Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 2G9Y
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 ASN 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.8 4.7 - - - +
43A LYS* 1.3 93.5 - - - +
45A ILE* 1.3 69.3 + - - +
311A SER* 5.9 0.2 - - - -
316A GLY* 3.2 8.1 - - - -
317A PHE* 3.0 59.6 + - + +
355A PHE* 3.9 6.7 - - - -
359A GLU* 3.8 17.4 - - - +
361A ASN 3.4 2.2 + - - -
362A THR* 3.1 27.6 + - + +
363A LEU 3.1 21.0 + - - -
446A LEU* 4.3 0.7 - - - -
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Residues in contact with ILE 45 (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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42A ALA* 4.5 2.2 - - + -
44A ASN* 1.3 81.1 - - - +
46A ILE* 1.3 77.3 + - - +
47A LEU* 4.2 1.1 - - + +
317A PHE* 3.0 8.0 + - - +
318A PHE* 3.5 25.8 - - + -
319A LEU* 2.9 26.5 + - - +
362A THR* 4.6 0.2 - - - -
363A LEU* 3.4 31.0 - - + +
365A ILE* 5.2 3.1 - - + -
442A MET* 3.5 54.3 - - + +
445A ALA* 4.2 2.7 - - + -
446A LEU* 3.6 20.6 - - + -
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Residues in contact with ILE 46 (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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45A ILE* 1.3 80.9 - - - +
47A LEU* 1.3 61.1 + - - +
48A LEU* 3.6 25.5 + - + -
303A THR* 5.5 1.6 - - + -
307A ILE* 3.8 30.3 - - + -
317A PHE* 4.1 13.7 - - + -
319A LEU* 3.3 20.6 - - + +
321A VAL* 4.7 4.3 - - + -
352A ALA* 3.9 18.2 - - + +
355A PHE* 4.1 17.9 - - + -
362A THR* 4.1 13.7 - - + -
363A LEU 2.9 9.3 + - - +
364A VAL* 3.4 8.9 - - + +
365A ILE* 3.0 25.8 + - - +
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Residues in contact with LEU 47 (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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45A ILE* 4.1 1.5 - - + -
46A ILE* 1.3 72.3 - - - +
48A LEU* 1.3 63.8 + - - +
49A ILE* 3.9 24.7 - - + -
109A TRP* 3.6 35.2 - - + +
318A PHE* 4.5 7.0 - - + -
319A LEU 2.8 12.7 + - - +
320A GLN* 3.2 16.0 - - - +
321A VAL 2.7 27.2 + - - +
365A ILE* 3.7 31.9 - - + +
367A THR* 4.6 0.9 - - + -
438A LEU* 4.2 10.3 - - + -
442A MET* 3.9 26.9 - - + -
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Residues in contact with LEU 48 (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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46A ILE* 3.6 23.8 - - + -
47A LEU* 1.3 74.6 - - - +
49A ILE* 1.3 64.1 - - - +
50A GLY 4.1 0.2 + - - -
303A THR* 5.1 0.9 - - + +
321A VAL* 3.1 24.9 - - + +
345A LEU* 4.5 8.3 - - + -
348A ALA* 3.8 19.5 - - + +
349A VAL* 3.8 35.0 - - + +
352A ALA* 3.8 7.2 - - + -
364A VAL* 3.8 24.2 - - + -
365A ILE 2.8 13.9 + - - +
366A VAL* 3.4 16.9 - - + +
367A THR 3.2 24.1 + - - +
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Residues in contact with ILE 49 (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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47A LEU* 3.9 27.1 - - + -
48A LEU* 1.3 79.7 - - - +
50A GLY* 1.3 65.8 + - - +
51A ASP* 4.0 6.1 - - - +
109A TRP* 3.8 45.3 - - + -
155A THR* 4.4 8.7 - - + +
320A GLN* 4.4 9.2 - - + -
321A VAL 2.7 11.3 + - - +
322A GLU* 3.2 10.1 - - + +
323A GLY 2.8 32.1 + - - -
345A LEU* 4.0 4.5 - - - +
367A THR* 3.5 19.7 - - + +
368A ALA 4.9 0.4 - - - +
369A ASP* 4.2 12.8 - - + +
438A LEU* 5.4 0.2 - - + -
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Residues in contact with GLY 50 (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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49A ILE* 1.3 73.4 - - - +
51A ASP* 1.3 66.8 + - - -
53A MET* 2.9 24.5 + - - +
323A GLY 3.9 6.1 - - - -
326A ILE* 4.1 2.7 - - - -
345A LEU* 3.6 23.3 - - - +
367A THR 2.9 11.5 + - - -
368A ALA* 3.0 14.7 - - - +
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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