Contacts of the strand formed by residues 240 - 247 (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 THR 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A HIS 3.3 25.8 + - - +
172A TYR* 3.8 9.1 - - + -
173A ASP* 2.8 42.0 + - - +
174A ARG 3.3 6.4 + - - -
238A GLY 3.9 1.4 + - - -
239A GLU* 1.3 71.5 - - - +
241A VAL* 1.3 64.5 + - - +
292A LEU* 4.1 19.5 - - + -
293A TYR 3.5 10.1 - - - +
294A THR* 2.7 23.8 + - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 4.5 0.2 - - - -
174A ARG* 3.3 32.8 - - + +
176A TYR* 3.7 26.0 - - + -
235A ALA* 4.3 8.7 - - + -
239A GLU* 4.5 3.8 - - + -
240A THR* 1.3 81.3 - - - +
242A LEU* 1.3 74.3 + - - +
243A LEU* 3.9 13.5 + - + +
291A ALA 3.6 1.9 - - - +
292A LEU* 3.5 5.9 - - - +
293A TYR* 2.9 34.5 + - + +
295A PHE* 4.0 24.7 - - + -
320A ILE* 6.4 0.4 - - + -
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Residues in contact with LEU 242 (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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155A MET* 3.3 34.8 - - + -
162A LEU* 4.4 12.1 - - + -
172A TYR* 3.9 36.9 - - + +
174A ARG 2.9 10.2 + - - +
175A ALA* 3.4 7.1 - - + -
176A TYR 2.9 27.7 + - - +
241A VAL* 1.3 74.1 - - - +
243A LEU* 1.3 59.5 + - - +
244A ILE* 4.0 15.5 - - + -
265A TRP* 5.2 2.7 - - + -
290A ALA* 4.1 19.7 - - + -
291A ALA 3.6 8.7 - - - +
292A LEU* 3.5 21.3 - - + -
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Residues in contact with LEU 243 (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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176A TYR* 3.8 16.6 - - + -
178A ILE* 4.6 8.3 - - + -
233A LEU* 4.3 16.6 - - + -
241A VAL* 4.1 23.3 - - + +
242A LEU* 1.3 72.5 - - - +
244A ILE* 1.3 64.3 + - - +
245A HIS* 3.9 2.3 + - - +
256A LEU* 5.0 11.0 - - + -
281A TRP* 5.2 7.4 + - + -
289A GLY 4.1 0.2 - - - +
290A ALA* 3.5 2.8 - - - -
291A ALA* 2.9 41.0 + - + +
293A TYR* 5.6 7.6 - - + -
295A PHE* 6.2 1.6 - - + -
303A TYR* 3.8 38.6 + - + +
320A ILE* 4.5 16.2 - - + -
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Residues in contact with ILE 244 (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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25A VAL* 4.4 14.1 - - + -
72A THR* 4.3 19.3 - - + -
131A THR* 4.1 11.4 - - + -
153A THR* 3.9 29.2 - - + +
155A MET* 4.1 26.7 - - + -
175A ALA* 4.9 3.1 - - + -
176A TYR 3.0 15.9 + - - +
177A THR* 3.7 11.8 - - - +
178A ILE* 2.8 31.6 + - - +
242A LEU* 4.0 24.0 - - + +
243A LEU* 1.3 73.9 - - - +
245A HIS* 1.3 63.4 + - - +
246A SER 5.2 0.2 - - - +
288A ALA* 5.1 0.4 - - + -
289A GLY 3.7 6.3 - - - +
290A ALA* 4.7 1.3 - - + +
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Residues in contact with HIS 245 (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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178A ILE* 3.4 10.7 - - + +
180A GLU* 3.0 32.0 + - + +
220A PHE* 3.7 19.5 - + - -
243A LEU 3.9 1.7 + - - +
244A ILE* 1.3 74.1 - - - +
246A SER* 1.3 73.9 + - - +
252A THR* 3.9 11.8 - - + +
254A PRO* 3.8 12.4 - - + +
281A TRP* 5.6 1.3 - - - +
283A ILE* 3.3 29.1 - - + +
288A ALA* 3.3 3.0 - - - -
289A GLY 3.1 32.0 + - - +
303A TYR* 2.6 40.4 + + - +
304A LEU 5.8 0.2 - - - -
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Residues in contact with SER 246 (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* 4.9 2.6 - - - +
133A VAL* 3.9 11.0 - - - -
151A SER* 5.4 3.5 + - - -
152A GLY* 4.6 9.8 + - - -
153A THR* 3.2 27.0 + - - -
177A THR* 5.6 0.7 + - - -
178A ILE 3.0 12.9 + - - -
179A GLY* 3.7 8.8 - - - -
180A GLU 3.0 26.9 + - - +
181A PHE* 6.0 0.2 - - - -
244A ILE 4.3 0.2 - - - -
245A HIS* 1.3 79.0 - - - +
247A GLN* 1.3 64.7 + - - +
248A ALA 5.4 0.2 - - - -
283A ILE* 4.8 0.2 - - - -
287A SER 3.7 3.6 - - - -
288A ALA* 3.9 9.4 - - - +
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Residues in contact with GLN 247 (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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133A VAL* 4.7 0.4 - - - -
180A GLU* 3.2 43.4 + - + +
182A ASP* 3.1 32.3 + - - +
218A ILE* 5.3 1.4 - - - +
246A SER* 1.3 74.1 - - - +
248A ALA* 1.3 52.4 + - - +
249A ASN 2.9 27.4 + - - -
250A ARG* 3.0 34.4 + - - +
251A ASP 5.0 0.6 + - - -
252A THR* 4.1 19.1 - - + -
283A ILE* 4.2 6.9 - - + +
285A GLY* 3.5 1.8 - - - -
286A GLY 2.7 28.2 + - - -
287A SER 3.1 15.6 + - - +
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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