Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 1BQ5
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 ARG 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.7 9.4 - - - -
173A ASP* 1.3 78.3 + - - +
175A ALA* 1.3 62.8 + - - +
176A TYR* 3.3 41.3 + - + -
234A THR* 3.1 21.7 + - - -
235A ALA* 4.7 1.0 - - - +
236A LYS* 6.2 1.2 - - - +
239A GLU* 2.5 38.9 + - - +
240A THR 3.3 1.0 + - - +
241A VAL* 3.3 20.3 - - + +
242A LEU 2.9 22.7 + - - -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO 4.3 1.4 - - - +
24A GLN* 4.7 1.4 - - - +
25A VAL* 4.1 31.3 + - + +
28A HIS* 4.8 6.7 - - + +
172A TYR* 3.9 21.7 - - + -
174A ARG* 1.3 77.1 - - - +
176A TYR* 1.3 71.2 + - - +
242A LEU* 3.4 19.7 - - + +
244A ILE* 4.9 3.4 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.3 16.6 - - + +
24A GLN* 4.0 18.6 - - + -
25A VAL* 4.4 2.2 - - - -
174A ARG* 3.3 34.6 + - + -
175A ALA* 1.3 79.3 - - - +
177A THR* 1.3 62.2 + - - +
178A ILE* 4.1 2.6 - - + +
233A LEU* 4.0 44.4 - - + -
234A THR* 2.6 42.5 + - - -
235A ALA* 5.6 0.7 - - + -
241A VAL* 3.7 21.8 - - + -
242A LEU 2.9 9.9 + - - +
243A LEU* 3.8 11.8 - - + +
244A ILE* 3.0 27.9 + - - +
320A ILE* 5.7 2.7 - - + -
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 4.2 16.2 - - + +
23A PRO* 2.8 42.8 + - + +
24A GLN 3.7 14.4 - - - +
25A VAL* 4.0 8.7 - - + +
69A PRO* 5.1 6.5 - - + +
72A THR* 2.8 29.4 + - - +
153A THR* 4.6 4.3 + - - -
176A TYR* 1.3 73.7 - - - +
178A ILE* 1.3 63.2 + - - +
179A GLY 4.2 0.4 - - - -
221A ASN* 3.6 6.2 + - - +
244A ILE* 3.7 18.7 + - - +
246A SER* 5.6 0.9 + - - -
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 5.4 1.6 - - + -
69A PRO* 4.7 0.7 - - - -
176A TYR* 5.3 2.2 - - + +
177A THR* 1.3 81.6 + - - +
179A GLY* 1.3 62.2 + - - +
180A GLU 4.0 0.2 + - - -
220A PHE* 3.7 35.9 - - + -
221A ASN* 3.5 6.1 - - - +
227A LEU* 3.7 20.2 - - + -
233A LEU* 4.2 22.0 - - + -
243A LEU* 4.6 10.5 - - + -
244A ILE 2.8 17.9 + - - +
245A HIS* 3.4 17.0 - - + +
246A SER* 3.0 26.3 + - - +
303A TYR* 3.6 29.6 - - + +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 3.8 12.5 - - - +
178A ILE* 1.3 74.1 - - - +
180A GLU* 1.3 61.2 + - - -
181A PHE* 3.4 20.9 - - - -
220A PHE* 3.5 2.1 - - - -
221A ASN* 2.8 38.4 + - - +
246A SER* 3.7 14.1 - - - -
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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