Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 8LDH
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 CYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ARG* 2.7 45.0 + - - +
174A MET* 4.0 26.5 - - + -
175A GLY* 3.6 34.5 - - - -
178A LEU* 4.6 1.8 - - - -
180A VAL* 4.1 13.7 - - - -
181A HIS 3.5 11.8 + - - -
182A SER 3.1 6.0 + - - +
183A CYS 3.5 0.2 - - - -
184A SER* 1.3 79.2 - - - +
186A HIS* 1.3 53.2 + - - +
205A ASN 3.8 5.2 - - - -
206A VAL* 4.1 13.2 - - + -
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Residues in contact with HIS 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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171A ARG* 3.7 6.7 + - - +
174A MET* 4.3 5.6 - - - +
183A CYS 3.5 15.2 + - - -
184A SER* 2.9 31.0 + - - -
185A CYS* 1.3 72.2 - - - +
187A GLY* 1.3 56.6 - - - +
188A TRP* 4.7 6.1 - - + +
203A GLY 3.6 2.8 - - - +
204A MET* 3.2 3.6 - - - +
205A ASN* 2.8 64.1 + - - +
207A ALA* 4.8 4.6 + - - -
331A CIT 2.6 50.0 + - - +
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Residues in contact with GLY 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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167A SER* 4.6 6.6 - - - -
170A PHE* 4.3 15.2 - - - -
171A ARG* 4.1 19.1 + - - +
174A MET* 4.5 2.4 - - - -
186A HIS* 1.3 73.5 - - - +
188A TRP* 1.3 77.7 + - - -
203A GLY 4.8 0.2 - - - -
204A MET* 3.9 22.7 - - - -
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Residues in contact with TRP 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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167A SER* 4.2 2.0 - - - -
170A PHE* 4.4 4.3 - - - -
171A ARG* 6.0 1.3 - - - -
186A HIS* 4.7 4.1 - - + +
187A GLY* 1.3 99.4 + - - +
189A VAL* 1.3 59.9 + - - +
190A ILE* 4.0 12.3 - - + -
199A SER* 3.6 1.7 - - - -
200A VAL* 2.8 48.5 + - + +
203A GLY* 5.3 8.5 - - - -
267A VAL* 3.6 38.6 - - + -
269A PRO* 3.1 48.2 - - + -
289A PRO* 4.0 22.7 - - + -
303A MET* 5.2 4.7 - - - -
331A CIT 3.6 35.1 + - + -
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Residues in contact with VAL 189 (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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163A CYS* 3.3 16.7 - - - +
166A ASP* 4.0 21.3 - - + +
167A SER* 3.1 24.2 + - - +
170A PHE* 4.0 33.0 - - + -
188A TRP* 1.3 75.3 - - - +
190A ILE* 1.3 61.5 - - - +
197A VAL* 3.6 35.2 - - + -
198A PRO 3.2 5.6 - - - +
199A SER* 4.2 11.7 - - - -
228A HIS* 4.3 12.6 - - + +
231A VAL* 5.1 2.5 - - + -
269A PRO* 4.1 4.3 - - - +
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Residues in contact with ILE 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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163A CYS* 3.9 6.8 - - - -
188A TRP* 4.2 14.6 - - + -
189A VAL* 1.3 79.2 - - - +
191A GLY* 1.3 59.5 + - - +
197A VAL* 3.7 3.8 - - - -
198A PRO* 2.4 66.1 + - + +
200A VAL* 4.2 15.0 - - + -
269A PRO* 5.1 1.8 - - + -
287A SER* 3.3 21.3 - - - +
288A LEU* 4.4 2.7 - - + -
289A PRO* 4.8 7.0 - - + -
303A MET* 3.8 37.7 - - + -
305A LEU* 4.9 4.0 - - + -
313A LEU* 3.7 17.9 - - + -
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Residues in contact with GLY 191 (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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141A ASP* 4.0 1.4 - - - +
163A CYS* 3.7 1.0 - - - -
190A ILE* 1.3 83.1 - - - +
192A GLU* 1.3 62.7 + - - -
193A HIS 3.4 3.6 + - - -
198A PRO* 3.5 9.6 - - - -
286A LEU* 4.0 8.4 - - - +
287A SER* 3.1 37.5 + - - -
313A LEU* 3.8 18.6 - - - -
316A SER* 5.5 0.7 - - - -
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Residues in contact with GLU 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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106A ARG* 3.5 28.7 + - - -
141A ASP* 3.1 16.8 - - + +
190A ILE 4.1 0.2 + - - -
191A GLY* 1.3 70.6 - - - -
193A HIS* 1.3 73.3 + - - +
194A GLY 3.1 0.3 + - - -
196A SER* 3.2 35.8 + - - -
197A VAL* 2.9 14.1 - - - +
198A PRO* 4.3 3.0 - - - +
286A LEU* 3.5 12.5 - - + +
316A SER* 3.3 26.2 + - - +
319A THR* 5.2 3.8 - - - +
320A LEU* 4.1 19.4 - - + +
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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