1 - - + +
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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