Contacts of the strand formed by residues 156 - 162 (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 VAL 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B PHE* 4.6 6.9 - - - -
124B PRO* 4.7 1.8 - - + -
151B PHE* 3.8 36.8 - - + -
154B ASP* 3.4 20.5 + - - +
155B HIS* 1.3 81.5 - - - +
157B GLU* 1.3 69.6 + - - +
158B LEU* 4.2 2.5 - - + +
177B PRO* 5.6 2.5 - - + -
191B LEU* 5.4 10.1 - - + -
213B VAL* 3.9 20.4 - - + -
214B GLN 3.2 11.4 - - - +
215B PHE* 4.3 8.7 - - + -
216B TYR* 4.5 2.5 - - - -
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Residues in contact with GLU 157 (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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10B PHE* 4.4 12.2 - - + -
156B VAL* 1.3 80.7 - - - +
158B LEU* 1.3 61.1 + - - +
159B SER* 4.1 2.2 + - - -
212B GLN* 3.6 1.9 - - - +
213B VAL* 3.4 2.2 - - - -
214B GLN* 2.7 49.3 + - + +
216B TYR* 2.5 33.8 + - + +
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Residues in contact with LEU 158 (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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146B CYS* 4.2 10.8 - - - -
148B ALA* 4.7 7.0 - - + -
156B VAL* 4.2 2.2 - - + -
157B GLU* 1.3 73.5 - - - +
159B SER* 1.3 72.2 + - - +
160B TRP* 4.1 5.4 - - + +
173B THR* 4.1 19.0 + - + +
191B LEU* 3.8 28.7 - - + +
192B SER 5.0 0.2 - - - -
193B SER* 3.3 34.8 - - - +
211B CYS* 4.1 11.4 - - - -
212B GLN 3.2 3.8 - - - +
213B VAL* 3.7 28.9 - - + +
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Residues in contact with SER 159 (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 4.9 2.0 + - - -
158B LEU* 1.3 80.5 - - - +
160B TRP* 1.3 65.9 + - - +
161B TRP* 3.0 23.4 + - - -
166B GLU* 3.4 24.6 - - - -
171B VAL* 6.2 0.9 - - - -
211B CYS* 3.7 1.6 - - - -
212B GLN* 2.7 55.1 + - - +
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Residues in contact with TRP 160 (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* 3.8 16.4 - - + -
144B LEU* 4.1 22.0 - - + -
145B VAL 4.2 0.2 - - - -
146B CYS* 3.3 36.6 - - + -
158B LEU* 4.1 2.4 - - + +
159B SER* 1.3 75.3 - - - +
161B TRP* 1.3 63.8 + - - +
162B VAL 4.3 0.2 - - - -
166B GLU* 3.2 9.5 - - - +
167B VAL* 3.0 40.6 + - + +
171B VAL* 3.5 27.5 - - + +
193B SER* 2.9 34.8 + - - -
194B ARG 3.5 7.0 + - - -
195B LEU* 3.5 42.8 - - + -
209B PHE* 5.2 0.7 - - + -
210B ARG 3.7 17.7 - - - -
211B CYS* 3.7 18.6 - - + -
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Residues in contact with TRP 161 (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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159B SER* 3.0 23.3 + - - -
160B TRP* 1.3 81.2 + - - +
162B VAL* 1.3 62.1 + - - +
163B ASN 3.9 0.6 + - - -
164B GLY 3.1 29.6 - - - -
165B LYS* 3.4 5.4 - - - +
166B GLU* 3.4 37.9 - - + +
195B LEU* 5.9 0.2 - - - -
208B HIS 3.6 1.9 - - - +
209B PHE* 3.7 0.7 - - - -
210B ARG* 2.8 67.3 + - + +
212B GLN* 2.9 44.6 + - + -
301B SO4 4.4 4.8 + - - +
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Residues in contact with VAL 162 (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 TRP* 1.3 73.2 - - - +
163B ASN* 1.3 88.5 + - - +
164B GLY 3.2 0.4 - - - -
165B LYS* 2.8 25.3 + - - +
167B VAL* 3.5 33.5 - - + +
195B LEU* 4.2 9.4 - - + -
201B PHE* 3.9 25.6 - - + -
208B HIS 3.1 8.5 - - - +
209B PHE* 3.9 22.2 - - + -
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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