Contacts of the strand formed by residues 194 - 200 (chain B) in PDB entry 4LDQ
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 LEU 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B LYS* 4.3 8.4 - - - +
162B VAL 3.3 11.0 - - - +
164B VAL* 3.8 22.4 - - + -
185B ILE* 3.7 35.9 - - + +
188B LEU* 3.5 8.8 + - + -
189B HIS* 3.8 29.3 - - + +
192B GLY 3.6 1.3 - - - -
193B ARG* 1.3 76.9 - - - +
195B GLU* 1.3 63.4 + - - +
196B HIS 3.2 29.2 - - - +
197B ALA* 4.3 4.9 - - + -
221B ILE* 3.7 22.4 - - + -
222B PRO* 4.7 7.3 - - + +
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Residues in contact with GLU 195 (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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161B LYS* 3.1 40.2 - - + +
162B VAL 2.8 17.1 + - - +
163B THR* 3.7 15.9 - - - +
194B LEU* 1.3 75.5 - - - +
196B HIS* 1.3 69.7 + - + +
222B PRO* 3.8 12.2 - - - +
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Residues in contact with HIS 196 (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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162B VAL 3.7 0.8 + - - -
163B THR* 3.3 17.7 + - + +
164B VAL 2.9 25.1 + - - -
194B LEU* 3.2 11.4 - - - +
195B GLU* 1.3 88.9 + - + +
197B ALA* 1.3 79.0 + - - +
198B PHE* 3.8 18.6 - + + -
222B PRO* 3.6 28.2 + - + +
223B ALA 3.3 9.5 - - - -
224B THR* 2.7 28.1 + - - -
238B ARG* 5.1 5.1 + - - -
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Residues in contact with ALA 197 (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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164B VAL 3.2 5.6 - - - +
166B THR* 6.3 0.4 - - + -
185B ILE* 4.3 13.5 - - + -
194B LEU* 4.3 8.5 - - + +
196B HIS* 1.3 76.3 - - - +
198B PHE* 1.3 63.9 + - - +
216B LEU* 4.2 27.1 - - + -
221B ILE* 4.3 7.6 - - + -
222B PRO 3.0 13.2 + - - +
223B ALA* 3.1 5.1 - - + +
224B THR 3.0 24.8 + - - -
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Residues in contact with PHE 198 (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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163B THR* 3.6 31.4 - - + -
164B VAL 2.6 11.9 + - - +
165B LEU* 3.2 22.6 - - + -
166B THR* 2.7 34.5 + - - +
185B ILE* 5.8 0.2 - - - +
196B HIS* 3.8 14.4 - + + -
197B ALA* 1.3 76.5 - - - +
199B CYS* 1.3 56.6 + - - +
224B THR* 3.4 35.9 - - + -
226B ILE* 4.3 19.5 - - + -
234B ALA* 5.0 3.6 - - + -
238B ARG* 3.7 56.1 - - + -
240B VAL* 3.9 11.4 - - + -
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Residues in contact with CYS 199 (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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318A ILE* 4.7 1.6 - - - -
166B THR* 3.6 8.7 - - + -
168B CYS 5.8 0.2 - - - +
197B ALA 4.2 0.4 + - - -
198B PHE* 1.3 75.0 - - - +
200B THR* 1.3 60.8 + - - +
208B GLY* 3.9 13.2 - - - -
212B THR* 3.7 24.9 - - + -
213B ALA* 4.3 7.9 - - - -
216B LEU* 4.1 18.4 - - + -
224B THR 3.0 9.7 + - - -
225B LEU* 3.4 29.9 - - - +
226B ILE* 3.1 26.2 + - - +
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Residues in contact with THR 200 (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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165B LEU* 4.5 8.7 - - + -
166B THR 3.2 14.6 + - - +
167B HIS* 2.7 32.8 + - - +
168B CYS 4.8 0.7 + - - -
199B CYS* 1.3 76.1 - - - +
201B GLU* 1.3 64.2 + - - +
202B THR* 3.0 7.4 + - - -
208B GLY* 3.1 22.0 - - - -
225B LEU* 3.8 2.7 - - - -
226B ILE* 3.5 13.2 - - + -
228B ASP* 3.5 14.1 + - - +
231B VAL* 3.6 30.5 - - + -
265B LEU* 4.7 2.0 - - + -
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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