Contacts of the strand formed by residues 171 - 179 (chain B) in PDB entry 4LP4
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.0 30.3 - - + +
165B VAL 3.7 15.0 - - - +
166B PRO* 4.1 7.2 - - + -
167B ASN* 2.5 35.7 + - - -
168B GLU 3.2 18.3 + - - +
169B LYS* 3.6 14.6 - - + +
170B GLY* 1.3 78.2 - - - +
172B SER* 1.3 61.8 + - - +
173B VAL* 4.7 2.0 - - + -
192B LEU* 3.8 25.6 - - + -
193B MET 3.5 3.1 - - - +
194B VAL* 4.4 10.3 - - + -
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Residues in contact with SER 172 (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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167B ASN* 4.4 7.0 - - - +
170B GLY 4.1 0.8 + - - -
171B VAL* 1.3 75.6 - - - +
173B VAL* 1.3 68.3 + - - +
174B LYS* 4.2 16.0 + - - +
191B GLU 3.7 0.9 - - - +
192B LEU* 3.9 0.5 - - - +
193B MET* 2.9 58.8 + - - +
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Residues in contact with VAL 173 (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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155B LEU 6.0 0.7 - - - +
157B TRP* 4.2 11.0 - - + +
164B LEU 5.6 2.0 - - - +
166B PRO* 4.0 32.0 - - + +
167B ASN* 5.0 2.8 + - - +
171B VAL* 4.7 3.1 - - + -
172B SER* 1.3 80.7 - - - +
174B LYS* 1.3 82.3 + - - +
175B GLU* 3.9 21.2 - - + +
190B SER* 3.4 24.7 - - - +
191B GLU 3.3 5.8 - - - +
192B LEU* 3.9 20.0 - - + -
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Residues in contact with LYS 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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172B SER* 4.2 19.0 + - - +
173B VAL* 1.3 87.9 + - - +
175B GLU* 1.3 64.9 + - - +
189B GLN 4.0 0.3 - - - +
190B SER* 3.3 4.3 - - - -
191B GLU* 2.8 49.4 + - + +
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Residues in contact with GLU 175 (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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154B THR* 5.9 3.8 - - - +
155B LEU* 4.1 17.9 + - - +
166B PRO* 6.1 1.0 - - - +
173B VAL* 3.9 19.4 - - + +
174B LYS* 1.3 81.1 - - - +
176B GLN* 1.3 64.7 - - - +
189B GLN 3.3 7.2 - - - +
190B SER* 4.5 7.0 + - - +
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Residues in contact with GLN 176 (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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175B GLU* 1.3 78.4 - - - +
177B THR* 1.3 71.0 + - - +
178B ARG* 3.3 36.9 + - + +
187B THR 3.9 0.4 - - - +
188B LEU* 3.4 5.4 - - - +
189B GLN* 2.8 55.2 + - + +
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Residues in contact with THR 177 (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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152B ALA* 4.8 4.6 - - + +
175B GLU* 6.1 0.2 - - - +
176B GLN* 1.3 76.5 - - - +
178B ARG* 1.3 70.9 + - - +
179B ARG* 6.1 0.2 - - - -
186B PHE* 3.5 32.5 - - + -
187B THR 3.5 3.1 - - - -
188B LEU* 3.3 23.8 - - + +
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Residues in contact with ARG 178 (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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145B VAL* 5.2 2.2 - - - +
176B GLN* 3.3 31.8 + - + +
177B THR* 1.3 81.3 - - - +
179B ARG* 1.3 63.8 + - - +
186B PHE* 3.3 8.1 - - - +
187B THR* 2.8 65.4 + - - +
189B GLN* 3.1 28.9 + - - +
301B NA 3.7 12.3 - - - -
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Residues in contact with ARG 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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178B ARG* 1.3 76.5 - - - +
180B HIS* 1.3 66.5 + - - +
181B PRO* 3.3 8.4 - - + +
184B GLY* 3.4 32.9 + - - +
185B LEU 3.6 2.5 - - - +
186B PHE* 3.5 34.5 - - + -
187B THR* 6.1 0.2 - - - -
301B NA 3.3 14.7 - - - -
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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