Contacts of the strand formed by residues 245 - 252 (chain A) in PDB entry 1QCY
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 LYS 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A THR* 4.2 11.3 + - - +
142A GLN 3.2 5.0 + - - +
143A LEU* 3.2 31.0 - - + +
144A ASP 3.0 24.8 + - - +
244A VAL* 1.3 75.5 - - - +
246A LYS* 1.3 77.2 + - - +
247A VAL* 4.2 4.3 - - + -
273A ASN* 2.9 30.3 + - + +
275A GLN* 3.5 32.1 - - - +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 3.6 10.1 - - + +
234A PHE* 3.7 48.5 + - + +
240A ALA* 5.3 8.3 - - - -
241A ARG 5.3 7.2 - - - +
244A VAL 3.6 9.2 + - - +
245A LYS* 1.3 83.9 - - - +
247A VAL* 1.3 63.7 + - - +
272A GLU* 4.5 21.6 + - - +
273A ASN 4.5 3.2 + - - +
274A ILE* 3.6 28.5 - - + +
275A GLN 3.0 23.4 + - - -
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.2 26.9 - - + -
144A ASP 2.9 10.1 + - - +
145A ILE* 3.3 10.7 - - + +
146A VAL 2.8 25.6 + - - -
234A PHE* 3.4 6.4 - - - -
245A LYS* 4.2 2.9 - - + +
246A LYS* 1.3 81.2 - - - +
248A MET* 1.3 65.8 + - - +
249A VAL* 4.6 5.6 - - + -
275A GLN* 3.4 24.9 - - - +
277A PHE* 3.8 30.1 - - + -
331A ILE* 4.2 19.1 - - + +
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Residues in contact with MET 248 (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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146A VAL 3.2 11.0 - - - +
148A VAL* 3.7 19.7 - - + -
226A THR* 3.6 38.4 - - - +
229A ALA* 4.1 5.8 - - + -
230A ARG 4.2 3.8 - - - +
234A PHE* 4.0 15.9 - - + -
247A VAL* 1.3 76.0 - - - +
249A VAL* 1.3 65.3 + - - +
250A ILE* 3.8 18.2 - - + -
269A CYS* 3.9 21.5 - - - -
274A ILE* 4.0 22.2 - - + +
275A GLN 2.8 8.6 + - - +
276A ARG* 3.5 8.3 - - + +
277A PHE* 2.9 26.0 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.2 17.3 - - + -
146A VAL 2.9 7.5 + - - -
147A ILE* 3.4 19.4 - - + +
148A VAL 2.7 33.3 + - - +
164A PHE* 4.8 3.6 - - + -
168A LEU* 5.3 3.4 - - + -
247A VAL* 4.6 3.6 - - + -
248A MET* 1.3 77.9 - - - +
250A ILE* 1.3 59.8 + - - +
251A VAL* 4.0 7.6 + - + -
277A PHE* 3.2 14.1 - - + +
279A ILE* 4.0 25.1 - - + -
327A LEU* 4.3 11.7 - - + -
331A ILE* 4.2 24.9 - - + -
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Residues in contact with ILE 250 (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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148A VAL* 3.5 17.7 - - + +
186A TYR* 4.6 7.2 - - - +
222A THR* 4.5 15.3 - - + -
226A THR* 3.7 26.9 - - + +
248A MET* 3.8 28.3 - - + +
249A VAL* 1.3 75.6 - - - +
251A VAL* 1.3 62.3 + - - +
252A THR* 4.2 4.2 - - + +
276A ARG* 4.9 6.7 - - + -
277A PHE 2.7 12.5 + - - +
278A SER* 3.5 6.4 - - - -
279A ILE* 2.7 35.9 + - - +
299A ILE* 5.4 0.6 - - + +
302A ILE* 3.2 35.7 - - + -
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Residues in contact with VAL 251 (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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147A ILE* 4.9 0.4 - - + -
148A VAL 2.9 8.9 + - - +
149A LEU* 3.8 28.9 - - + -
150A ASP* 2.9 31.3 + - - +
155A ILE* 5.3 2.9 - - + +
161A VAL* 5.6 4.3 - - + -
164A PHE* 4.1 13.5 - - + -
186A TYR* 4.2 2.1 + - - -
249A VAL* 4.4 8.1 - - + +
250A ILE* 1.3 76.9 - - - +
252A THR* 1.3 63.6 + - - +
279A ILE* 3.6 28.9 - - + +
281A ILE* 3.9 27.4 - - + -
320A LEU* 4.6 11.9 - - + -
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Residues in contact with THR 252 (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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150A ASP* 2.7 23.5 + - - -
155A ILE* 4.9 1.8 - - - -
186A TYR* 3.4 20.5 + - - +
220A THR* 3.7 2.4 - - - +
222A THR* 4.1 3.3 + - + +
250A ILE* 5.2 7.0 - - + -
251A VAL* 1.3 77.4 - - - +
253A ASP* 1.3 63.4 + - - +
254A GLY 3.4 13.6 + - - +
279A ILE 3.1 12.3 + - - +
280A ALA* 3.4 1.6 - - - -
281A ILE* 2.9 26.5 + - - +
295A PHE* 3.7 2.4 - - + -
299A ILE* 3.4 36.6 - - + -
302A ILE* 5.8 0.2 - - + -
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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