Contacts of the strand formed by residues 244 - 255 (chain A) in PDB entry 2AGQ
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 SER 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ARG* 3.4 13.2 - - - +
243A LYS* 1.3 81.7 - - - +
245A ILE* 1.3 67.4 + - - +
336A ARG* 2.8 39.9 + - - -
337A PHE 3.0 16.2 - - - -
338A SER* 4.0 8.1 - - - -
340A PHE* 3.6 2.9 - - - -
7C G 3.6 8.1 - - - +
8C T 2.7 23.6 + - - +
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Residues in contact with ILE 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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242A ARG* 4.0 13.0 - - - -
244A SER* 1.3 80.4 - - - +
246A GLY* 1.3 60.1 + - - +
272A SER* 3.9 11.2 - - - +
275A LYS* 3.5 36.3 - - + +
276A LEU* 3.8 25.1 - - + -
279A ARG* 2.9 47.3 - - - +
336A ARG* 4.0 2.5 - - - -
337A PHE* 2.7 43.2 + - - +
340A PHE* 3.8 6.4 - - + -
7C G 3.6 7.6 - - - +
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Residues in contact with GLY 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 1.3 77.9 - - - +
247A ARG* 1.3 61.7 + - - -
272A SER* 3.6 9.0 - - - -
275A LYS* 3.0 24.1 + - - -
335A VAL 3.1 13.9 - - - -
336A ARG* 3.3 17.1 - - - +
6C A 4.2 4.6 + - - +
7C G 2.9 13.6 + - - -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLY* 1.3 75.7 - - - +
248A ILE* 1.3 66.9 + - - +
249A VAL* 3.4 25.0 - - + +
268A ALA* 3.6 25.8 - - + +
271A GLU* 2.8 32.2 + - + +
272A SER* 3.4 17.8 + - - +
275A LYS* 4.4 7.6 - - - +
334A GLY* 3.1 2.1 - - - -
335A VAL* 2.8 30.4 + - - +
336A ARG* 4.5 0.6 - - - +
5C G 3.6 23.2 + - - -
6C A 2.9 30.7 + - - -
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Residues in contact with ILE 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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247A ARG* 1.3 79.6 + - - +
249A VAL* 1.3 71.5 + - - +
287A VAL* 4.3 17.0 - - + +
289A VAL* 5.1 3.6 - - + -
332A ARG* 3.1 63.5 - - + +
333A ILE 3.5 18.6 - - - +
334A GLY* 3.7 5.2 - - - +
335A VAL 5.7 0.2 - - - +
5C G 3.8 20.5 - - + +
6C A 2.9 22.1 + - + +
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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
----------------------------------------------------------
247A ARG* 3.4 44.0 - - + +
248A ILE* 1.3 78.5 - - - +
250A THR* 1.3 64.8 + - - +
264A TYR* 3.9 43.5 - - + +
267A ARG* 5.7 4.7 - - + +
268A ALA* 4.8 6.7 - - + +
271A GLU* 5.0 4.0 - - - +
332A ARG* 3.2 3.5 - - - -
333A ILE* 2.9 40.4 + - - +
5C G 4.0 5.2 - - - +
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Residues in contact with THR 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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34A SER* 4.0 28.7 + - - +
36A ARG* 3.6 29.4 - - + +
249A VAL* 1.3 75.9 - - - +
251A MET* 1.3 75.9 + - - +
252A LYS 3.9 0.3 + - - -
264A TYR* 3.9 11.4 - - - -
331A ARG* 3.9 14.4 - - + +
332A ARG* 3.3 17.0 - - + +
4C T 4.2 3.5 + - - -
5C G 2.5 28.2 + - - -
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Residues in contact with MET 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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35A GLY 6.4 0.2 - - - -
36A ARG* 2.8 24.5 + - - +
249A VAL 4.7 0.9 - - - +
250A THR* 1.3 76.7 - - - +
252A LYS* 1.3 68.0 + - - +
253A ARG 3.1 12.3 - - - +
255A SER* 4.0 12.8 - - - +
260A GLU* 5.1 1.1 - - - +
261A ILE* 3.9 28.3 - - + -
264A TYR* 3.4 43.5 - - + -
330A ILE* 2.9 50.0 - - + +
331A ARG 3.1 14.1 + - - +
333A ILE* 4.3 9.9 - - + -
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Residues in contact with LYS 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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35A GLY 3.6 18.3 + - - +
36A ARG* 3.4 42.6 + - - +
37A PHE* 5.4 1.0 - - - +
250A THR 3.9 1.2 + - - -
251A MET* 1.3 71.8 - - - +
253A ARG* 1.3 63.8 + - + +
264A TYR* 2.8 20.9 + - - +
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Residues in contact with ARG 253 (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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36A ARG* 3.2 10.5 - - - +
251A MET* 3.1 16.3 - - - +
252A LYS* 1.3 83.8 - - + +
254A ASN* 1.3 74.9 + - - +
255A SER* 3.7 2.6 + - - -
260A GLU* 3.0 36.8 + - - +
264A TYR* 4.6 0.7 + - - -
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Residues in contact with ASN 254 (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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36A ARG* 2.7 34.4 + - - +
251A MET* 4.5 0.2 - - - -
253A ARG* 1.3 89.0 + - - +
255A SER* 1.3 63.6 + - - +
291A GLU* 3.7 26.2 + - - +
329A LYS* 4.2 22.5 + - + +
330A ILE 3.2 10.5 - - - +
331A ARG* 3.1 25.1 - - - +
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Residues in contact with SER 255 (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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251A MET* 4.0 2.9 - - - +
253A ARG* 3.7 3.6 + - - -
254A ASN* 1.3 79.8 - - - +
256A ARG* 1.3 69.7 + - - +
257A ASN* 2.8 18.2 + - - +
260A GLU* 2.6 36.1 + - - +
261A ILE* 3.7 11.1 - - - +
329A LYS* 4.1 9.1 - - - +
330A ILE* 2.6 43.9 + - - +
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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