Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 3SDI
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 45 (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* 2.8 33.6 + - - +
43A THR 3.7 0.6 - - - -
44A ASN* 1.3 79.2 - - - +
46A VAL* 1.3 64.3 + - - +
147A PHE* 3.6 11.8 - - - -
186A LEU* 4.1 15.5 - - - -
215A ILE 3.1 15.3 - - - -
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Residues in contact with VAL 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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40A ILE 3.5 18.4 - - - +
41A LYS* 3.9 9.2 - - + -
45A GLY* 1.3 78.5 - - - +
47A VAL* 1.3 68.8 + - - +
48A ILE 4.3 0.4 + - - -
139A ALA* 3.4 29.2 - - + -
140A GLY 4.5 2.7 - - - +
147A SER* 3.7 44.6 - - + +
148A LEU* 4.3 12.6 - - + -
186A LEU* 4.0 4.6 - - - +
214A ILE* 3.2 6.4 - - - +
215A ILE* 2.8 36.0 + - + +
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Residues in contact with VAL 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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38A LEU* 5.4 0.6 - - - +
39A GLY* 3.1 3.5 - - - -
40A ILE* 2.8 55.9 + - + +
46A VAL* 1.3 77.1 - - - +
48A ILE* 1.3 70.1 + - - +
186A LEU* 4.5 1.3 - - + +
189A ALA* 3.6 31.4 - - + +
190A ILE* 4.4 7.6 - - + -
193A ALA* 4.2 11.0 - - + -
212A LEU* 3.6 31.2 - - + -
213A ALA 3.6 7.4 - - - +
214A ILE* 4.2 10.8 - - + -
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Residues in contact with ILE 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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38A LEU 3.3 10.1 - - - +
39A GLY* 4.1 7.2 - - - -
46A VAL 4.3 0.6 - - - +
47A VAL* 1.3 78.4 - - - +
49A ALA* 1.3 62.0 + - - +
67A VAL* 3.7 27.7 - - + +
75A GLY* 4.0 8.5 - - - +
76A ALA* 3.8 31.4 - - - +
77A VAL* 4.1 14.8 - - + +
137A LEU* 4.7 3.8 - - + +
139A ALA* 3.8 26.2 - - + +
148A LEU* 4.2 8.5 - - + -
211A GLU 4.1 0.3 - - - +
212A LEU* 3.5 1.9 - - - -
213A ALA* 2.9 43.4 + - + +
214A ILE* 5.6 0.4 - - - -
215A ILE* 5.8 3.1 - - + -
221A PHE* 4.9 0.7 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 3.3 2.9 - - - -
38A LEU* 2.9 49.4 + - + +
47A VAL 4.3 0.2 - - - -
48A ILE* 1.3 77.1 - - - +
50A THR* 1.3 65.8 + - - +
67A VAL* 5.4 0.4 - - - -
77A VAL* 4.4 3.7 - - - +
193A ALA* 4.6 9.0 - - + +
197A LEU* 4.2 11.9 - - + -
211A GLU 3.2 9.4 - - - +
212A LEU* 3.8 23.1 - - + -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR 2.9 18.1 + - - -
37A SER* 3.6 14.2 - - - +
49A ALA* 1.3 78.1 - - - +
51A GLU* 1.3 66.4 + - - +
66A LYS* 3.0 41.0 + - + -
67A VAL* 4.3 1.1 - - + -
77A VAL* 3.6 20.2 - - + -
197A LEU* 3.7 13.2 - - - +
210A ILE* 3.7 3.1 - - - -
211A GLU* 2.8 45.9 + - + +
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Residues in contact with GLU 51 (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 VAL* 3.4 19.8 - - + +
36A THR* 3.7 7.0 + - - +
50A THR* 1.3 80.5 + - - +
52A LYS* 1.3 67.1 + - - +
53A LYS* 3.1 30.6 + - - +
66A LYS* 2.9 26.1 + - - +
197A LEU* 4.4 2.2 - - + +
200A SER 4.4 2.1 - - - +
202A VAL* 3.7 40.0 - - + +
203A GLU* 3.3 27.9 - - - +
204A GLY 5.7 0.2 + - - -
209A THR* 3.6 12.8 - - + +
210A ILE* 3.8 3.6 - - + -
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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