Contacts of the strand formed by residues 173 - 179 (chain B) in PDB entry 3LKB
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 GLN 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 4.0 15.5 - - - +
144B ALA 3.1 7.5 + - - +
145B LYS* 3.4 33.3 + - + +
146B VAL 2.8 26.1 + - - -
171B GLY 4.6 4.4 + - - +
172B LEU* 1.3 74.4 - - - +
174B ILE* 1.3 63.1 + - - +
175B VAL* 3.2 6.1 + - + +
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Residues in contact with ILE 174 (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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134B LEU* 5.0 2.9 - - + -
146B VAL* 3.3 20.9 - - + +
148B LEU* 4.1 33.7 - - + -
163B ALA* 4.0 15.9 - - + +
164B ARG* 4.3 19.1 + - + +
167B ALA* 3.7 28.3 - - + -
172B LEU 3.9 1.6 + - - -
173B GLN* 1.3 70.3 - - - +
175B VAL* 1.3 59.8 + - - +
176B ASP 4.0 15.9 - - - +
177B VAL* 4.0 17.3 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 4.4 15.7 - - + -
146B VAL 3.0 21.2 + - - +
173B GLN* 3.2 6.5 + - + +
174B ILE* 1.3 72.3 - - - +
176B ASP* 1.3 61.2 + - + +
197B ALA* 3.7 31.0 - - + +
199B VAL* 3.7 25.4 - - + -
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.3 7.8 - - + +
148B LEU 3.0 22.0 + - - -
174B ILE* 3.5 4.0 + - - +
175B VAL* 1.3 86.8 - - + +
177B VAL* 1.3 74.1 + - - +
178B GLN* 3.0 28.9 - - - +
193B ARG* 4.9 11.8 + - - +
194B PHE* 3.6 32.1 - - + -
197B ALA* 6.0 0.9 - - + -
199B VAL* 5.4 0.2 - - + -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.1 25.8 - - + +
150B VAL* 5.7 4.5 - - + -
160B VAL* 4.9 9.9 - - + -
164B ARG* 3.7 39.3 - - - +
174B ILE* 4.0 12.6 - - + -
176B ASP* 1.3 87.2 + - - +
178B GLN* 1.3 65.9 + - - +
179B GLU* 5.5 6.9 - - + +
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Residues in contact with GLN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU 2.7 9.7 + - - +
149B VAL* 3.3 7.8 - - + -
150B VAL* 2.9 28.6 + - - +
176B ASP* 3.0 30.9 - - - +
177B VAL* 1.3 76.2 - - - +
179B GLU* 1.3 64.0 + - - +
180B VAL* 4.0 4.4 - - + +
190B LEU* 3.1 30.0 - - + +
193B ARG* 3.0 31.0 + - - +
194B PHE* 4.0 7.6 - - + -
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Residues in contact with GLU 179 (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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150B VAL* 3.0 19.0 - - + +
152B PRO* 3.6 22.7 - - + +
157B ARG* 3.0 52.7 + - - +
177B VAL* 5.5 6.6 - - + +
178B GLN* 1.3 80.8 + - - +
180B VAL* 1.3 62.2 + - - +
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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