Contacts of the strand formed by residues 208 - 215 (chain B) in PDB entry 4LCC
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 HIS 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TRP 3.6 0.9 + - - +
162B VAL* 3.1 8.4 - - - +
163B ASN* 2.6 49.6 + - - +
206B ARG 3.8 0.4 + - - +
207B ASN* 1.3 72.3 - - - +
209B PHE* 1.3 63.7 + - - +
210B ARG* 3.7 23.8 - - + +
239B GLU* 2.6 35.8 + - + +
240B ALA 4.4 1.1 - - - -
241B TRP* 3.3 48.1 + + + -
301B SO4 3.5 34.4 + - - -
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Residues in contact with PHE 209 (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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128B VAL* 5.5 1.1 - - - +
144B LEU* 3.5 28.3 - - + -
160B TRP* 5.2 3.6 - - + -
161B TRP 3.7 2.5 - - - -
162B VAL* 3.9 20.9 - - + -
195B LEU* 4.3 8.3 - - + -
197B VAL* 4.4 11.7 - - + -
201B PHE* 3.5 46.0 - + - -
202B TRP* 3.4 35.0 - + - -
207B ASN* 4.0 19.1 - - + -
208B HIS* 1.3 74.5 - - - +
210B ARG* 1.3 60.7 + - - +
238B ALA 4.0 0.2 - - - +
239B GLU* 3.2 3.1 - - - +
240B ALA* 2.7 58.0 + - + +
242B GLY* 4.2 4.5 - - - -
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Residues in contact with ARG 210 (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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160B TRP* 3.7 7.1 - - - -
161B TRP* 2.8 67.9 + - - +
208B HIS* 3.7 17.0 - - + +
209B PHE* 1.3 75.0 - - - +
211B CYS* 1.3 63.9 + - - +
212B GLN* 3.2 32.8 + - - +
235B ILE* 5.1 0.6 - - - +
237B SER* 3.1 29.7 + - - -
238B ALA 3.1 15.9 - - - +
239B GLU* 4.3 6.7 - - + -
301B SO4 2.9 40.2 + - - -
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Residues in contact with CYS 211 (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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126B VAL* 4.2 3.0 - - - +
128B VAL* 3.4 19.7 - - + +
146B CYS* 2.0 52.9 - - - -
158B LEU* 4.1 17.9 - - - -
159B SER 3.9 2.5 - - - -
160B TRP* 3.7 16.6 - - + -
210B ARG* 1.3 71.2 - - - +
212B GLN* 1.3 61.5 + - - +
213B VAL* 4.2 0.6 + - - -
236B VAL 4.2 0.3 - - - +
237B SER* 3.2 5.9 - - - -
238B ALA* 2.5 38.6 + - + +
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Residues in contact with GLN 212 (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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157B GLU 3.6 1.1 - - - +
158B LEU* 3.2 3.3 - - - +
159B SER* 2.7 52.4 + - - +
161B TRP* 2.9 41.9 + - + +
210B ARG* 3.2 24.3 + - - +
211B CYS* 1.3 74.9 - - - +
213B VAL* 1.3 67.0 + - - +
214B GLN* 4.8 4.5 + - + +
235B ILE* 3.4 41.6 - - + +
236B VAL 4.3 1.6 - - - -
237B SER* 4.3 1.8 - - - -
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Residues in contact with VAL 213 (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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124B PRO* 3.9 24.4 - - + +
126B VAL* 3.7 28.5 - - + -
148B ALA* 4.2 8.1 - - + -
156B VAL* 3.9 24.0 - - + -
157B GLU 3.4 4.7 - - - +
158B LEU* 3.7 27.4 - - + -
211B CYS* 4.8 0.7 - - - -
212B GLN* 1.3 79.6 - - - +
214B GLN* 1.3 62.9 - - - +
215B PHE 3.7 0.7 + - - -
235B ILE* 3.5 4.3 - - - -
236B VAL* 3.1 37.7 + - - +
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Residues in contact with GLN 214 (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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156B VAL* 3.2 10.0 - - - +
157B GLU* 2.7 47.3 + - + +
212B GLN* 4.1 5.1 + - - +
213B VAL* 1.3 72.6 - - - +
215B PHE* 1.3 77.2 + - - +
216B TYR* 3.6 31.3 - - + +
233B THR* 3.5 17.2 - - - +
234B GLN 3.5 13.2 + - - -
235B ILE* 3.3 31.0 - - + +
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Residues in contact with PHE 215 (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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121B VAL* 4.4 4.7 - - + -
122B PHE 3.3 25.4 - - - -
123B PRO* 4.0 14.6 - - + -
124B PRO* 3.5 30.7 - - + -
151B PHE* 4.3 3.6 - - + -
152B TYR 3.8 9.4 - - - -
153B PRO* 3.8 20.4 - - + -
155B HIS 3.5 15.0 - - - -
156B VAL* 4.3 5.8 - - + -
213B VAL 3.7 0.8 + - - +
214B GLN* 1.3 77.0 + - - +
216B TYR* 1.3 71.8 + - - +
217B GLY* 3.5 22.0 - - - -
231B PRO 3.9 7.2 - - - -
232B VAL 3.3 20.0 - - - -
233B THR* 3.2 21.7 - - - +
234B GLN* 2.9 22.8 + - + +
236B VAL* 5.6 0.2 - - + -
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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