Contacts of the strand formed by residues 351 - 359 (chain A) in PDB entry 2Q8I
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 GLY 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 3.4 13.0 - - - -
289A GLY 4.0 1.6 - - - -
290A GLY 3.8 2.7 - - - -
291A GLY* 3.5 12.4 - - - +
346A SER* 3.1 4.5 + - - -
347A MET* 2.8 35.3 + - - +
350A VAL* 1.3 87.3 - - - +
352A THR* 1.3 63.4 + - - -
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Residues in contact with THR 352 (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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285A ILE 3.5 3.3 - - - +
286A SER* 3.5 0.3 - - - -
287A ASP* 3.0 34.9 + - - +
291A GLY* 3.3 2.3 - - - -
292A VAL* 4.0 1.2 - - + +
344A LEU* 3.7 29.6 - - + -
345A TYR 3.5 12.8 - - - +
346A SER* 3.2 16.7 + - - -
351A GLY* 1.3 77.8 - - - -
353A ASP* 1.3 67.4 + - - +
408A RDC 2.9 48.3 + - + -
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Residues in contact with ASP 353 (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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284A LYS* 4.2 22.7 + - + +
285A ILE 3.3 4.0 - - - +
286A SER* 2.8 31.5 + - - -
287A ASP 5.5 0.3 - - - +
343A LYS 4.0 0.2 - - - +
344A LEU* 3.5 4.5 - - - +
345A TYR* 2.8 48.8 + - + +
352A THR* 1.3 75.5 - - - +
354A ALA* 1.3 60.5 + - - +
355A VAL* 4.9 5.6 - - + -
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Residues in contact with ALA 354 (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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248A LEU* 4.1 29.1 - - + +
283A ILE 3.5 1.4 - - - +
284A LYS* 3.3 1.9 - - - -
285A ILE* 2.8 44.4 + - + +
342A LEU* 5.0 1.6 - - + -
343A LYS 3.4 5.6 - - - +
344A LEU* 3.6 18.8 - - + -
353A ASP* 1.3 75.6 - - - +
355A VAL* 1.3 63.0 + - - +
356A ILE 4.2 0.2 - - - -
408A RDC 4.2 8.1 - - + +
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Residues in contact with VAL 355 (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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282A SER* 4.4 3.8 - - - -
283A ILE 3.2 17.3 - - - +
284A LYS* 4.2 23.6 - - + -
342A LEU* 3.4 5.0 - - - +
343A LYS* 2.8 38.4 + - + +
345A TYR* 4.7 15.5 - - + -
353A ASP* 4.9 1.8 - - + -
354A ALA* 1.3 81.3 - - - +
356A ILE* 1.3 68.9 + - - +
357A TYR* 3.5 41.2 - - + +
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Residues in contact with ILE 356 (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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241A LEU* 4.7 2.0 - - + -
244A MET* 4.0 31.6 - - + -
245A LEU* 4.0 24.2 - - + -
248A LEU* 3.7 30.3 - - + -
281A LEU 3.7 1.0 - - - +
282A SER* 3.3 4.3 - - - -
283A ILE* 2.9 51.2 + - + +
285A ILE* 5.3 0.2 - - + -
341A ASP 3.7 7.6 - - - +
342A LEU* 4.2 10.5 - - + +
355A VAL* 1.3 73.2 - - - +
357A TYR* 1.3 62.9 + - - +
358A LEU* 3.7 30.3 - - + -
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Residues in contact with TYR 357 (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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280A ASP* 4.5 17.9 - - - -
281A LEU 3.6 1.8 - - - -
282A SER* 3.6 26.2 - - - -
340A GLY* 3.0 6.9 - - - -
341A ASP* 2.9 44.6 + - + +
343A LYS* 4.1 30.7 - - + -
345A TYR* 5.4 5.2 + + - -
355A VAL* 3.5 41.5 - - + +
356A ILE* 1.3 71.5 - - - +
358A LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 358 (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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234A VAL* 4.9 6.1 - - + -
236A TYR* 3.5 53.2 - - + +
241A LEU* 4.3 19.5 - - + -
244A MET* 4.0 9.0 - - + -
280A ASP* 3.6 8.5 - - - +
281A LEU* 2.8 55.1 + - + +
283A ILE* 5.0 0.2 - - + -
335A ALA* 5.0 6.1 - - - +
340A GLY* 4.4 4.7 - - - +
356A ILE* 3.7 21.3 - - + -
357A TYR* 1.3 82.8 - - - +
359A LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 359 (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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234A VAL* 3.9 14.2 - - - +
235A VAL 5.5 0.2 - - - +
236A TYR* 5.7 3.3 - - - -
279A GLU* 3.6 19.7 + - - +
280A ASP* 5.0 7.2 + - - +
281A LEU* 4.6 0.7 - - - -
338A PHE 3.9 18.7 + - - +
339A GLN* 3.5 30.6 + - + +
340A GLY* 4.9 0.8 - - - -
358A LEU* 1.3 77.2 - - - +
360A ALA* 1.3 64.6 + - - +
361A LEU 3.4 8.3 + - - +
364A GLU* 3.7 37.1 + - + +
365A SER* 3.5 22.1 + - - +
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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