Contacts of the strand formed by residues 45 - 51 (chain G) 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 CYS 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41G ARG* 3.7 0.2 - - - -
42G GLY* 2.8 35.3 + - - -
43G LYS 4.9 0.2 - - - -
44G ASP* 1.3 85.9 - - - +
46G THR* 1.3 69.7 + - - +
47G VAL* 4.5 3.6 - - - -
141G VAL* 3.7 3.4 - - - -
146G PRO* 3.1 11.0 - - - +
184G SER 5.0 1.3 - - - -
186G TRP* 3.7 39.5 - - + -
189G VAL* 4.0 14.8 - - - -
214G VAL* 4.7 0.7 - - + -
215G ALA 3.2 15.5 - - - +
216G THR* 4.2 5.6 - - + -
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Residues in contact with THR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G VAL 3.4 13.7 - - - +
41G ARG* 4.6 0.9 - - - -
42G GLY 4.5 0.4 - - - +
45G CYS* 1.3 80.5 + - - +
47G VAL* 1.3 66.8 + - - +
48G VAL 4.4 0.2 + - - -
139G VAL* 3.6 36.2 - - + +
140G SER 3.1 23.7 + - - -
146G PRO* 3.3 10.4 - - - +
147G SER 3.3 3.6 + - - +
148G ILE* 3.7 17.0 - - + -
213G GLY 4.0 0.5 - - - +
214G VAL* 3.6 2.1 - - - +
215G ALA* 2.8 35.7 + - - +
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU* 4.0 0.3 - - - +
39G ALA* 3.2 5.2 - - - +
40G VAL* 2.9 42.6 + - + +
45G CYS* 4.5 3.1 - - - -
46G THR* 1.3 79.6 - - - +
48G VAL* 1.3 67.6 + - - +
49G ILE* 3.7 27.7 - - + +
186G TRP 4.4 0.9 - - - +
189G VAL* 3.7 23.6 - - + -
190G VAL* 3.6 37.9 - - + +
193G ALA* 4.3 2.2 - - + -
212G VAL* 4.4 1.3 - - + -
213G GLY 3.5 6.7 - - - +
214G VAL* 4.3 10.3 - - + -
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU 3.4 4.0 - - - +
39G ALA* 3.6 15.7 - - + -
46G THR 4.4 0.2 + - - -
47G VAL* 1.3 72.4 - - - +
49G ILE* 1.3 65.3 + - - +
67G ILE* 4.1 15.1 - - + +
76G MET 6.1 0.4 - - - -
77G VAL* 4.3 28.5 - - + +
137G THR* 4.9 0.4 - - + -
139G VAL* 3.5 42.8 - - + -
212G VAL* 3.5 4.3 - - - +
213G GLY* 2.9 55.7 + - - +
221G PHE* 4.5 4.9 - - + -
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Residues in contact with ILE 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G SER* 3.1 4.4 - - - -
38G LEU* 2.8 40.4 + - + +
47G VAL* 3.7 13.9 - - + +
48G VAL* 1.3 77.8 - - - +
50G SER* 1.3 65.9 + - - +
67G ILE* 5.4 0.4 - - - -
190G VAL* 4.2 4.5 - - - +
193G ALA* 2.8 47.1 - - + -
194G ILE* 3.9 9.2 - - + +
197G MET* 4.0 20.8 - - + +
210G LEU* 3.6 30.5 - - + -
211G GLU 3.5 4.9 - - - +
212G VAL* 4.2 16.2 - - + -
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Residues in contact with SER 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ILE* 3.3 14.9 - - - +
36G ASN 3.3 5.6 - - - -
37G SER* 3.9 11.4 - - - -
49G ILE* 1.3 81.4 - - - +
51G GLN* 1.3 75.6 + - - +
66G TYR* 4.8 6.1 - - - +
67G ILE* 4.7 4.0 - - - +
77G VAL* 4.1 17.0 - - - +
78G VAL 5.7 0.3 + - - -
197G MET* 5.5 0.2 - - - -
210G LEU* 3.7 4.5 - - - +
211G GLU* 3.0 42.9 + - - +
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ILE* 3.3 24.7 - - + +
36G ASN* 2.8 49.1 + - + +
50G SER* 1.3 85.0 + - - +
52G LYS* 1.3 59.8 + - - +
53G LYS* 4.0 25.9 + - + +
66G TYR* 5.6 2.9 - - - -
197G MET* 4.7 5.8 - - - -
201G LEU* 3.5 26.8 - - + +
203G THR* 5.4 2.2 + - - -
205G PHE* 3.7 26.5 - - + -
209G ASP 3.7 5.4 - - - +
210G LEU* 4.5 2.0 - - + -
211G GLU* 5.0 2.8 - - - +
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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